1052 Citations
Hit-to-lead optimization is a critical phase in drug discovery Herein we report on the fragment-based discovery and optimization of -aminopyridine derivatives as a novel lead-like structure for the treatment of the dangerous opportunistic pathogen Pseudomonas aeruginosa We pursue an innovative treatment strategy by interfering with the Pseudomonas quinolone signal PQS quorum sensing QS system leading to an abolishment of bacterial pathogenicity Our compounds act on the PQS receptor PqsR a key transcription factor controlling the expression of various pathogenicity determinants In this target-driven approach we made use of biophysical screening via surface plasmon resonance SPR followed by isothermal titration calorimetry ... More
Hit-to-lead optimization is a critical phase in drug discovery. Herein, we report on the fragment-based discovery and optimization of 2-aminopyridine derivatives as a novel lead-like structure for the treatment of the dangerous opportunistic pathogen Pseudomonas aeruginosa. We pursue an innovative treatment strategy by interfering with the Pseudomonas quinolone signal (PQS) quorum sensing (QS) system leading to an abolishment of bacterial pathogenicity. Our compounds act on the PQS receptor (PqsR), a key transcription factor controlling the expression of various pathogenicity determinants. In this target-driven approach, we made use of biophysical screening via surface plasmon resonance (SPR) followed by isothermal titration calorimetry (ITC)-enabled enthalpic efficiency (EE) evaluation. Hit optimization then involved growth vector identification and exploitation. Astonishingly, the latter was successfully achieved by introducing flexible linkers rather than rigid motifs leading to a boost in activity on the target receptor and anti-virulence potency. Less
Well-ordered HIV- envelope glycoprotein Env trimers are prioritized for clinical evaluation and there is a need for an improved understanding about how elicited B cell responses evolve following immunization To accomplish this we prime-boosted rhesus macaques with clade C NFL trimers and identified unique Ab lineages from single-sorted Env-specific memory B cells We traced all lineages in high-throughput heavy chain HC repertoire Rep-seq data generated from multiple immune compartments and time points and expressed several as monoclonal Abs mAbs Our results revealed broad dissemination and high levels of somatic hypermutation SHM of most lineages including tier virus neutralizing lineages following ... More
Well-ordered HIV-1 envelope glycoprotein (Env) trimers are prioritized for clinical evaluation, and there is a need for an improved understanding about how elicited B cell responses evolve following immunization. To accomplish this, we prime-boosted rhesus macaques with clade C NFL trimers and identified 180 unique Ab lineages from ∼1,000 single-sorted Env-specific memory B cells. We traced all lineages in high-throughput heavy chain (HC) repertoire (Rep-seq) data generated from multiple immune compartments and time points and expressed several as monoclonal Abs (mAbs). Our results revealed broad dissemination and high levels of somatic hypermutation (SHM) of most lineages, including tier 2 virus neutralizing lineages, following boosting. SHM was highest in the Ab complementarity determining regions (CDRs) but also surprisingly high in the framework regions (FRs), especially FR3. Our results demonstrate the capacity of the immune system to affinity-mature large numbers of Env-specific B cell lineages simultaneously, supporting the use of regimens consisting of repeated boosts to improve each Ab, even those belonging to less expanded lineages. Less
A multiprotein complex polarisome nucleates actin cables for polarized cell growth in budding yeast and filamentous fungi However the dynamic regulations of polarisome proteins in polymerizing actin under physiological and stress conditions remains unknown We identify a previously functionally unknown polarisome member actin-interacting-protein Aip which promotes actin assembly synergistically with formin Bni Aip -C terminus is responsible for its activities by interacting with G-actin and Bni Through N-terminal intrinsically disordered region Aip forms high-order oligomers and generate cytoplasmic condensates under the stresses conditions The molecular dynamics and reversibility of Aip condensates are regulated by scaffolding protein Spa via liquid-liquid phase ... More
A multiprotein complex polarisome nucleates actin cables for polarized cell growth in budding yeast and filamentous fungi. However, the dynamic regulations of polarisome proteins in polymerizing actin under physiological and stress conditions remains unknown. We identify a previously functionally unknown polarisome member, actin-interacting-protein 5 (Aip5), which promotes actin assembly synergistically with formin Bni1. Aip5-C terminus is responsible for its activities by interacting with G-actin and Bni1. Through N-terminal intrinsically disordered region, Aip5 forms high-order oligomers and generate cytoplasmic condensates under the stresses conditions. The molecular dynamics and reversibility of Aip5 condensates are regulated by scaffolding protein Spa2 via liquid-liquid phase separation both in vitro and in vivo. In the absence of Spa2, Aip5 condensates hamper cell growth and actin cable structures under stress treatment. The present study reveals the mechanisms of actin assembly for polarity establishment and the adaptation in stress conditions to protect actin assembly by protein phase separation. Less
The investigational drugs E indisulam and tasisulam aryl-sulfonamides promote the degradation of the splicing factor RBM in a proteasome-dependent mechanism While the activity critically depends on the Cullin RING ligase substrate receptor DCAF the molecular details remain elusive Here we present the cryo-EM structure of the DDB -DCAF -DDA core ligase complex bound to RBM and E at resolution together with crystal structures of engineered subcomplexes We show that DCAF adopts a novel fold stabilized by DDA and that extensive protein-protein contacts between the ligase and substrate mitigate low affinity interactions between aryl-sulfonamides and DCAF Our data demonstrates how aryl-sulfonamides ... More
The investigational drugs E7820, indisulam and tasisulam (aryl-sulfonamides) promote the degradation of the splicing factor RBM39 in a proteasome-dependent mechanism. While the activity critically depends on the Cullin RING ligase substrate receptor DCAF15, the molecular details remain elusive. Here we present the cryo-EM structure of the DDB1-DCAF15-DDA1 core ligase complex bound to RBM39 and E7820 at 4.4 Å resolution, together with crystal structures of engineered subcomplexes. We show that DCAF15 adopts a novel fold stabilized by DDA1, and that extensive protein-protein contacts between the ligase and substrate mitigate low affinity interactions between aryl-sulfonamides and DCAF15. Our data demonstrates how aryl-sulfonamides neo-functionalize a shallow, non-conserved pocket on DCAF15 to selectively bind and degrade RBM39 and the closely related splicing factor RBM23 without the requirement for a high affinity ligand, which has broad implications for the de novo discovery of molecular glue degraders. Less
Indanomycin is biosynthesized by a hybrid nonribosomal peptide synthase polyketide synthase NRPS PKS followed by a number of tailoring' steps to form the two ring systems that are present in the mature product It had previously been hypothesized that the indane ring of indanomycin was formed by the action of IdmH using a Diels Alder reaction Here the crystal structure of a selenomethionine-labelled truncated form of IdmH IdmH- was solved using single-wavelength anomalous dispersion SAD phasing This truncated variant allows consistent and easy crystallization but importantly the structure was used as a search model in molecular replacement allowing the full-length ... More
Indanomycin is biosynthesized by a hybrid nonribosomal peptide synthase/polyketide synthase (NRPS/PKS) followed by a number of `tailoring' steps to form the two ring systems that are present in the mature product. It had previously been hypothesized that the indane ring of indanomycin was formed by the action of IdmH using a Diels–Alder reaction. Here, the crystal structure of a selenomethionine-labelled truncated form of IdmH (IdmH-Δ99–107) was solved using single-wavelength anomalous dispersion (SAD) phasing. This truncated variant allows consistent and easy crystallization, but importantly the structure was used as a search model in molecular replacement, allowing the full-length IdmH structure to be determined to 2.7 Å resolution. IdmH is a homodimer, with the individual protomers consisting of an α+β barrel. Each protomer contains a deep hydrophobic pocket which is proposed to constitute the active site of the enzyme. To investigate the reaction catalysed by IdmH, 88% of the backbone NMR resonances were assigned, and using chemical shift perturbation of [15N]-labelled IdmH it was demonstrated that indanomycin binds in the active-site pocket. Finally, combined quantum mechanical/molecular mechanical (QM/MM) modelling of the IdmH reaction shows that the active site of the enzyme provides an appropriate environment to promote indane-ring formation, supporting the assignment of IdmH as the key Diels–Alderase catalysing the final step in the biosynthesis of indanomycin through a similar mechanism to other recently characterized Diels–Alderases involved in polyketide-tailoring reactions. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at https://proteopedia.org/w/Journal:IUCrJ:S2052252519012399. Less
The class B family of G-protein-coupled receptors GPCRs has long been a paradigm for peptide hormone recognition and signal transduction One class B GPCR the glucagon-like peptide- receptor GLP- R has been considered as an anti-diabetes drug target and there are several peptidic drugs available for the treatment of this overwhelming disease The previously determined structures of inactive GLP- R in complex with two negative allosteric modulators include ten thermal-stabilizing mutations that were selected from a total of designed mutations Here we systematically summarize all mutations we have tested and the results suggest that the mutagenesis strategy that strengthens inter-helical ... More
The class B family of G-protein-coupled receptors (GPCRs) has long been a paradigm for peptide hormone recognition and signal transduction. One class B GPCR, the glucagon-like peptide-1 receptor (GLP-1R), has been considered as an anti-diabetes drug target and there are several peptidic drugs available for the treatment of this overwhelming disease. The previously determined structures of inactive GLP-1R in complex with two negative allosteric modulators include ten thermal-stabilizing mutations that were selected from a total of 98 designed mutations. Here we systematically summarize all 98 mutations we have tested and the results suggest that the mutagenesis strategy that strengthens inter-helical hydrophobic interactions shows the highest success rate. We further investigate four back mutations by thermal-shift assay, crystallization and molecular dynamic simulations, and conclude that mutation I1962.66bF increases thermal stability intrinsically and that mutation S2714.47bA decreases crystal packing entropy extrinsically, while mutations S1932.63bC and M2333.36bC may be dispensable since these two cysteines are not disulfide-linked. Our results indicate intrinsic connections between different regions of GPCR transmembrane helices and the current data suggest a general mutagenesis principle for structural determination of GPCRs and other membrane proteins. Less
Redesigning existing food protein formulations is necessary in situations where food authorities propose dose adjustments or removal of currently employed additives Redesigning formulations involves evaluating substitute additives to obtain similar long-term physical stability as the original formulation Such formulation screening experiments benefit from comprehensive data visualization understanding the effects of substitute additives on long-term physical stability and identification of short-term optimization targets This work employs empirical phase diagrams to reach these benefits by combining multidimensional long-term protein physical stability data with short-term empirical protein properties A case study was performed where multidimensional protein phase diagrams formulations allowed for identification of ... More
Redesigning existing food protein formulations is necessary in situations where food authorities propose dose adjustments or removal of currently employed additives. Redesigning formulations involves evaluating substitute additives to obtain similar long-term physical stability as the original formulation. Such formulation screening experiments benefit from comprehensive data visualization, understanding the effects of substitute additives on long-term physical stability, and identification of short-term optimization targets. This work employs empirical phase diagrams to reach these benefits by combining multidimensional long-term protein physical stability data with short-term empirical protein properties. A case study was performed where multidimensional protein phase diagrams (1152 formulations) allowed for identification of stabilizing effects as a result of pH, methionine, sugars, salt, and minimized glycerol content. Corresponding empirical protein property diagrams (144 formulations) resulted in the identification of normalized surface tension as a short-term empirical protein property to reach long-term physical stability presumably similar to the original product, namely via preferential hydration. Additionally, changes in pH and salt were identified as environmental optimization targets to reach stability via repulsive electrostatic forces. This case study shows the applicability of the empirical phase diagram method to rationally perform formulation redesign screenings, while simultaneously expanding knowledge on protein long-term physical stability. Less
Purpose The overall goal of this study was to investigate the dissolution performance and crystallization kinetics of amorphous solid dispersions ASDs of a weakly basic compound posaconazole dispersed in a pH-sensitive polymeric matrix consisting of hydroxypropyl methylcellulose acetate succinate HPMC-AS using fasted-state simulated media Methods ASDs with three different drug loadings and wt and the commercially available tablets were exposed to acidic media pH followed by transfer to and dissolution in intestinal media pH Parallel single stage dissolution experiments in only simulated intestinal media were also performed to better understand the impact of the gastric stage Different analytical methods including ... More
Purpose
The overall goal of this study was to investigate the dissolution performance and crystallization kinetics of amorphous solid dispersions (ASDs) of a weakly basic compound, posaconazole, dispersed in a pH-sensitive polymeric matrix consisting of hydroxypropyl methylcellulose acetate succinate (HPMC-AS), using fasted-state simulated media.
Methods
ASDs with three different drug loadings, 10, 25 and 50 wt.%, and the commercially available tablets were exposed to acidic media (pH 1.6), followed by transfer to, and dissolution in, intestinal media (pH 6.5). Parallel single stage dissolution experiments in only simulated intestinal media were also performed to better understand the impact of the gastric stage. Different analytical methods, including nanoparticle tracking analysis, powder x-ray diffraction, second harmonic generation and two-photon excitation ultraviolet fluorescence microscopy, were used to characterize the phase behavior of these systems at different stages of dissolution.
Results
Results revealed that all ASDs exhibited some degree of drug release upon suspension in acidic media, and were also vulnerable to matrix crystallization. Upon transfer to intestinal media conditions, supersaturation was observed. This was short-lived for some dispersions due to the release of the crystals formed in the acid immersion stage which acted as seeds for crystal growth. Lower drug loading ASDs also exhibited transient formation of amorphous nanodroplets prior to crystallization.
Conclusions
This work emphasizes the significance of assessing the impact of pH change on dissolution and provides a fundamental basis of understanding the phase behavior kinetics of ASDs of weakly basic drugs when formulated with pH sensitive polymers. Less
The overall goal of this study was to investigate the dissolution performance and crystallization kinetics of amorphous solid dispersions (ASDs) of a weakly basic compound, posaconazole, dispersed in a pH-sensitive polymeric matrix consisting of hydroxypropyl methylcellulose acetate succinate (HPMC-AS), using fasted-state simulated media.
Methods
ASDs with three different drug loadings, 10, 25 and 50 wt.%, and the commercially available tablets were exposed to acidic media (pH 1.6), followed by transfer to, and dissolution in, intestinal media (pH 6.5). Parallel single stage dissolution experiments in only simulated intestinal media were also performed to better understand the impact of the gastric stage. Different analytical methods, including nanoparticle tracking analysis, powder x-ray diffraction, second harmonic generation and two-photon excitation ultraviolet fluorescence microscopy, were used to characterize the phase behavior of these systems at different stages of dissolution.
Results
Results revealed that all ASDs exhibited some degree of drug release upon suspension in acidic media, and were also vulnerable to matrix crystallization. Upon transfer to intestinal media conditions, supersaturation was observed. This was short-lived for some dispersions due to the release of the crystals formed in the acid immersion stage which acted as seeds for crystal growth. Lower drug loading ASDs also exhibited transient formation of amorphous nanodroplets prior to crystallization.
Conclusions
This work emphasizes the significance of assessing the impact of pH change on dissolution and provides a fundamental basis of understanding the phase behavior kinetics of ASDs of weakly basic drugs when formulated with pH sensitive polymers. Less
Recently two groups of rhodopsin genes were identified in large double-stranded DNA viruses The structure and function of viral rhodopsins are unknown We present functional characterization and high-resolution structure of an Organic Lake Phycodnavirus rhodopsin II OLPVRII of group It forms a pentamer with a symmetrical bottle-like central channel with the narrow vestibule in the cytoplasmic part covered by a ring of arginines whereas phenylalanines form a hydrophobic barrier in its exit The proton donor E is placed in the helix B The structure is unique among the known rhodopsins Structural and functional data and molecular dynamics suggest that OLPVRII ... More
Recently, two groups of rhodopsin genes were identified in large double-stranded DNA viruses. The structure and function of viral rhodopsins are unknown. We present functional characterization and high-resolution structure of an Organic Lake Phycodnavirus rhodopsin II (OLPVRII) of group 2. It forms a pentamer, with a symmetrical, bottle-like central channel with the narrow vestibule in the cytoplasmic part covered by a ring of 5 arginines, whereas 5 phenylalanines form a hydrophobic barrier in its exit. The proton donor E42 is placed in the helix B. The structure is unique among the known rhodopsins. Structural and functional data and molecular dynamics suggest that OLPVRII might be a light-gated pentameric ion channel analogous to pentameric ligand-gated ion channels, however, future patch clamp experiments should prove this directly. The data shed light on a fundamentally distinct branch of rhodopsins and may contribute to the understanding of virus-host interactions in ecologically important marine protists. Less
Macrophage migration inhibitory factor MIF is a pleiotropic cytokine that increasingly is being studied in cancers and inflammatory diseases Though murine models have been instrumental in understanding the functional role of MIF in different pathological conditions the information obtained from these models is biased towards a specific species In experimental science results obtained from multiple clinically relevant animal models always provide convincing data that might recapitulate in humans Syrian golden hamster Mesocricetus auratus is a clinically relevant animal model for multiple human diseases Hence the major objectives of this study were to characterize structure and function of hamster MIF and ... More
Macrophage migration inhibitory factor (MIF) is a pleiotropic cytokine that increasingly is being studied in cancers and inflammatory diseases. Though murine models have been instrumental in understanding the functional role of MIF in different pathological conditions, the information obtained from these models is biased towards a specific species. In experimental science, results obtained from multiple clinically relevant animal models always provide convincing data that might recapitulate in humans. Syrian golden hamster (Mesocricetus auratus), is a clinically relevant animal model for multiple human diseases. Hence, the major objectives of this study were to characterize structure and function of hamster MIF, and finally evaluate its effect on pancreatic tumor growth in vivo. Initially, the recombinant hamster MIF (rha-MIF) was cloned, expressed and purified in bacterial expression system. The rha-MIF primary sequence, biochemical properties and crystal structure analysis showed a greater similarity with human MIF. The crystal structure of hamster MIF illustrates that it forms a homotrimer as known in human and mouse. However, hamster MIF exhibits some minor structural variations when compared to human and mouse MIF. The in vitro functional studies show that rha-MIF has tautomerase activity and enhances activation and migration of hamster peripheral blood mononuclear cells (PBMCs). Interestingly, injection of rha-MIF into HapT1 pancreatic tumor bearing hamsters significantly enhanced the tumor growth and tumor associated angiogenesis. Together, the current study shows a structural and functional similarity between hamster and human MIF. Moreover, it has demonstrated that a high-level of circulating MIF originating from non-tumor cells might also promote pancreatic tumor growth in vivo. Less
Macrophage migration inhibitory factor MIF is a pleiotropic cytokine that increasingly is being studied in cancers and inflammatory diseases Though murine models have been instrumental in understanding the functional role of MIF in different pathological conditions the information obtained from these models is biased towards a specific species In experimental science results obtained from multiple clinically relevant animal models always provide convincing data that might recapitulate in humans Syrian golden hamster Mesocricetus auratus is a clinically relevant animal model for multiple human diseases Hence the major objectives of this study were to characterize the structure and function of Mesocricetus auratus ... More
Macrophage migration inhibitory factor (MIF) is a pleiotropic cytokine that increasingly is being studied in cancers and inflammatory diseases. Though murine models have been instrumental in understanding the functional role of MIF in different pathological conditions, the information obtained from these models is biased towards a specific species. In experimental science, results obtained from multiple clinically relevant animal models always provide convincing data that might recapitulate in humans. Syrian golden hamster (Mesocricetus auratus), is a clinically relevant animal model for multiple human diseases. Hence, the major objectives of this study were to characterize the structure and function of Mesocricetus auratus MIF (MaMIF) and finally evaluate its effect on pancreatic tumor growth in vivo. Initially, the recombinant MaMIF was cloned, expressed and purified in a bacterial expression system. The MaMIF primary sequence, biochemical properties, and crystal structure analysis showed greater similarity with human MIF. The crystal structure of MaMIF illustrates that it forms a homotrimer as known in human and mouse. However, MaMIF exhibits some minor structural variations when compared to human and mouse MIF. The in vitro functional studies show that MaMIF has tautomerase activity and enhances activation and migration of hamster peripheral blood mononuclear cells (PBMCs). Interestingly, injection of MaMIF into HapT1 pancreatic tumor-bearing hamsters significantly enhanced the tumor growth and tumor-associated angiogenesis. Together, the current study shows a structural and functional similarity between the hamster and human MIF. Moreover, it has demonstrated that a high level of circulating MIF originating from non-tumor cells might also promote pancreatic tumor growth in vivo. Less
Rational structure-based drug design SBDD relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process While SBDD has proven successful for many drug-discovery projects its application to G protein-coupled receptors GPCRs has been limited owing to extreme difficulties with their crystallization Here a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands taking advantage of the serial femtosecond crystallography approach which obviates the need for large crystals and ... More
Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. While SBDD has proven successful for many drug-discovery projects, its application to G protein-coupled receptors (GPCRs) has been limited owing to extreme difficulties with their crystallization. Here, a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands, taking advantage of the serial femtosecond crystallography approach, which obviates the need for large crystals and requires only submilligram quantities of purified protein. The method was applied to the human β2-adrenergic receptor, resulting in eight room-temperature co-crystal structures with six different ligands, including previously unreported structures with carvedilol and propranolol. The generality of the proposed method was tested with three other receptors. This approach has the potential to enable SBDD for GPCRs and other difficult-to-crystallize membrane proteins. Less
Co-inhibitory immune receptors can contribute to T cell dysfunction in patients with cancer Blocking antibodies against cytotoxic T-lymphocyte-associated protein CTLA- and programmed cell death PD- partially reverse this effect and are becoming standard of care in an increasing number of malignancies However many of the other axes by which tumours become inhospitable to T cells are not fully understood Here we report that V-domain immunoglobulin suppressor of T cell activation VISTA engages and suppresses T cells selectively at acidic pH such as that found in tumour microenvironments Multiple histidine residues along the rim of the VISTA extracellular domain mediate binding ... More
Co-inhibitory immune receptors can contribute to T cell dysfunction in patients with cancer1,2. Blocking antibodies against cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) and programmed cell death 1 (PD-1) partially reverse this effect and are becoming standard of care in an increasing number of malignancies3. However, many of the other axes by which tumours become inhospitable to T cells are not fully understood. Here we report that V-domain immunoglobulin suppressor of T cell activation (VISTA) engages and suppresses T cells selectively at acidic pH such as that found in tumour microenvironments. Multiple histidine residues along the rim of the VISTA extracellular domain mediate binding to the adhesion and co-inhibitory receptor P-selectin glycoprotein ligand-1 (PSGL-1). Antibodies engineered to selectively bind and block this interaction in acidic environments were sufficient to reverse VISTA-mediated immune suppression in vivo. These findings identify a mechanism by which VISTA may engender resistance to anti-tumour immune responses, as well as an unexpectedly determinative role for pH in immune co-receptor engagement. Less
The tricarboxylic acid cycle intermediate succinate is involved in metabolic processes and plays a crucial role in the homeostasis of mitochondrial reactive oxygen species The receptor responsible for succinate signalling SUCNR also known as GPR is a member of the G-protein-coupled-receptor family and links succinate signalling to renin-induced hypertension retinal angiogenesis and inflammation Because SUCNR senses succinate as an immunological danger signal which has relevance for diseases including ulcerative colitis liver fibrosis diabetes and rheumatoid arthritis it is of interest as a therapeutic target Here we report the high-resolution crystal structure of rat SUCNR in complex with an intracellular binding ... More
The tricarboxylic acid cycle intermediate succinate is involved in metabolic processes and plays a crucial role in the homeostasis of mitochondrial reactive oxygen species1. The receptor responsible for succinate signalling, SUCNR1 (also known as GPR91), is a member of the G-protein-coupled-receptor family2 and links succinate signalling to renin-induced hypertension, retinal angiogenesis and inflammation3,4,5. Because SUCNR1 senses succinate as an immunological danger signal6—which has relevance for diseases including ulcerative colitis, liver fibrosis7, diabetes and rheumatoid arthritis3,8—it is of interest as a therapeutic target. Here we report the high-resolution crystal structure of rat SUCNR1 in complex with an intracellular binding nanobody in the inactive conformation. Structure-based mutagenesis and radioligand-binding studies, in conjunction with molecular modelling, identified key residues for species-selective antagonist binding and enabled the determination of the high-resolution crystal structure of a humanized rat SUCNR1 in complex with a high-affinity, human-selective antagonist denoted NF-56-EJ40. We anticipate that these structural insights into the architecture of the succinate receptor and its antagonist selectivity will enable structure-based drug discovery and will further help to elucidate the function of SUCNR1 in vitro and in vivo. Less
Influenza A virus IAV nonstructural protein NS a potent antagonist of the host immune response is capable of interacting with RNA and a wide range of cellular proteins NS consists of an RNA-binding domain RBD and an effector domain ED separated by a flexible linker region LR H N -NS has a characteristic -residue deletion in the LR with either G minor group or E major group at the st position and non-H N -NS contains E with an intact linker Based on the orientation of the ED with respect to the RBD previous crystallographic studies have shown that minor ... More
Influenza A virus (IAV) nonstructural protein 1 (NS1), a potent antagonist of the host immune response, is capable of interacting with RNA and a wide range of cellular proteins. NS1 consists of an RNA-binding domain (RBD) and an effector domain (ED) separated by a flexible linker region (LR). H5N1-NS1 has a characteristic 5-residue deletion in the LR, with either G (minor group) or E (major group) at the 71st position, and non-H5N1-NS1 contains E71 with an intact linker. Based on the orientation of the ED with respect to the RBD, previous crystallographic studies have shown that minor group H5N1-NS1(G71), a non-H5N1-NS1 [H6N6-NS1(E71)], and the LR deletion mutant H6N6-NS1(Δ80-84/E71) mimicking the major group H5N1-NS1 exhibit “open,” “semiopen,” and “closed” conformations, respectively, suggesting that NS1 exhibits a strain-dependent conformational preference. Here we report the first crystal structure of a naturally occurring H5N1-NS1(E71) and show that it adopts an open conformation similar to that of the minor group of H5N1-NS1 [H5N1-NS1(G71)]. We also show that H6N6-NS1(Δ80-84/E71) under a different crystallization condition and H6N6-NS1(Δ80-84/G71) also exhibit open conformations, suggesting that NS1 can adopt an open conformation irrespective of E or G at the 71st position. Our single-molecule fluorescence resonance energy transfer (FRET) analysis to investigate the conformational preference of NS1 in solution showed that all NS1 constructs predominantly exist in an open conformation. Further, our coimmunoprecipitation and binding studies showed that they all bind to cellular factors with similar affinities. Taken together, our studies suggest that NS1 exhibits strain-independent structural plasticity that allows it to interact with a wide variety of cellular ligands during viral infection. Less
Musashi- MSI belongs to Musashi family of RNA binding proteins RBP Like Musashi- MSI it is overexpressed in a variety of cancers and is a promising therapeutic target Both MSI proteins contain two N-terminal RNA recognition motifs and play roles in posttranscriptional regulation of target mRNAs Previously we have identified several inhibitors of MSI all of which bind to MSI as well In order to design MSI -specific inhibitors and compare the differences of binding mode of the inhibitors we set out to solve the structure of MSI -RRM the key motif that is responsible for the binding Here we ... More
Musashi-2 (MSI2) belongs to Musashi family of RNA binding proteins (RBP). Like Musashi-1 (MSI1), it is overexpressed in a variety of cancers and is a promising therapeutic target. Both MSI proteins contain two N-terminal RNA recognition motifs and play roles in posttranscriptional regulation of target mRNAs. Previously, we have identified several inhibitors of MSI1, all of which bind to MSI2 as well. In order to design MSI2-specific inhibitors and compare the differences of binding mode of the inhibitors, we set out to solve the structure of MSI2-RRM1, the key motif that is responsible for the binding. Here, we report the crystal structure and the first NMR solution structure of MSI2-RRM1, and compare these to the structures of MSI1-RBD1 and other RBPs. A high degree of structural similarity was observed between the crystal and solution NMR structures. MSI2-RRM1 shows a highly similar overall folding topology to MSI1-RBD1 and other RBPs. The structural information of MSI2-RRM1 will be helpful for understanding MSI2-RNA interaction and for guiding rational drug design of MSI2-specific inhibitors. Less
The G protein coupled cysteinyl leukotriene receptor CysLT R mediates inflammatory processes and plays a major role in numerous disorders including asthma allergic rhinitis cardiovascular disease and cancer Selective CysLT R antagonists are widely prescribed as antiasthmatic drugs however these drugs demonstrate low effectiveness in some patients and exhibit a variety of side effects To gain deeper understanding into the functional mechanisms of CysLTRs we determined the crystal structures of CysLT R bound to two chemically distinct antagonists zafirlukast and pranlukast The structures reveal unique ligand-binding modes and signaling mechanisms including lateral ligand access to the orthosteric pocket between transmembrane ... More
The G protein–coupled cysteinyl leukotriene receptor CysLT1R mediates inflammatory processes and plays a major role in numerous disorders, including asthma, allergic rhinitis, cardiovascular disease, and cancer. Selective CysLT1R antagonists are widely prescribed as antiasthmatic drugs; however, these drugs demonstrate low effectiveness in some patients and exhibit a variety of side effects. To gain deeper understanding into the functional mechanisms of CysLTRs, we determined the crystal structures of CysLT1R bound to two chemically distinct antagonists, zafirlukast and pranlukast. The structures reveal unique ligand-binding modes and signaling mechanisms, including lateral ligand access to the orthosteric pocket between transmembrane helices TM4 and TM5, an atypical pattern of microswitches, and a distinct four-residue–coordinated sodium site. These results provide important insights and structural templates for rational discovery of safer and more effective drugs. Less
Protein-crystallization imaging and classification is a labor-intensive process typically performed either by humans or by instruments that currently cost well over This cost puts the use of crystallization-trial imaging outside the reach of most academic laboratories and also start-up biotechnology firms where resources are scarce An imaging system has been designed and prototyped which automatically captures images from multi-well protein-crystallization experiments using both standard and fluorescent imaging techniques at a cost times lower than current market rates The machine uses a Panowin F D printer as a base and controls it using G-code commands sent from a Python script running ... More
Protein-crystallization imaging and classification is a labor-intensive process typically performed either by humans or by instruments that currently cost well over $100 000. This cost puts the use of crystallization-trial imaging outside the reach of most academic laboratories, and also start-up biotechnology firms, where resources are scarce. An imaging system has been designed and prototyped which automatically captures images from multi-well protein-crystallization experiments using both standard and fluorescent imaging techniques at a cost 28 times lower than current market rates. The machine uses a Panowin F1 3D printer as a base and controls it using G-code commands sent from a Python script running on a desktop computer. A graphical user interface (GUI) was developed to enable users to control the machine and facilitate image capture, classification and editing. A 488 nm laser diode and a 525 nm filter were incorporated to allow in situ fluorescent imaging of proteins trace-labeled with a fluorophore, Alexa Fluor 488. The instrument was primarily designed using a 3D printer and augmented using commercially available parts, and this publication aims to serve as a guide for comparable in-laboratory robotics projects. Less
Protein trafficking requires coat complexes that couple recognition of sorting motifs in transmembrane cargoes with biogenesis of transport carriers The mechanisms of cargo transport through the endosomal network are poorly understood Here we identify a sorting motif for endosomal recycling of cargoes including the cation-independent mannose- -phosphate receptor and semaphorin C by the membrane tubulating BAR domain-containing sorting nexins SNX and SNX Crystal structures establish that this motif folds into a -hairpin which binds a site in the SNX SNX phox homology domains Over sixty cargoes share this motif and require SNX SNX for their recycling These include cargoes involved ... More
Protein trafficking requires coat complexes that couple recognition of sorting motifs in transmembrane cargoes with biogenesis of transport carriers. The mechanisms of cargo transport through the endosomal network are poorly understood. Here, we identify a sorting motif for endosomal recycling of cargoes, including the cation-independent mannose-6-phosphate receptor and semaphorin 4C, by the membrane tubulating BAR domain-containing sorting nexins SNX5 and SNX6. Crystal structures establish that this motif folds into a β-hairpin, which binds a site in the SNX5/SNX6 phox homology domains. Over sixty cargoes share this motif and require SNX5/SNX6 for their recycling. These include cargoes involved in neuronal migration and a Drosophila snx6 mutant displays defects in axonal guidance. These studies identify a sorting motif and provide molecular insight into an evolutionary conserved coat complex, the ‘Endosomal SNX–BAR sorting complex for promoting exit 1’ (ESCPE-1), which couples sorting motif recognition to the BAR-domain-mediated biogenesis of cargo-enriched tubulo-vesicular transport carriers. Less
The influence of process parameters during freeze thaw FT operations is essential for the preservation of the protein stability activity during production and storage processes in the biopharmaceutical industry Process parameters such as FT ramps the final storage time and temperature affect the occurring FT stress onto the target protein in different ways FT stress includes cold denaturation freeze concentration and ice crystal formation which can result in protein aggregation To visualize the impact of variations in FT ramps descriptors such as solubility phase behavior and crystal morphology were evaluated The phase diagram-based toolbox in combination with an HTS-compatible cryo-device ... More
The influence of process parameters during freeze/thaw (FT) operations is essential for the preservation of the protein stability/activity during production and storage processes in the biopharmaceutical industry. Process parameters, such as FT ramps, the final storage time and temperature, affect the occurring FT stress onto the target protein in different ways. FT stress includes cold denaturation, freeze concentration, and ice crystal formation which can result in protein aggregation. To visualize the impact of variations in FT ramps, descriptors such as solubility, phase behavior and crystal morphology were evaluated. The phase diagram-based toolbox in combination with an HTS-compatible cryo-device allowed the identification of suitable ramping schemes during FT operations. It could be clearly shown that rapid operations are needed above the glass transition temperature of the target protein to circumvent precipitation during FT cycles. Finally, a stability index is introduced which allows ranking of the systems investigated. Less
Microfluidic devices have been increasingly used for low-volume liquid handling operations However laboratory automation of such delicate devices has lagged behind due to the lack of world-to-chip macro-to-micro interfaces In this paper we have presented the first pipette-free robotic microfluidic interface using a microfluidic-embedded container cap referred to as a microfluidic cap-to-dispense CD to achieve a seamless integration of liquid handling and robotic automation without any traditional pipetting steps The CD liquid handling platform offers a generic and modular way to connect the robotic device to standard liquid containers It utilizes the high accuracy and high flexibility of the robotic ... More
Microfluidic devices have been increasingly used for low-volume liquid handling operations. However, laboratory automation of such delicate devices has lagged behind due to the lack of world-to-chip (macro-to-micro) interfaces. In this paper, we have presented the first pipette-free robotic–microfluidic interface using a microfluidic-embedded container cap, referred to as a microfluidic cap-to-dispense (μCD), to achieve a seamless integration of liquid handling and robotic automation without any traditional pipetting steps. The μCD liquid handling platform offers a generic and modular way to connect the robotic device to standard liquid containers. It utilizes the high accuracy and high flexibility of the robotic system to recognize, capture and position; and then using microfluidic adaptive printing it can achieve high-precision on-demand volume distribution. With its modular connectivity, nanoliter processability, high adaptability, and multitask capacity, μCD shows great potential as a generic robotic–microfluidic interface for complete pipette-free liquid handling automation. Less
Human leukocyte antigen HLA alleles have been implicated as risk factors for immune-mediated adverse drug reactions The authors recently reported a strong association between HLA-A and vancomycin-induced drug reaction with eosinophilia and systemic symptoms Identification of individuals with the risk allele before or shortly after the initiation of vancomycin therapy is of great clinical importance to prevent morbidity and mortality and improve drug safety and antibiotic treatment options A prerequisite to the success of pharmacogenetic screening tests is the development of simple robust cost-effective single HLA allele test that can be implemented in routine diagnostic laboratories In this study the ... More
Human leukocyte antigen (HLA) alleles have been implicated as risk factors for immune-mediated adverse drug reactions. The authors recently reported a strong association between HLA-A*32:01 and vancomycin-induced drug reaction with eosinophilia and systemic symptoms. Identification of individuals with the risk allele before or shortly after the initiation of vancomycin therapy is of great clinical importance to prevent morbidity and mortality, and improve drug safety and antibiotic treatment options. A prerequisite to the success of pharmacogenetic screening tests is the development of simple, robust, cost-effective single HLA allele test that can be implemented in routine diagnostic laboratories. In this study, the authors developed a simple, real-time allele-specific PCR for typing the HLA-A*32:01 allele. Four-hundred and fifty-eight DNA samples including 30 HLA-A*32:01–positive samples were typed by allele-specific PCR. Compared with American Society for Histocompatibility and Immunogenetics–accredited, sequence-based, high-resolution, full-allelic HLA typing, this assay demonstrates 100% accuracy, 100% sensitivity (95% CI, 88.43% to 100%), and 100% specificity (95% CI, 99.14% to 100%). The lowest limit of detection of this assay using PowerUp SYBR Green is 10 ng of template DNA. The assay demonstrates a sensitivity and specificity to differentiate the HLA-A*32:01 allele from closely related non–HLA-A*32 alleles and may be used in clinical settings to identify individuals with the risk allele before or during the course of vancomycin therapy. Less
Yersinia pestis the causative agent of bubonic plague is one of the most lethal pathogens in recorded human history Today the concern is the possible misuse of Y pestis as an agent in bioweapons and bioterrorism Current therapies for the treatment of plague include the use of a small number of antibiotics but clinical cases of antibiotic resistance have been reported in some areas of the world Therefore the discovery of new drugs is required to combat potential Y pestis infection Here the crystal structure of the Y pestis UDP-glucose pyrophosphorylase UGP a metabolic enzyme implicated in the survival of ... More
Yersinia pestis, the causative agent of bubonic plague, is one of the most lethal pathogens in recorded human history. Today, the concern is the possible misuse of Y. pestis as an agent in bioweapons and bioterrorism. Current therapies for the treatment of plague include the use of a small number of antibiotics, but clinical cases of antibiotic resistance have been reported in some areas of the world. Therefore, the discovery of new drugs is required to combat potential Y. pestis infection. Here, the crystal structure of the Y. pestis UDP-glucose pyrophosphorylase (UGP), a metabolic enzyme implicated in the survival of Y. pestis in mouse macrophages, is described at 2.17 Å resolution. The structure provides a foundation that may enable the rational design of inhibitors and open new avenues for the development of antiplague therapeutics. Less
Second harmonic generation SHG microscopy and Raman microscopy were used for qualitative and quantitative analysis of pharmaceutical materials Prototype instruments and algorithms for sampling strategies and data analyses were developed to achieve pharmaceutical materials analysis with low limits of detection and short measurement times Manufacturing an amorphous solid dispersion ASD in which an amorphous active pharmaceutical ingredient API within polymer matrix is an effective approach to improve the solubility and bioavailability of a drug However since ASDs are generally metastable materials they can often transform to produce crystalline API with higher thermodynamic stability Analytical methods with low limits of detection ... More
Second harmonic generation (SHG) microscopy and Raman microscopy were used for
qualitative and quantitative analysis of pharmaceutical materials. Prototype instruments and
algorithms for sampling strategies and data analyses were developed to achieve pharmaceutical
materials analysis with low limits of detection and short measurement times.
Manufacturing an amorphous solid dispersion (ASD), in which an amorphous active
pharmaceutical ingredient (API) within polymer matrix, is an effective approach to improve the
solubility and bioavailability of a drug. However, since ASDs are generally metastable materials,
they can often transform to produce crystalline API with higher thermodynamic stability.
Analytical methods with low limits of detection for crystalline APIs were used to assess the
stability of ASDs. With high selectivity to noncentrosymmetric crystals, SHG microscopy was
demonstrated as an analytical tool, which exhibited a limit of detection of 10 ppm for ritonavir
Form II crystals. SHG microscopy was employed for accelerated stability testing of ASDs, which
provided a four-decade dynamic range of crystallinity for kinetic modeling. An established model
was validated by investigating nucleation and crystal growth based on SHG images. To achieve in
situ accelerated stability testing, controlled environment for in situ stability testing (CEiST) was
designed and built to provide elevated temperature and humidity, which is compatible with a
commercial SHG microscope based on our research prototype. The combination of CEiST and
SHG microscopy enabled assessment of individual crystal growth rates by single-particle tracking
and nucleation rates for individual fields of view with low Poisson noise. In addition, SHG
microscopy coupled with CEiST enabled the study of heterogeneity of crystallization kinetics
within pharmaceutical materials.
Polymorphism of APIs plays an important role in drug formulation development. Different
polymorphs of identical APIs may exhibit different physiochemical properties, e.g., solubility,
stability, and bioavailability, due to their crystal structures. Moreover, polymorph transitions may take place during the manufacturing process and storage. Therefore, analytical methods with high
speed for polymorph characterization, which can provide real-time feedback for the polymorphic
transition, have broad applications in pharmaceutical materials characterization. Raman
spectroscopy is able to determine the API polymorphism, but is hampered by the long
measurement times. In this study, two analytical methods with high speed were developed to
characterize API polymorphs. One is SHG microscopy-guided Raman spectroscopy, which
achieved the speed of 10 ms/particle for clopidogrel bisulfate. Initial classification of two different
polymorphs was based on SHG images, followed acquisition of Raman spectroscopy at the
selected positions to determine the API crystal form. Another approach is implementing of
dynamic sampling into confocal Raman microscopy to accelerate Raman image acquisition for 6-
folds. Instead of raster scanning, dynamic sampling algorithm enabled acquiring Raman spectra at
the most informative locations. The reconstructed Raman image of pharmaceutical materials has
<0.5% loss of image quality with 15.8% sampling rate. Less
qualitative and quantitative analysis of pharmaceutical materials. Prototype instruments and
algorithms for sampling strategies and data analyses were developed to achieve pharmaceutical
materials analysis with low limits of detection and short measurement times.
Manufacturing an amorphous solid dispersion (ASD), in which an amorphous active
pharmaceutical ingredient (API) within polymer matrix, is an effective approach to improve the
solubility and bioavailability of a drug. However, since ASDs are generally metastable materials,
they can often transform to produce crystalline API with higher thermodynamic stability.
Analytical methods with low limits of detection for crystalline APIs were used to assess the
stability of ASDs. With high selectivity to noncentrosymmetric crystals, SHG microscopy was
demonstrated as an analytical tool, which exhibited a limit of detection of 10 ppm for ritonavir
Form II crystals. SHG microscopy was employed for accelerated stability testing of ASDs, which
provided a four-decade dynamic range of crystallinity for kinetic modeling. An established model
was validated by investigating nucleation and crystal growth based on SHG images. To achieve in
situ accelerated stability testing, controlled environment for in situ stability testing (CEiST) was
designed and built to provide elevated temperature and humidity, which is compatible with a
commercial SHG microscope based on our research prototype. The combination of CEiST and
SHG microscopy enabled assessment of individual crystal growth rates by single-particle tracking
and nucleation rates for individual fields of view with low Poisson noise. In addition, SHG
microscopy coupled with CEiST enabled the study of heterogeneity of crystallization kinetics
within pharmaceutical materials.
Polymorphism of APIs plays an important role in drug formulation development. Different
polymorphs of identical APIs may exhibit different physiochemical properties, e.g., solubility,
stability, and bioavailability, due to their crystal structures. Moreover, polymorph transitions may take place during the manufacturing process and storage. Therefore, analytical methods with high
speed for polymorph characterization, which can provide real-time feedback for the polymorphic
transition, have broad applications in pharmaceutical materials characterization. Raman
spectroscopy is able to determine the API polymorphism, but is hampered by the long
measurement times. In this study, two analytical methods with high speed were developed to
characterize API polymorphs. One is SHG microscopy-guided Raman spectroscopy, which
achieved the speed of 10 ms/particle for clopidogrel bisulfate. Initial classification of two different
polymorphs was based on SHG images, followed acquisition of Raman spectroscopy at the
selected positions to determine the API crystal form. Another approach is implementing of
dynamic sampling into confocal Raman microscopy to accelerate Raman image acquisition for 6-
folds. Instead of raster scanning, dynamic sampling algorithm enabled acquiring Raman spectra at
the most informative locations. The reconstructed Raman image of pharmaceutical materials has
<0.5% loss of image quality with 15.8% sampling rate. Less
Curli amyloid fibrils secreted by Enterobacteriaceae mediate host cell adhesion and contribute to biofilm formation thereby promoting bacterial resistance to environmental stressors Here we present crystal structures of amyloid-forming segments from the major curli subunit CsgA revealing steric zipper fibrils of tightly mated -sheets demonstrating a structural link between curli and human pathological amyloids D-enantiomeric peptides originally developed to interfere with Alzheimer s disease-associated amyloid- inhibited CsgA fibrillation and reduced biofilm formation in Salmonella typhimurium Moreover as previously shown CsgA fibrils cross-seeded fibrillation of amyloid- providing support for the proposed structural resemblance and potential for cross-species amyloid interactions The presented ... More
Curli amyloid fibrils secreted by Enterobacteriaceae mediate host cell adhesion and contribute to biofilm formation, thereby promoting bacterial resistance to environmental stressors. Here, we present crystal structures of amyloid-forming segments from the major curli subunit, CsgA, revealing steric zipper fibrils of tightly mated β-sheets, demonstrating a structural link between curli and human pathological amyloids. D-enantiomeric peptides, originally developed to interfere with Alzheimer’s disease-associated amyloid-β, inhibited CsgA fibrillation and reduced biofilm formation in Salmonella typhimurium. Moreover, as previously shown, CsgA fibrils cross-seeded fibrillation of amyloid-β, providing support for the proposed structural resemblance and potential for cross-species amyloid interactions. The presented findings provide structural insights into amyloidogenic regions important for curli formation, suggest a novel strategy for disrupting amyloid-structured biofilms, and hypothesize on the formation of self-propagating prion-like species originating from a microbial source that could influence neurodegenerative diseases. Less
Phosphate acquisition by plants is an essential process that is directly implicated in the optimization of crop yields Purple acid phosphatases PAPs are ubiquitous metalloenzymes which catalyze the hydrolysis of a wide range of phosphate esters and anhydrides While some plant PAPs display a preference for ATP as the substrate others are efficient in hydrolyzing phytate or -phosphoenolpyruvate PEP PAP from red kidney bean rkbPAP is an efficient ATP- and ADPase but has no activity towards phytate The crystal structure of this enzyme in complex with an ATP analogue to resolution provides insight into the amino acid residues that play ... More
Phosphate acquisition by plants is an essential process that is directly implicated in the optimization of crop yields. Purple acid phosphatases (PAPs) are ubiquitous metalloenzymes, which catalyze the hydrolysis of a wide range of phosphate esters and anhydrides. While some plant PAPs display a preference for ATP as the substrate, others are efficient in hydrolyzing phytate or 2-phosphoenolpyruvate (PEP). PAP from red kidney bean (rkbPAP) is an efficient ATP- and ADPase, but has no activity towards phytate. The crystal structure of this enzyme in complex with an ATP analogue (to 2.20 Å resolution) provides insight into the amino acid residues that play an essential role in binding this substrate. Homology modelling was used to generate three-dimensional structures for the active sites of PAPs from tobacco (NtPAP) and Arabidopsis thaliana (AtPAP12 and AtPAP26) that are efficient in hydrolyzing phytate and PEP as substrates, respectively. In combination with substrate docking simulations and a phylogenetic analysis of 49 plant PAP sequences (including the first PAP sequences reported from Eucalyptus), several active site residues were identified that are important in defining the substrate specificities of plant PAPs. These results may inform bioengineering studies aimed at identifying and incorporating suitable plant PAP genes into crops to improve phosphorus use efficiency. Organic phosphorus sources increasingly supplement or replace inorganic fertilizer, and efficient phosphorus use of crops will lower the environmental footprint of agriculture while enhancing food production. Less
The CC chemokine receptor CCR balances immunity and tolerance by homeostatic trafficking of immune cells In cancer CCR -mediated trafficking leads to lymph node metastasis suggesting the receptor as a promising therapeutic target Here we present the crystal structure of human CCR fused to the protein Sialidase NanA by using data up to resolution The structure shows the ligand Cmp bound to an intracellular allosteric binding pocket A sulfonamide group characteristic for various chemokine receptor ligands binds to a patch of conserved residues in the Gi protein binding region between transmembrane helix and helix We demonstrate how structural data can ... More
The CC chemokine receptor 7 (CCR7) balances immunity and tolerance by homeostatic trafficking of immune cells. In cancer, CCR7-mediated trafficking leads to lymph node metastasis, suggesting the receptor as a promising therapeutic target. Here, we present the crystal structure of human CCR7 fused to the protein Sialidase NanA by using data up to 2.1 Å resolution. The structure shows the ligand Cmp2105 bound to an intracellular allosteric binding pocket. A sulfonamide group, characteristic for various chemokine receptor ligands, binds to a patch of conserved residues in the Gi protein binding region between transmembrane helix 7 and helix 8. We demonstrate how structural data can be used in combination with a compound repository and automated thermal stability screening to identify and modulate allosteric chemokine receptor antagonists. We detect both novel (CS-1 and CS-2) and clinically relevant (CXCR1-CXCR2 phase-II antagonist Navarixin) CCR7 modulators with implications for multi-target strategies against cancer. Less
Elucidating the cellular architecture of the human cerebral cortex is central to understanding our cognitive abilities and susceptibility to disease Here we used single-nucleus RNA-sequencing analysis to perform a comprehensive study of cell types in the middle temporal gyrus of human cortex We identified a highly diverse set of excitatory and inhibitory neuron types that are mostly sparse with excitatory types being less layer-restricted than expected Comparison to similar mouse cortex single-cell RNA-sequencing datasets revealed a surprisingly well-conserved cellular architecture that enables matching of homologous types and predictions of properties of human cell types Despite this general conservation we also ... More
Elucidating the cellular architecture of the human cerebral cortex is central to understanding our cognitive abilities and susceptibility to disease. Here we used single-nucleus RNA-sequencing analysis to perform a comprehensive study of cell types in the middle temporal gyrus of human cortex. We identified a highly diverse set of excitatory and inhibitory neuron types that are mostly sparse, with excitatory types being less layer-restricted than expected. Comparison to similar mouse cortex single-cell RNA-sequencing datasets revealed a surprisingly well-conserved cellular architecture that enables matching of homologous types and predictions of properties of human cell types. Despite this general conservation, we also found extensive differences between homologous human and mouse cell types, including marked alterations in proportions, laminar distributions, gene expression and morphology. These species-specific features emphasize the importance of directly studying human brain. Less
Compositions devices methods and systems are provided for differential functionalization of a surface of a structure to support biopolymer synthesis Provided herein are processes which include use of lamps lasers and or microcontact printing to add functional groups to surfaces for the efficient and uniform synthesis of oligonucleic acids
A H N virus predominated recent influenza seasons which has resulted in the rigorous investigation of haemagglutinin but whether neuraminidase NA has undergone antigenic change and contributed to the predominance of A H N virus is unknown Here we show that the NA of the circulating A H N viruses has experienced significant antigenic drift since compared with the A Hong Kong vaccine strain This antigenic drift was mainly caused by amino acid mutations at NA residues S N S T introducing an N-linked glycosylation site at residue and As a result the binding of the NA of A H ... More
A(H3N2) virus predominated recent influenza seasons, which has resulted in the rigorous investigation of haemagglutinin, but whether neuraminidase (NA) has undergone antigenic change and contributed to the predominance of A(H3N2) virus is unknown. Here, we show that the NA of the circulating A(H3N2) viruses has experienced significant antigenic drift since 2016 compared with the A/Hong Kong/4801/2014 vaccine strain. This antigenic drift was mainly caused by amino acid mutations at NA residues 245, 247 (S245N/S247T; introducing an N-linked glycosylation site at residue 245) and 468. As a result, the binding of the NA of A(H3N2) virus by some human monoclonal antibodies, including those that have broad reactivity to the NA of the 1957 A(H2N2) and 1968 A(H3N2) reference pandemic viruses as well as contemporary A(H3N2) strains, was reduced or abolished. This antigenic drift also reduced NA-antibody-based protection against in vivo virus challenge. X-ray crystallography showed that the glycosylation site at residue 245 is within a conserved epitope that overlaps the NA active site, explaining why it impacts antibody binding. Our findings suggest that NA antigenic drift impacts protection against influenza virus infection, thus highlighting the importance of including NA antigenicity for consideration in the optimization of influenza vaccines. Less
We previously generated rotavirus-specific RV-specific recombinant monoclonal antibodies mAbs derived from B cells isolated from human intestinal resections Twenty-four of these mAbs were specific for the VP fragment of RV VP and most of were non-neutralizing when tested in the conventional MA cell based assay We reexamined the ability of these mAbs to neutralize RVs in human intestinal epithelial cells including ileal enteroids and HT- cells Most of of the non-neutralizing VP mAbs efficiently neutralized human RV in HT- cells or enteroids Serum RV neutralization titers in adults and infants were significantly higher in HT- than MA cells and adsorption ... More
We previously generated 32 rotavirus-specific (RV-specific) recombinant monoclonal antibodies (mAbs) derived from B cells isolated from human intestinal resections. Twenty-four of these mAbs were specific for the VP8* fragment of RV VP4, and most (20 of 24) were non-neutralizing when tested in the conventional MA104 cell–based assay. We reexamined the ability of these mAbs to neutralize RVs in human intestinal epithelial cells, including ileal enteroids and HT-29 cells. Most (18 of 20) of the “non-neutralizing” VP8* mAbs efficiently neutralized human RV in HT-29 cells or enteroids. Serum RV neutralization titers in adults and infants were significantly higher in HT-29 than MA104 cells and adsorption of these sera with recombinant VP8* lowered the neutralization titers in HT-29 but not MA104 cells. VP8* mAbs also protected suckling mice from diarrhea in an in vivo challenge model. X-ray crystallographic analysis of one VP8* mAb (mAb9) in complex with human RV VP8* revealed that the mAb interaction site was distinct from the human histo-blood group antigen binding site. Since MA104 cells are the most commonly used cell line to detect anti-RV neutralization activity, these findings suggest that prior vaccine and other studies of human RV neutralization responses may have underestimated the contribution of VP8* antibodies to the overall neutralization titer. Less
Viral discovery is accelerating at an unprecedented rate due to continuing advances in culture-independent sequence-based analyses One important facet of this discovery is identification of the hosts of these recently characterized uncultured viruses To this end we have adapted the viral tagging approach which bypasses the need for culture-based methods to identify host phage pairings Fluorescently labelled anonymous virions adsorb to unlabelled anonymous bacterial host cells which are then individually sorted as host phage pairs followed by genome amplification and high-throughput sequencing to establish the identities of both the host and the attached virus es We demonstrate single-cell viral tagging ... More
Viral discovery is accelerating at an unprecedented rate due to continuing advances in culture-independent sequence-based analyses. One important facet of this discovery is identification of the hosts of these recently characterized uncultured viruses. To this end, we have adapted the viral tagging approach, which bypasses the need for culture-based methods to identify host–phage pairings. Fluorescently labelled anonymous virions adsorb to unlabelled anonymous bacterial host cells, which are then individually sorted as host–phage pairs, followed by genome amplification and high-throughput sequencing to establish the identities of both the host and the attached virus(es). We demonstrate single-cell viral tagging using the faecal microbiome, including cross-tagging of viruses and bacteria between human subjects. A total of 363 unique host–phage pairings were predicted, most of which were subject-specific and involved previously uncharacterized viruses despite the majority of their bacterial hosts having known taxonomy. One-fifth of these pairs were confirmed by multiple individual tagged cells. Viruses targeting more than one bacterial species were conspicuously absent in the host–phage network, suggesting that phages are not major vectors of inter-species horizontal gene transfer in the human gut. A high level of cross-reactivity between phages and bacteria from different subjects was noted despite subject-specific viral profiles, which has implications for faecal microbiota transplant therapy. Less
Image-based protein phase diagram analysis is key for understanding and exploiting protein phase behavior in the biopharmaceutical field However required data analysis has become a notorious time-consuming task since high-throughput screening approaches were implemented A variety of computational tools have been developed to support analysis but these tools primarily use end point visible light images This study investigates the combined effect of end point and time-dependent image features obtained from cross-polarized and ultraviolet light features supplementary to visible light on protein phase diagram image classification In addition external validation was performed to evaluate the classification algorithm s applicability to support ... More
Image-based protein phase diagram analysis is key for understanding and exploiting protein phase behavior in the biopharmaceutical field. However, required data analysis has become a notorious time-consuming task since high-throughput screening approaches were implemented. A variety of computational tools have been developed to support analysis, but these tools primarily use end point visible light images. This study investigates the combined effect of end point and time-dependent image features obtained from cross-polarized and ultraviolet light features, supplementary to visible light, on protein phase diagram image classification. In addition, external validation was performed to evaluate the classification algorithm’s applicability to support protein phase diagram scoring. The predicted protein phase behavior classes were subsequently used to automatically construct multidimensional protein phase diagrams to prevent image information loss without complicating the used image classification algorithm. Combining end point and time-dependent features from 3 light sources resulted in a balanced accuracy of 86.4 ± 4.3%, which is comparable to or better than more complex classifiers reported in literature. External validation resulted in a correct formulation classification rate of 91.7%. Subsequent automated construction of the multidimensional protein phase diagrams, using predicted classes, allowed visualization of details such as crystallization rate and protein phase behavior type coexistence. Less
Detection and activation of HIV broadly neutralizing antibody precursor B cells using anti-idiotypes
Many tested vaccines fail to provide protection against disease despite the induction of antibodies that bind the pathogen of interest In light of this there is much interest in rationally designed subunit vaccines that direct the antibody response to protective epitopes Here we produced a panel of anti-idiotype antibodies able to specifically recognize the inferred germline version of the human immunodeficiency virus HIV- broadly neutralizing antibody b iglb We determined the crystal structure of two anti-idiotypes in complex with iglb and used these anti-idiotypes to identify rare naive human B cells expressing B cell receptors with similarity to iglb Immunization ... More
Many tested vaccines fail to provide protection against disease despite the induction of antibodies that bind the pathogen of interest. In light of this, there is much interest in rationally designed subunit vaccines that direct the antibody response to protective epitopes. Here, we produced a panel of anti-idiotype antibodies able to specifically recognize the inferred germline version of the human immunodeficiency virus 1 (HIV-1) broadly neutralizing antibody b12 (iglb12). We determined the crystal structure of two anti-idiotypes in complex with iglb12 and used these anti-idiotypes to identify rare naive human B cells expressing B cell receptors with similarity to iglb12. Immunization with a multimerized version of this anti-idiotype induced the proliferation of transgenic murine B cells expressing the iglb12 heavy chain in vivo, despite the presence of deletion and anergy within this population. Together, our data indicate that anti-idiotypes are a valuable tool for the study and induction of potentially protective antibodies. Less
Human anti-HIV- broadly neutralizing antibodies bNAbs protect against infection in animal models However bNAbs have not been elicited by vaccination in diverse wild-type animals or humans in part because B cells expressing the precursors of these antibodies do not recognize most HIV- envelopes Envs Immunogens have been designed that activate these B cell precursors in vivo but they also activate competing off-target responses Here we report on a complementary approach to expand specific B cells using an anti-idiotypic antibody iv that selects for naive human B cells expressing immunoglobulin light chains with amino acid complementarity determining region s a key ... More
Human anti-HIV-1 broadly neutralizing antibodies (bNAbs) protect against infection in animal models. However, bNAbs have not been elicited by vaccination in diverse wild-type animals or humans, in part because B cells expressing the precursors of these antibodies do not recognize most HIV-1 envelopes (Envs). Immunogens have been designed that activate these B cell precursors in vivo, but they also activate competing off-target responses. Here we report on a complementary approach to expand specific B cells using an anti-idiotypic antibody, iv8, that selects for naive human B cells expressing immunoglobulin light chains with 5–amino acid complementarity determining region 3s, a key feature of anti-CD4 binding site (CD4bs)–specific VRC01-class antibodies. In mice, iv8 induced target cells to expand and mature in the context of a polyclonal immune system and produced serologic responses targeting the CD4bs on Env. In summary, the results demonstrate that an anti-idiotypic antibody can specifically recognize and expand rare B cells that express VRC01-class antibodies against HIV-1. Less
RNase H dependent PCR-enabled T-cell receptor sequencing rhTCRseq can be used to determine paired alpha beta T-cell receptor TCR clonotypes in single cells or perform alpha and beta TCR repertoire analysis in bulk RNA samples With the enhanced specificity of RNase H dependent PCR rhPCR it achieves TCR-specific amplification and addition of dual-index barcodes in a single PCR step For single cells the protocol includes sorting of single cells into plates generation of cDNA libraries a TCR-specific amplification step a second PCR on pooled sample to generate a sequencing library and sequencing In the bulk method sorting and cDNA library ... More
RNase H–dependent PCR-enabled T-cell receptor sequencing (rhTCRseq) can be used to determine paired alpha/beta T-cell receptor (TCR) clonotypes in single cells or perform alpha and beta TCR repertoire analysis in bulk RNA samples. With the enhanced specificity of RNase H–dependent PCR (rhPCR), it achieves TCR-specific amplification and addition of dual-index barcodes in a single PCR step. For single cells, the protocol includes sorting of single cells into plates, generation of cDNA libraries, a TCR-specific amplification step, a second PCR on pooled sample to generate a sequencing library, and sequencing. In the bulk method, sorting and cDNA library steps are replaced with a reverse-transcriptase (RT) reaction that adds a unique molecular identifier (UMI) to each cDNA molecule to improve the accuracy of repertoire-frequency measurements. Compared to other methods for TCR sequencing, rhTCRseq has a streamlined workflow and the ability to analyze single cells in 384-well plates. Compared to TCR reconstruction from single-cell transcriptome sequencing data, it improves the success rate for obtaining paired alpha/beta information and ensures recovery of complete complementarity-determining region 3 (CDR3) sequences, a prerequisite for cloning/expression of discovered TCRs. Although it has lower throughput than droplet-based methods, rhTCRseq is well-suited to analysis of small sorted populations, especially when analysis of 96 or 384 single cells is sufficient to identify predominant T-cell clones. For single cells, sorting typically requires 2–4 h and can be performed days, or even months, before library construction and data processing, which takes ~4 d; the bulk RNA protocol takes ~3 d. Less
Balanced fusion and fission are key for the proper function and physiology of mitochondria Remodelling of the mitochondrial inner membrane is mediated by the dynamin-like protein mitochondrial genome maintenance Mgm in fungi or the related protein optic atrophy OPA in animals Mgm is required for the preservation of mitochondrial DNA in yeast whereas mutations in the OPA gene in humans are a common cause of autosomal dominant optic atrophy a genetic disorder that affects the optic nerve Mgm and OPA are present in mitochondria as a membrane-integral long form and a short form that is soluble in the intermembrane space ... More
Balanced fusion and fission are key for the proper function and physiology of mitochondria1,2. Remodelling of the mitochondrial inner membrane is mediated by the dynamin-like protein mitochondrial genome maintenance 1 (Mgm1) in fungi or the related protein optic atrophy 1 (OPA1) in animals3,4,5. Mgm1 is required for the preservation of mitochondrial DNA in yeast6, whereas mutations in the OPA1 gene in humans are a common cause of autosomal dominant optic atrophy—a genetic disorder that affects the optic nerve7,8. Mgm1 and OPA1 are present in mitochondria as a membrane-integral long form and a short form that is soluble in the intermembrane space. Yeast strains that express temperature-sensitive mutants of Mgm19,10 or mammalian cells that lack OPA1 display fragmented mitochondria11,12, which suggests that Mgm1 and OPA1 have an important role in inner-membrane fusion. Consistently, only the mitochondrial outer membrane—not the inner membrane—fuses in the absence of functional Mgm113. Mgm1 and OPA1 have also been shown to maintain proper cristae architecture10,14; for example, OPA1 prevents the release of pro-apoptotic factors by tightening crista junctions15. Finally, the short form of OPA1 localizes to mitochondrial constriction sites, where it presumably promotes mitochondrial fission16. How Mgm1 and OPA1 perform their diverse functions in membrane fusion, scission and cristae organization is at present unknown. Here we present crystal and electron cryo-tomography structures of Mgm1 from Chaetomium thermophilum. Mgm1 consists of a GTPase (G) domain, a bundle signalling element domain, a stalk, and a paddle domain that contains a membrane-binding site. Biochemical and cell-based experiments demonstrate that the Mgm1 stalk mediates the assembly of bent tetramers into helical filaments. Electron cryo-tomography studies of Mgm1-decorated lipid tubes and fluorescence microscopy experiments on reconstituted membrane tubes indicate how the tetramers assemble on positively or negatively curved membranes. Our findings convey how Mgm1 and OPA1 filaments dynamically remodel the mitochondrial inner membrane. Less
The -oxopurine phosphoribosyltransferases PRTs are drug targets for the treatment of parasitic diseases This is due to the fact that parasites are auxotrophic for the -oxopurine bases relying on salvage enzymes for the synthesis of their -oxopurine nucleoside monophosphates In Trypanosoma brucei the parasite that is the aetiological agent for sleeping sickness there are three -oxopurine PRT isoforms Two are specific for hypoxanthine and guanine whilst the third characterized here uses all three naturally occurring bases with similar efficiency Here we have determined crystal structures for TbrHGXPRT in complex with GMP XMP and IMP to investigate the structural basis for ... More
The 6-oxopurine phosphoribosyltransferases (PRTs) are drug targets for the treatment of parasitic diseases. This is due to the fact that parasites are auxotrophic for the 6-oxopurine bases relying on salvage enzymes for the synthesis of their 6-oxopurine nucleoside monophosphates. In Trypanosoma brucei, the parasite that is the aetiological agent for sleeping sickness, there are three 6-oxopurine PRT isoforms. Two are specific for hypoxanthine and guanine, whilst the third, characterized here, uses all three naturally occurring bases with similar efficiency. Here, we have determined crystal structures for TbrHGXPRT in complex with GMP, XMP and IMP to investigate the structural basis for substrate specificity. The results show that Y201 and E208, not commonly observed within the purine binding pocket of 6-oxopurine PRTs, contribute to the versatility of this enzyme. The structures further show that a nearby water can act as an adaptor to facilitate the binding of XMP and GMP. When GMP binds, a water can accept a proton from the 2-amino group but when XMP binds, the equivalent water can donate its proton to the 2-oxo group. However, when IMP is bound, no water molecule is observed at that location. Less
Discovery of novel Mnk inhibitors using mutation-based induced-fit virtual high-throughput screening
Mnk kinases Mnk and are downstream effectors of Map kinase pathways and regulate phosphorylation of eukaryotic initiation factor E Engagement of the Mnk pathway is critical in acute myeloid leukemia AML leukemogenesis and Mnk inhibitors have potent antileukemic properties in vitro and in vivo suggesting that targeting Mnk kinases may provide a novel approach for treating AML Here we report the development and application of a mutation-based induced-fit in silico screen to identify novel Mnk inhibitors The Mnk structure was modeled by temporarily mutating an amino acid that obstructs the ATP-binding site in the Mnk crystal structure while carrying out ... More
Mnk kinases (Mnk1 and 2) are downstream effectors of Map kinase pathways and regulate phosphorylation of eukaryotic initiation factor 4E. Engagement of the Mnk pathway is critical in acute myeloid leukemia (AML) leukemogenesis and Mnk inhibitors have potent antileukemic properties in vitro and in vivo, suggesting that targeting Mnk kinases may provide a novel approach for treating AML. Here, we report the development and application of a mutation-based induced-fit in silico screen to identify novel Mnk inhibitors. The Mnk1 structure was modeled by temporarily mutating an amino acid that obstructs the ATP-binding site in the Mnk1 crystal structure while carrying out docking simulations of known inhibitors. The hit compounds display activity in Mnk biochemical and cellular assays, including acute myeloid leukemia progenitors. This approach will enable further rational structure-based drug design of new Mnk inhibitors and potentially novel ways of therapeutically targeting this kinase. Less
Objective To optimize post-differentiation freeze thaw and culture conditions for induced pluripotent stem cell-derived brain microvascular endothelial cell iPSC-BMEC maturation functionality and reproducibility Methods Human iPSCs were spontaneously differentiated into BMECs protocol based on Lippmann et al Nat Biotech Dissociation and sub-culture conditions were investigated using Design of Experiments DoE an unbiased method based on structured statistical analysis of variance ANOVA DoE efficiently identifies interactions amongst experimental variables and predicts responses Our design focused on maximizing trans-endothelial electrical resistance TEER We incorporated a Mantis liquid handler to execute precise culture conditions in -well transwell systems and measured TEER over time ... More
Objective: To optimize post-differentiation freeze, thaw, and culture conditions for induced pluripotent stem cell-derived brain microvascular endothelial cell (iPSC-BMEC) maturation, functionality, and reproducibility. Methods: Human iPSCs were spontaneously differentiated into BMECs (protocol based on Lippmann et al. Nat Biotech 2012). Dissociation and sub-culture conditions were investigated using Design of Experiments (DoE), an unbiased method based on structured statistical analysis of variance (ANOVA). DoE efficiently identifies interactions amongst experimental variables and predicts responses. Our design focused on maximizing trans-endothelial electrical resistance (TEER). We incorporated a Mantis liquid handler to execute precise culture conditions in 96-well transwell systems and measured TEER over time. Top hit conditions were validated on multiple batches of iPSC-BMECs, these included post-thaw cell viability, hourly TEER reads, and immunocytochemistry (ICC). Results: We have identified a robust cryopreservation method, time course and medium formulation for sub-culturing spontaneously differentiated iPSC-BMEC. The optimized cryopreservation protocol yields high cell viability recovery allowing the ability to produce bulk batches of iPSC-BMECs, thereby minimizing interexperimental variability. Surprisingly, we found that the removal of retinoic acid and the extension to at least 7 days in culture reproducibly resulted in prolonged high TEER, approximately 500 ohms * cm2 greater than TEER peak at 48 h, in iPSC-BMEC mono-culture transwells. Our sub-culture method generates iPSC-BMECs that express the endothelial surface marker PECAM1, relevant blood–brain barrier (BBB) tight junction proteins (claudin-5, ZO-1, occludin), and transporters enriched on brain microvessels (Glut-1, transferrin receptor, insulin receptor). Conclusion: We demonstrate the power of applying DoE to fine-tune complex culture conditions to maximize cell performance. Our cryopreservation and sub-culture protocols robustly produce functional endothelial cells of the BBB that are suited to address basic cerebral vascular biology questions, study the vascular phenotype of neurological disorders, and enable high-throughput screening for drug discovery. Less
The structure of BgaR a transcriptional regulator of the lactose operon in Clostridium perfringens has been solved by SAD phasing using a mercury derivative BgaR is an exquisite sensor of lactose with a binding affinity in the low-micromolar range This sensor and regulator has been captured bound to lactose and to lactulose as well as in a nominal apo form and was compared with AraC another saccharide-binding transcriptional regulator It is shown that the saccharides bind in the N-terminal region of a jelly-roll fold but that part of the saccharide is exposed to bulk solvent This differs from the classical ... More
The structure of BgaR, a transcriptional regulator of the lactose operon in�Clostridium perfringens, has been solved by SAD phasing using a mercury derivative. BgaR is an exquisite sensor of lactose, with a binding affinity in the low-micromolar range. This sensor and regulator has been captured bound to lactose and to lactulose as well as in a nominal apo form, and was compared with AraC, another saccharide-binding transcriptional regulator. It is shown that the saccharides bind in the N-terminal region of a jelly-roll fold, but that part of the saccharide is exposed to bulk solvent. This differs from the classical AraC saccharide-binding site, which is mostly sequestered from the bulk solvent. The structures of BgaR bound to lactose and to lactulose highlight how specific and nonspecific interactions lead to a higher binding affinity of BgaR for lactose compared with lactulose. Moreover, solving multiple structures of BgaR in different space groups, both bound to saccharides and unbound, verified that the dimer interface along a C-terminal helix is similar to the dimer interface observed in AraC. Less
Designing peptides that fold and assemble in response to metal ions tests our understanding of how peptide folding and metal binding influence one another Here histidine residues are introduced into the hydrophobic core of a coiled-coil trimer generating a peptide that self-assembles upon the addition of metal ions HisAD the resulting peptide is unstructured in the absence of metal and folds selectively to form an -helical construct upon complexation with Cu II and Ni II but not Co II or Zn II The structure and metal-binding ability of HisAD is probed using a combination of circular dichroism CD spectroscopy analytical ... More
Designing peptides that fold and assemble in response to metal ions tests our understanding of how peptide folding and metal binding influence one another. Here, histidine residues are introduced into the hydrophobic core of a coiled-coil trimer, generating a peptide that self-assembles upon the addition of metal ions. HisAD, the resulting peptide, is unstructured in the absence of metal and folds selectively to form an α-helical construct upon complexation with Cu(II) and Ni(II) but not Co(II) or Zn(II). The structure, and metal-binding ability, of HisAD is probed using a combination of circular dichroism (CD) spectroscopy, analytical ultracentrifugation (AUC), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. These show the peptide is trimeric and binds to both Cu(II) and Ni(II) in a 1 : 1 ratio with the histidine residues involved in the metal coordination, as designed. The X-ray crystal structure of the HisAD-Cu(II) complex reveals the trimeric HisAD peptide coordinates three Cu(II) ions; this is the first example of such a structure. Additionally, HisAD demonstrates an unprecedented discrimination between transition metal ions, the basis of which is likely to be related to the stability of the peptide-metal complexes formed. Less
To enable rapid selection of traits in marker-assisted breeding markers must be technically simple low-cost high-throughput and randomly distributed in a genome We developed such a technology designated as Multiplex Restriction Amplicon Sequencing MRASeq which reduces genome complexity by polymerase chain reaction PCR amplification of amplicons flanked by restriction sites The first PCR primers contain restriction site sequences at -ends preceded by - bases of specific or degenerate nucleotide sequences and then by a unique M -tail sequence which serves as a binding site for a second PCR that adds sequencing primers and barcodes to allow sample multiplexing for sequencing ... More
To enable rapid selection of traits in marker-assisted breeding, markers must be technically simple, low-cost, high-throughput and randomly distributed in a genome. We developed such a technology, designated as Multiplex Restriction Amplicon Sequencing (MRASeq), which reduces genome complexity by polymerase chain reaction (PCR) amplification of amplicons flanked by restriction sites. The first PCR primers contain restriction site sequences at 3’-ends, preceded by 6-10 bases of specific or degenerate nucleotide sequences and then by a unique M13-tail sequence which serves as a binding site for a second PCR that adds sequencing primers and barcodes to allow sample multiplexing for sequencing. The sequences of restriction sites and adjacent nucleotides can be altered to suit different species. Physical mapping of MRASeq SNPs from a biparental population of allohexaploid wheat (Triticum aestivum L.) showed a random distribution of SNPs across the genome. MRASeq generated thousands of SNPs from a wheat biparental population and natural populations of wheat and barley (Hordeum vulgare L.). This novel, next-generation sequencing-based genotyping platform can be used for linkage mapping to screen quantitative trait loci (QTL), background selection in breeding and many other genetics and breeding applications of various species. Less
DNA is an emerging medium for digital data and its adoption can be accelerated by synthesis processes specialized for storage applications Here we describe a de novo enzymatic synthesis strategy designed for data storage which harnesses the template-independent polymerase terminal deoxynucleotidyl transferase TdT in kinetically controlled conditions Information is stored in transitions between non-identical nucleotides of DNA strands To produce strands representing user-defined content nucleotide substrates are added iteratively yielding short homopolymeric extensions whose lengths are controlled by apyrase-mediated substrate degradation With this scheme we synthesize DNA strands carrying bits including addressing and demonstrate retrieval with streaming nanopore sequencing We ... More
DNA is an emerging medium for digital data and its adoption can be accelerated by synthesis processes specialized for storage applications. Here, we describe a de novo enzymatic synthesis strategy designed for data storage which harnesses the template-independent polymerase terminal deoxynucleotidyl transferase (TdT) in kinetically controlled conditions. Information is stored in transitions between non-identical nucleotides of DNA strands. To produce strands representing user-defined content, nucleotide substrates are added iteratively, yielding short homopolymeric extensions whose lengths are controlled by apyrase-mediated substrate degradation. With this scheme, we synthesize DNA strands carrying 144 bits, including addressing, and demonstrate retrieval with streaming nanopore sequencing. We further devise a digital codec to reduce requirements for synthesis accuracy and sequencing coverage, and experimentally show robust data retrieval from imperfectly synthesized strands. This work provides distributive enzymatic synthesis and information-theoretic approaches to advance digital information storage in DNA. Less
Transient receptor potential TRP channels are polymodal sensory transducers that respond to chemicals temperature mechanical stress and membrane voltage and are involved in vision taste olfaction hearing touch thermal perception and nociception TRP channels are implicated in numerous devastating diseases including various forms of cancer and represent important drug targets The large sizes low expression levels and conformational dynamics of TRP channels make them challenging targets for structural biology Here we present the methodology used in structural studies of TRPV a TRP channel that is highly selective for calcium and mediates Ca uptake in epithelial tissues We provide a protocol ... More
Transient receptor potential (TRP) channels are polymodal sensory transducers that respond to chemicals, temperature, mechanical stress, and membrane voltage and are involved in vision, taste, olfaction, hearing, touch, thermal perception, and nociception. TRP channels are implicated in numerous devastating diseases, including various forms of cancer, and represent important drug targets. The large sizes, low expression levels, and conformational dynamics of TRP channels make them challenging targets for structural biology. Here, we present the methodology used in structural studies of TRPV6, a TRP channel that is highly selective for calcium and mediates Ca2+ uptake in epithelial tissues. We provide a protocol for the expression, purification, and crystallization of TRPV6. Similar approaches can be used to determine crystal structures of other membrane proteins, including different members of the TRP channel family. Less
Human NimA-related kinases Neks have multiple mitotic and non-mitotic functions but few substrates are known We systematically determined the phosphorylation-site motifs for the entire Nek kinase family except for Nek While all Nek kinases strongly select for hydrophobic residues in the position the family separates into four distinct groups based on specificity for a serine versus threonine phospho-acceptor and preference for basic or acidic residues in other positions Unlike Nek -Nek Nek is a dual-specificity kinase that efficiently phosphorylates itself and peptide substrates on serine and tyrosine and its activity is enhanced by tyrosine auto-phosphorylation Nek dual-specificity depends on residues ... More
Human NimA-related kinases (Neks) have multiple mitotic and non-mitotic functions, but few substrates are known. We systematically determined the phosphorylation-site motifs for the entire Nek kinase family, except for Nek11. While all Nek kinases strongly select for hydrophobic residues in the −3 position, the family separates into four distinct groups based on specificity for a serine versus threonine phospho-acceptor, and preference for basic or acidic residues in other positions. Unlike Nek1-Nek9, Nek10 is a dual-specificity kinase that efficiently phosphorylates itself and peptide substrates on serine and tyrosine, and its activity is enhanced by tyrosine auto-phosphorylation. Nek10 dual-specificity depends on residues in the HRD+2 and APE-4 positions that are uncommon in either serine/threonine or tyrosine kinases. Finally, we show that the phosphorylation-site motifs for the mitotic kinases Nek6, Nek7 and Nek9 are essentially identical to that of their upstream activator Plk1, suggesting that Nek6/7/9 function as phospho-motif amplifiers of Plk1 signaling. Less
The universally conserved N -threonylcarbamoyladenosine t A modification of tRNA is essential for translational fidelity In bacteria t A biosynthesis starts with the TsaC TsaC -catalyzed synthesis of the intermediate threonylcarbamoyl adenylate TC AMP followed by transfer of the threonylcarbamoyl TC moiety to adenine- of tRNA by the TC-transfer complex comprised of TsaB TsaD and TsaE subunits and possessing an ATPase activity required for multi-turnover of the t A cycle We report a - crystal structure of the T maritima TC-transfer complex TmTsaB D E bound to Mg -ATP in the ATPase site and substrate analog carboxy-AMP in the TC-transfer ... More
The universally conserved N6-threonylcarbamoyladenosine (t6A) modification of tRNA is essential for translational fidelity. In bacteria, t6A biosynthesis starts with the TsaC/TsaC2-catalyzed synthesis of the intermediate threonylcarbamoyl adenylate (TC–AMP), followed by transfer of the threonylcarbamoyl (TC) moiety to adenine-37 of tRNA by the TC-transfer complex comprised of TsaB, TsaD and TsaE subunits and possessing an ATPase activity required for multi-turnover of the t6A cycle. We report a 2.5-Å crystal structure of the T. maritima TC-transfer complex (TmTsaB2D2E2) bound to Mg2+-ATP in the ATPase site, and substrate analog carboxy-AMP in the TC-transfer site. Site directed mutagenesis results show that residues in the conserved Switch I and Switch II motifs of TsaE mediate the ATP hydrolysis-driven reactivation/reset step of the t6A cycle. Further, SAXS analysis of the TmTsaB2D2-tRNA complex in solution reveals bound tRNA lodged in the TsaE binding cavity, confirming our previous biochemical data. Based on the crystal structure and molecular docking of TC–AMP and adenine-37 in the TC-transfer site, we propose a model for the mechanism of TC transfer by this universal biosynthetic system. Less
Toxin-antitoxin TA gene pairs have been identified in nearly all bacterial genomes sequenced to date and are thought to facilitate persistence and antibiotic tolerance TA loci are classified into various types based upon the characteristics of their antitoxins with those in type II expressing proteic antitoxins Many toxins from type II modules are ribonucleases that maintain a PilT N-terminal PIN domain containing conserved amino acids considered essential for activity The vapBC virulence-associated protein TA system is the largest subfamily in this class and has been linked to pathogenesis of nontypeable Haemophilus influenzae NTHi In this study the crystal structure of ... More
Toxin-antitoxin (TA) gene pairs have been identified in nearly all bacterial genomes sequenced to date and are thought to facilitate persistence and antibiotic tolerance. TA loci are classified into various types based upon the characteristics of their antitoxins, with those in type II expressing proteic antitoxins. Many toxins from type II modules are ribonucleases that maintain a PilT N-terminal (PIN) domain containing conserved amino acids considered essential for activity. The vapBC (virulence-associated protein) TA system is the largest subfamily in this class and has been linked to pathogenesis of nontypeable Haemophilus influenzae (NTHi). In this study, the crystal structure of the VapBC-1 complex from NTHi was determined to 2.20 Å resolution. Based on this structure, aspartate-to-asparagine and glutamate-to-glutamine mutations of four conserved residues in the PIN domain of the VapC-1 toxin were constructed and the effects of the mutations on protein-protein interactions, growth of Escherichia coli, and pathogenesis ex vivo were tested. Finally, a novel model system was designed and utilized that consists of an NTHi ΔvapBC-1 strain complemented in cis with the TA module containing a mutated or wild-type toxin at an ectopic site on the chromosome. This enabled the analysis of the effect of PIN domain toxin mutants in tandem with their wild-type antitoxin under the control of the vapBC-1 native promoter and in single copy. This is the first report of a system facilitating the study of TA mutant operons in the background of NTHi during infections of primary human tissues ex vivo. Less
The HLA-A -restricted decapeptide EAAGIGILTV derived from melanoma antigen recognized by T-cells- MART- protein represents one of the best-studied tumor associated T-cell epitopes but clinical results targeting this peptide have been disappointing This limitation may reflect the dominance of the nonapeptide AAGIGILTV at the melanoma cell surface The decapeptide and nonapeptide are presented in distinct conformations by HLA-A and TCRs from clinically relevant T-cell clones recognize the nonapeptide poorly Here we studied the MEL TCR that potently recognizes the nonapeptide The structure of the MEL -HLA-A -AAGIGILTV complex revealed an induced fit mechanism of antigen recognition involving altered peptide MHC ... More
The HLA-A*02:01-restricted decapeptide EAAGIGILTV, derived from melanoma antigen recognized by T-cells-1 (MART-1) protein, represents one of the best-studied tumor associated T-cell epitopes, but clinical results targeting this peptide have been disappointing. This limitation may reflect the dominance of the nonapeptide, AAGIGILTV, at the melanoma cell surface. The decapeptide and nonapeptide are presented in distinct conformations by HLA-A*02:01 and TCRs from clinically relevant T-cell clones recognize the nonapeptide poorly. Here, we studied the MEL5 TCR that potently recognizes the nonapeptide. The structure of the MEL5-HLA-A*02:01-AAGIGILTV complex revealed an induced fit mechanism of antigen recognition involving altered peptide–MHC anchoring. This “flexing” at the TCR–peptide–MHC interface to accommodate the peptide antigen explains previously observed incongruences in this well-studied system and has important implications for future therapeutic approaches. Finally, this study expands upon the mechanisms by which molecular plasticity can influence antigen recognition by T cells. Less
The human protein tyrosine phosphatase non-receptor type PTPN is a PDZ PSD- Dlg ZO- domain-containing phosphatase with a tumor-suppressive or a tumor-promoting role in many cancers Interestingly the high-risk genital human papillomavirus HPV types and target the PDZ domain of PTPN The presence of a PDZ binding motif PBM on E confers interaction with a number of different cellular PDZ domain-containing proteins and is a marker of high oncogenic potential Here we report the molecular basis of interaction between the PDZ domain of PTPN and the PBM of the HPV E protein We combined biophysical NMR and X-ray experiments to ... More
The human protein tyrosine phosphatase non-receptor type 3 (PTPN3) is a PDZ (PSD-95/Dlg/ZO-1) domain-containing phosphatase with a tumor-suppressive or a tumor-promoting role in many cancers. Interestingly, the high-risk genital human papillomavirus (HPV) types 16 and 18 target the PDZ domain of PTPN3. The presence of a PDZ binding motif (PBM) on E6 confers interaction with a number of different cellular PDZ domain-containing proteins and is a marker of high oncogenic potential. Here, we report the molecular basis of interaction between the PDZ domain of PTPN3 and the PBM of the HPV E6 protein. We combined biophysical, NMR and X-ray experiments to investigate the structural and functional properties of the PDZ domain of PTPN3. We showed that the C-terminal sequences from viral proteins encompassing a PBM interact with PTPN3-PDZ with similar affinities to the endogenous PTPN3 ligand MAP kinase p38γ. PBM binding stabilizes the PDZ domain of PTPN3. We solved the X-ray structure of the PDZ domain of PTPN3 in complex with the PBM of the HPV E6 protein. The crystal structure and the NMR chemical shift mapping of the PTPN3-PDZ/peptide complex allowed us to pinpoint the main structural determinants of recognition of the C-terminal sequence of the E6 protein and the long-range perturbations induced upon PBM binding. Less