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HCV Broadly Neutralizing Antibodies Use a CDRH3 Disulfide Motif to Recognize an E2 Glycoprotein Site that Can Be Targeted for Vaccine Design.
Flyak AI, Ruiz S, Colbert MD, Luong T, Crowe JE, Bailey JR, Bjorkman PJ
(2018) Cell Host Microbe 24: 703-716.e3
MeSH Terms: Antibodies, Neutralizing, Antibodies, Viral, Binding Sites, Disulfides, Drug Design, Epitopes, Hepacivirus, Hepatitis C, Hepatitis C Antibodies, Humans, Immunoglobulin G, Models, Molecular, Protein Conformation, Sequence Alignment, Viral Envelope Proteins, Viral Hepatitis Vaccines, X-Ray Diffraction
Show Abstract · Added March 31, 2019
Hepatitis C virus (HCV) vaccine efforts are hampered by the extensive genetic diversity of HCV envelope glycoproteins E1 and E2. Structures of broadly neutralizing antibodies (bNAbs) (e.g., HEPC3, HEPC74) isolated from individuals who spontaneously cleared HCV infection facilitate immunogen design to elicit antibodies against multiple HCV variants. However, challenges in expressing HCV glycoproteins previously limited bNAb-HCV structures to complexes with truncated E2 cores. Here we describe crystal structures of full-length E2 ectodomain complexes with HEPC3 and HEPC74, revealing lock-and-key antibody-antigen interactions, E2 regions (including a target of immunogen design) that were truncated or disordered in E2 cores, and an antibody CDRH3 disulfide motif that exhibits common interactions with a conserved epitope despite different bNAb-E2 binding orientations. The structures display unusual features relevant to common genetic signatures of HCV bNAbs and demonstrate extraordinary plasticity in antibody-antigen interactions. In addition, E2 variants that bind HEPC3/HEPC74-like germline precursors may represent candidate vaccine immunogens.
Copyright © 2018 Elsevier Inc. All rights reserved.
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17 MeSH Terms
Analysis of Functional Dynamics of Modular Multidomain Proteins by SAXS and NMR.
Thompson MK, Ehlinger AC, Chazin WJ
(2017) Methods Enzymol 592: 49-76
MeSH Terms: DNA Primase, Humans, Multiprotein Complexes, Nuclear Magnetic Resonance, Biomolecular, Protein Conformation, Protein Domains, Replication Protein A, Scattering, Small Angle, X-Ray Diffraction
Show Abstract · Added March 24, 2018
Multiprotein machines drive virtually all primary cellular processes. Modular multidomain proteins are widely distributed within these dynamic complexes because they provide the flexibility needed to remodel structure as well as rapidly assemble and disassemble components of the machinery. Understanding the functional dynamics of modular multidomain proteins is a major challenge confronting structural biology today because their structure is not fixed in time. Small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy have proven particularly useful for the analysis of the structural dynamics of modular multidomain proteins because they provide highly complementary information for characterizing the architectural landscape accessible to these proteins. SAXS provides a global snapshot of all architectural space sampled by a molecule in solution. Furthermore, SAXS is sensitive to conformational changes, organization and oligomeric states of protein assemblies, and the existence of flexibility between globular domains in multiprotein complexes. The power of NMR to characterize dynamics provides uniquely complementary information to the global snapshot of the architectural ensemble provided by SAXS because it can directly measure domain motion. In particular, NMR parameters can be used to define the diffusion of domains within modular multidomain proteins, connecting the amplitude of interdomain motion to the architectural ensemble derived from SAXS. Our laboratory has been studying the roles of modular multidomain proteins involved in human DNA replication using SAXS and NMR. Here, we present the procedure for acquiring and analyzing SAXS and NMR data, using DNA primase and replication protein A as examples.
© 2017 Elsevier Inc. All rights reserved.
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9 MeSH Terms
Protonation-dependent conformational dynamics of the multidrug transporter EmrE.
Dastvan R, Fischer AW, Mishra S, Meiler J, Mchaourab HS
(2016) Proc Natl Acad Sci U S A 113: 1220-5
MeSH Terms: Antiporters, Electron Spin Resonance Spectroscopy, Escherichia coli Proteins, Models, Molecular, Protein Conformation, Protons, X-Ray Diffraction
Show Abstract · Added February 5, 2016
The small multidrug transporter from Escherichia coli, EmrE, couples the energetically uphill extrusion of hydrophobic cations out of the cell to the transport of two protons down their electrochemical gradient. Although principal mechanistic elements of proton/substrate antiport have been described, the structural record is limited to the conformation of the substrate-bound state, which has been shown to undergo isoenergetic alternating access. A central but missing link in the structure/mechanism relationship is a description of the proton-bound state, which is an obligatory intermediate in the transport cycle. Here we report a systematic spin labeling and double electron electron resonance (DEER) study that uncovers the conformational changes of EmrE subsequent to protonation of critical acidic residues in the context of a global description of ligand-induced structural rearrangements. We find that protonation of E14 leads to extensive rotation and tilt of transmembrane helices 1-3 in conjunction with repacking of loops, conformational changes that alter the coordination of the bound substrate and modulate its access to the binding site from the lipid bilayer. The transport model that emerges from our data posits a proton-bound, but occluded, resting state. Substrate binding from the inner leaflet of the bilayer releases the protons and triggers alternating access between inward- and outward-facing conformations of the substrate-loaded transporter, thus enabling antiport without dissipation of the proton gradient.
1 Communities
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7 MeSH Terms
A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers.
Vandavasi VG, Putnam DK, Zhang Q, Petridis L, Heller WT, Nixon BT, Haigler CH, Kalluri U, Coates L, Langan P, Smith JC, Meiler J, O'Neill H
(2016) Plant Physiol 170: 123-35
MeSH Terms: Arabidopsis, Arabidopsis Proteins, Catalytic Domain, Cellulose, Escherichia coli, Glucosyltransferases, Microscopy, Electron, Transmission, Models, Molecular, Multiprotein Complexes, Protein Multimerization, Protein Structure, Secondary, Recombinant Proteins, Scattering, Small Angle, X-Ray Diffraction
Show Abstract · Added February 5, 2016
A cellulose synthesis complex with a "rosette" shape is responsible for synthesis of cellulose chains and their assembly into microfibrils within the cell walls of land plants and their charophyte algal progenitors. The number of cellulose synthase proteins in this large multisubunit transmembrane protein complex and the number of cellulose chains in a microfibril have been debated for many years. This work reports a low resolution structure of the catalytic domain of CESA1 from Arabidopsis (Arabidopsis thaliana; AtCESA1CatD) determined by small-angle scattering techniques and provides the first experimental evidence for the self-assembly of CESA into a stable trimer in solution. The catalytic domain was overexpressed in Escherichia coli, and using a two-step procedure, it was possible to isolate monomeric and trimeric forms of AtCESA1CatD. The conformation of monomeric and trimeric AtCESA1CatD proteins were studied using small-angle neutron scattering and small-angle x-ray scattering. A series of AtCESA1CatD trimer computational models were compared with the small-angle x-ray scattering trimer profile to explore the possible arrangement of the monomers in the trimers. Several candidate trimers were identified with monomers oriented such that the newly synthesized cellulose chains project toward the cell membrane. In these models, the class-specific region is found at the periphery of the complex, and the plant-conserved region forms the base of the trimer. This study strongly supports the "hexamer of trimers" model for the rosette cellulose synthesis complex that synthesizes an 18-chain cellulose microfibril as its fundamental product.
© 2016 American Society of Plant Biologists. All Rights Reserved.
1 Communities
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14 MeSH Terms
BCL::SAXS: GPU accelerated Debye method for computation of small angle X-ray scattering profiles.
Putnam DK, Weiner BE, Woetzel N, Lowe EW, Meiler J
(2015) Proteins 83: 1500-12
MeSH Terms: Algorithms, Humans, Models, Molecular, Proteins, ROC Curve, Scattering, Small Angle, X-Ray Diffraction
Show Abstract · Added February 5, 2016
Small angle X-ray scattering (SAXS) is an experimental technique used for structural characterization of macromolecules in solution. Here, we introduce BCL::SAXS--an algorithm designed to replicate SAXS profiles from rigid protein models at different levels of detail. We first show our derivation of BCL::SAXS and compare our results with the experimental scattering profile of hen egg white lysozyme. Using this protein we show how to generate SAXS profiles representing: (1) complete models, (2) models with approximated side chain coordinates, and (3) models with approximated side chain and loop region coordinates. We evaluated the ability of SAXS profiles to identify a correct protein topology from a non-redundant benchmark set of proteins. We find that complete SAXS profiles can be used to identify the correct protein by receiver operating characteristic (ROC) analysis with an area under the curve (AUC) > 99%. We show how our approximation of loop coordinates between secondary structure elements improves protein recognition by SAχS for protein models without loop regions and side chains. Agreement with SAXS data is a necessary but not sufficient condition for structure determination. We conclude that experimental SAXS data can be used as a filter to exclude protein models with large structural differences from the native.
© 2015 Wiley Periodicals, Inc.
1 Communities
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7 MeSH Terms
Structural studies of truncated forms of the prion protein PrP.
Wan W, Wille H, Stöhr J, Kendall A, Bian W, McDonald M, Tiggelaar S, Watts JC, Prusiner SB, Stubbs G
(2015) Biophys J 108: 1548-1554
MeSH Terms: Amyloid, Animals, Brain, Escherichia coli, GPI-Linked Proteins, Humans, Mice, Mice, Transgenic, Microscopy, Electron, Nerve Tissue Proteins, Prions, Protein Conformation, Recombinant Proteins, X-Ray Diffraction
Show Abstract · Added February 15, 2016
Prions are proteins that adopt self-propagating aberrant folds. The self-propagating properties of prions are a direct consequence of their distinct structures, making the understanding of these structures and their biophysical interactions fundamental to understanding prions and their related diseases. The insolubility and inherent disorder of prions have made their structures difficult to study, particularly in the case of the infectious form of the mammalian prion protein PrP. Many investigators have therefore preferred to work with peptide fragments of PrP, suggesting that these peptides might serve as structural and functional models for biologically active prions. We have used x-ray fiber diffraction to compare a series of different-sized fragments of PrP, to determine the structural commonalities among the fragments and the biologically active, self-propagating prions. Although all of the peptides studied adopted amyloid conformations, only the larger fragments demonstrated a degree of structural complexity approaching that of PrP. Even these larger fragments did not adopt the prion structure itself with detailed fidelity, and in some cases their structures were radically different from that of pathogenic PrP(Sc).
Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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14 MeSH Terms
A structure-specific nucleic acid-binding domain conserved among DNA repair proteins.
Mason AC, Rambo RP, Greer B, Pritchett M, Tainer JA, Cortez D, Eichman BF
(2014) Proc Natl Acad Sci U S A 111: 7618-23
MeSH Terms: Adenosine Triphosphate, Animals, Chromatography, Affinity, Chromatography, Agarose, Chromatography, Gel, Chromatography, Ion Exchange, Cloning, Molecular, Crystallization, DNA Helicases, DNA Repair, Hydrolysis, Likelihood Functions, Mice, Models, Molecular, Nucleic Acids, Protein Structure, Tertiary, Scattering, Small Angle, X-Ray Diffraction
Show Abstract · Added May 19, 2014
SMARCAL1, a DNA remodeling protein fundamental to genome integrity during replication, is the only gene associated with the developmental disorder Schimke immuno-osseous dysplasia (SIOD). SMARCAL1-deficient cells show collapsed replication forks, S-phase cell cycle arrest, increased chromosomal breaks, hypersensitivity to genotoxic agents, and chromosomal instability. The SMARCAL1 catalytic domain (SMARCAL1(CD)) is composed of an SNF2-type double-stranded DNA motor ATPase fused to a HARP domain of unknown function. The mechanisms by which SMARCAL1 and other DNA translocases repair replication forks are poorly understood, in part because of a lack of structural information on the domains outside of the common ATPase motor. In the present work, we determined the crystal structure of the SMARCAL1 HARP domain and examined its conformation and assembly in solution by small angle X-ray scattering. We report that this domain is conserved with the DNA mismatch and damage recognition domains of MutS/MSH and NER helicase XPB, respectively, as well as with the putative DNA specificity motif of the T4 phage fork regression protein UvsW. Loss of UvsW fork regression activity by deletion of this domain was rescued by its replacement with HARP, establishing the importance of this domain in UvsW and demonstrating a functional complementarity between these structurally homologous domains. Mutation of predicted DNA-binding residues in HARP dramatically reduced fork binding and regression activities of SMARCAL1(CD). Thus, this work has uncovered a conserved substrate recognition domain in DNA repair enzymes that couples ATP-hydrolysis to remodeling of a variety of DNA structures, and provides insight into this domain's role in replication fork stability and genome integrity.
1 Communities
2 Members
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18 MeSH Terms
Fungal prion HET-s as a model for structural complexity and self-propagation in prions.
Wan W, Stubbs G
(2014) Proc Natl Acad Sci U S A 111: 5201-6
MeSH Terms: Asparagine, Fungal Proteins, Kinetics, Models, Structural, Mutagenesis, Site-Directed, Nuclear Magnetic Resonance, Biomolecular, Podospora, Prions, Protein Conformation, Surface Properties, X-Ray Diffraction
Show Abstract · Added February 15, 2016
The highly ordered and reproducible structure of the fungal prion HET-s makes it an excellent model system for studying the inherent properties of prions, self-propagating infectious proteins that have been implicated in a number of fatal diseases. In particular, the HET-s prion-forming domain readily folds into a relatively complex two-rung β-solenoid amyloid. The faithful self-propagation of this fold involves a diverse array of inter- and intramolecular structural features. These features include a long flexible loop connecting the two rungs, buried polar residues, salt bridges, and asparagine ladders. We have used site-directed mutagenesis and X-ray fiber diffraction to probe the relative importance of these features for the formation of β-solenoid structure, as well as the cumulative effects of multiple mutations. Using fibrillization kinetics and chemical stability assays, we have determined the biophysical effects of our mutations on the assembly and stability of the prion-forming domain. We have found that a diversity of structural features provides a level of redundancy that allows robust folding and stability even in the face of significant sequence alterations and suboptimal environmental conditions. Our findings provide fundamental insights into the structural interactions necessary for self-propagation. Propagation of prion structure seems to require an obligatory level of complexity that may not be reproducible in short peptide models.
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11 MeSH Terms
Fiber diffraction of the prion-forming domain HET-s(218-289) shows dehydration-induced deformation of a complex amyloid structure.
Wan W, Stubbs G
(2014) Biochemistry 53: 2366-70
MeSH Terms: Amyloid, Models, Molecular, Molecular Structure, Prions, Water, X-Ray Diffraction
Show Abstract · Added February 15, 2016
Amyloids are filamentous protein aggregates that can be formed by many different proteins and are associated with both disease and biological functions. The pathogenicities or biological functions of amyloids are determined by their particular molecular structures, making accurate structural models a requirement for understanding their biological effects. One potential factor that can affect amyloid structures is hydration. Previous studies of simple stacked β-sheet amyloids have suggested that dehydration does not impact structure, but other studies indicated dehydration-related structural changes of a putative water-filled nanotube. Our results show that dehydration significantly affects the molecular structure of the fungal prion-forming domain HET-s(218-289), which forms a β-solenoid with no internal solvent-accessible regions. The dehydration-related structural deformation of HET-s(218-289) indicates that water can play a significant role in complex amyloid structures, even when no obvious water-accessible cavities are present.
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6 MeSH Terms
Heterogeneous seeding of HET-s(218-289) and the mutability of prion structures.
Wan W, Stubbs G
(2014) Prion 8:
MeSH Terms: Mutation, Nuclear Magnetic Resonance, Biomolecular, Prions, X-Ray Diffraction
Show Abstract · Added February 15, 2016
One fundamental property of prions is the formation of strains-prions that have distinct biological effects, despite a common amino acid sequence. The strain phenomenon is thought to be caused by the formation of different molecular structures, each encoding for a particular biological activity. While the precise mechanism of the formation of strains is unknown, they tend to arise following environmental changes, such as passage between different species. One possible mechanism discussed here is heterogeneous seeding; the formation of a prion nucleated by a different molecular structure. While heterogeneous seeding is not the only mechanism of prion mutation, it is consistent with some observations on species adaptation and drug resistance. Heterogeneous seeding provides a useful framework to understand how prions can adapt to new environmental conditions and change biological phenotypes.
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4 MeSH Terms