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Thames T, J Bryer A, Qiao X, Jeon J, Weed R, Janicki K, Hu B, Gor’kov PL, Hung I, Gan Z, Perilla JR, Chen B. Curvature of the Retroviral Capsid Assembly Is Modulated by a Molecular Switch. J Phys Chem Lett 2021; 12:7768-7776. [PMID: 34374542 PMCID: PMC9083439 DOI: 10.1021/acs.jpclett.1c01769] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
During the maturation step, the retroviral capsid proteins (CAs) assemble into polymorphic capsids. Their acute curvature is largely determined by 12 pentamers inserted into the hexameric lattice. However, how the CA switches its conformation to control assembly curvature remains unclear. We report the high-resolution structural model of the Rous sarcoma virus (RSV) CA T = 1 capsid, established by molecular dynamics simulations combining solid-state NMR and prior cryoelectron tomography restraints. Comparing this with our previous model of the RSV CA tubular assembly, we identify the key residues for dictating the incorporation of acute curvatures. These residues undergo large torsion angle changes, resulting in a 34° rotation of the C-terminal domain relative to its N-terminal domain around the flexible interdomain linker, without substantial changes of either the conformation of individual domains or the assembly contact interfaces. This knowledge provides new insights to help decipher the mechanism of the retroviral capsid assembly.
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Affiliation(s)
- Tyrone Thames
- Department of Physics, University of Central Florida, Orlando, FL 32816, USA
| | - Alexander J Bryer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Xin Qiao
- Department of Physics, University of Central Florida, Orlando, FL 32816, USA
| | - Jaekyun Jeon
- Laboratory of Chemical Physics, NIDDK, NIH, Bethesda, MD 20892, USA
| | - Ryan Weed
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA
| | - Kaylie Janicki
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA
| | - Bingwen Hu
- State Key Laboratory of Precision Spectroscopy, Shanghai Key Laboratory of Magnetic Resonance, Institute of Functional Materials, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China
| | - Peter L. Gor’kov
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Ivan Hung
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Zhehong Gan
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Bo Chen
- Department of Physics, University of Central Florida, Orlando, FL 32816, USA
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2
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Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nat Commun 2021; 12:3226. [PMID: 34050170 PMCID: PMC8163826 DOI: 10.1038/s41467-021-23506-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 05/03/2021] [Indexed: 02/08/2023] Open
Abstract
Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.
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3
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Cottee MA, Letham SC, Young GR, Stoye JP, Taylor IA. Structure of Drosophila melanogaster ARC1 reveals a repurposed molecule with characteristics of retroviral Gag. SCIENCE ADVANCES 2020; 6:eaay6354. [PMID: 31911950 PMCID: PMC6938703 DOI: 10.1126/sciadv.aay6354] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/06/2019] [Indexed: 06/10/2023]
Abstract
The tetrapod neuronal protein ARC and its Drosophila melanogaster homolog, dARC1, have important but differing roles in neuronal development. Both are thought to originate through exaptation of ancient Ty3/Gypsy retrotransposon Gag, with their novel function relying on an original capacity for self-assembly and encapsidation of nucleic acids. Here, we present the crystal structure of dARC1 CA and examine the relationship between dARC1, mammalian ARC, and the CA protein of circulating retroviruses. We show that while the overall architecture is highly related to that of orthoretroviral and spumaretroviral CA, there are substantial deviations in both amino- and carboxyl-terminal domains, potentially affecting recruitment of partner proteins and particle assembly. The degree of sequence and structural divergence suggests that Ty3/Gypsy Gag has been exapted on two separate occasions and that, although mammalian ARC and dARC1 share functional similarity, the structures have undergone different adaptations after appropriation into the tetrapod and insect genomes.
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Affiliation(s)
- Matthew A. Cottee
- Macromolecular Structure Laboratory, The Francis Crick Institute, Midland Road, London NW1 1AT, UK
| | - Suzanne C. Letham
- Macromolecular Structure Laboratory, The Francis Crick Institute, Midland Road, London NW1 1AT, UK
| | - George R. Young
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Midland Road, London NW1 1AT, UK
| | - Jonathan P. Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Midland Road, London NW1 1AT, UK
- Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, Midland Road, London NW1 1AT, UK
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4
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Smaga SS, Xu C, Summers BJ, Digianantonio KM, Perilla JR, Xiong Y. MxB Restricts HIV-1 by Targeting the Tri-hexamer Interface of the Viral Capsid. Structure 2019; 27:1234-1245.e5. [PMID: 31155311 PMCID: PMC7183857 DOI: 10.1016/j.str.2019.04.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/15/2019] [Accepted: 04/24/2019] [Indexed: 11/21/2022]
Abstract
The human antiviral protein MxB is a restriction factor that fights HIV infection. Previous experiments have demonstrated that MxB targets the HIV capsid, a protein shell that protects the viral genome. To make the conical-shaped capsid, HIV CA proteins are organized into a lattice composed of hexamer and pentamer building blocks, providing many interfaces for host proteins to recognize. Through extensive biochemical and biophysical studies and molecular dynamics simulations, we show that MxB is targeting the HIV capsid by recognizing the region created at the intersection of three CA hexamers. We are further able to map this interaction to a few CA residues, located in a negatively charged well at the interface between the three CA hexamers. This work provides detailed residue-level mapping of the targeted capsid interface and how MxB interacts. This information could inspire the development of capsid-targeting therapies for HIV.
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Affiliation(s)
- Sarah Sierra Smaga
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Brady James Summers
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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5
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Pornillos O, Ganser-Pornillos BK. Maturation of retroviruses. Curr Opin Virol 2019; 36:47-55. [PMID: 31185449 PMCID: PMC6730672 DOI: 10.1016/j.coviro.2019.05.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/29/2019] [Accepted: 05/03/2019] [Indexed: 01/10/2023]
Abstract
During retrovirus maturation, cleavage of the precursor structural Gag polyprotein by the viral protease induces architectural rearrangement of the virus particle from an immature into a mature, infectious form. The structural rearrangement encapsidates the viral RNA genome in a fullerene capsid, producing a diffusible viral core that can initiate infection upon entry into the cytoplasm of a host cell. Maturation is an important therapeutic window against HIV-1. In this review, we highlight recent breakthroughs in understanding of the structures of retroviral immature and mature capsid lattices that define the boundary conditions of maturation and provide novel insights on capsid transformation. We also discuss emerging insights on encapsidation of the viral genome in the mature capsid, as well as remaining questions for further study.
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Affiliation(s)
- Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
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6
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Abstract
The retrovirus capsid core is a metastable structure that disassembles during the early phase of viral infection after membrane fusion. The core is intact and permeable to essential nucleotides during reverse transcription, but it undergoes disassembly for nuclear entry and genome integration. Increasing or decreasing the stability of the capsid core has a substantial negative impact on virus infectivity, which makes the core an attractive anti-viral target. The retrovirus capsid core also encounters a variety of virus- and organism-specific host cellular factors that promote or restrict viral replication. This review describes the structural elements fundamental to the formation and stability of the capsid core. The physical and chemical properties of the capsid core that are critical to its functional role in reverse transcription and interaction with host cellular factors are highlighted to emphasize areas of current research.
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In vitro assembly of the Rous Sarcoma Virus capsid protein into hexamer tubes at physiological temperature. Sci Rep 2017; 7:2913. [PMID: 28588198 PMCID: PMC5460288 DOI: 10.1038/s41598-017-02060-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/06/2017] [Indexed: 12/21/2022] Open
Abstract
During a proteolytically-driven maturation process, the orthoretroviral capsid protein (CA) assembles to form the convex shell that surrounds the viral genome. In some orthoretroviruses, including Rous Sarcoma Virus (RSV), CA carries a short and hydrophobic spacer peptide (SP) at its C-terminus early in the maturation process, which is progressively removed as maturation proceeds. In this work, we show that RSV CA assembles in vitro at near-physiological temperatures, forming hexamer tubes that effectively model the mature capsid surface. Tube assembly is strongly influenced by electrostatic effects, and is a nucleated process that remains thermodynamically favored at lower temperatures, but is effectively arrested by the large Gibbs energy barrier associated with nucleation. RSV CA tubes are multi-layered, being formed by nested and concentric tubes of capsid hexamers. However the spacer peptide acts as a layering determinant during tube assembly. If only a minor fraction of CA-SP is present, multi-layered tube formation is blocked, and single-layered tubes predominate. This likely prevents formation of biologically aberrant multi-layered capsids in the virion. The generation of single-layered hexamer tubes facilitated 3D helical image reconstruction from cryo-electron microscopy data, revealing the basic tube architecture.
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Jeon J, Qiao X, Hung I, Mitra AK, Desfosses A, Huang D, Gor’kov PL, Craven RC, Kingston RL, Gan Z, Zhu F, Chen B. Structural Model of the Tubular Assembly of the Rous Sarcoma Virus Capsid Protein. J Am Chem Soc 2017; 139:2006-2013. [DOI: 10.1021/jacs.6b11939] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jaekyun Jeon
- Department
of Physics, University of Central Florida, Orlando, Florida 32816, United States
| | - Xin Qiao
- Department
of Physics, University of Central Florida, Orlando, Florida 32816, United States
| | - Ivan Hung
- National
High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Alok K. Mitra
- School
of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Ambroise Desfosses
- School
of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Daniel Huang
- Department
of Physics, University of Central Florida, Orlando, Florida 32816, United States
| | - Peter L. Gor’kov
- National
High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Rebecca C. Craven
- Department
of Microbiology and Immunology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Richard L. Kingston
- School
of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Zhehong Gan
- National
High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Fangqiang Zhu
- Department
of Physics, Indiana University−Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Bo Chen
- Department
of Physics, University of Central Florida, Orlando, Florida 32816, United States
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9
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Bayro MJ, Tycko R. Structure of the Dimerization Interface in the Mature HIV-1 Capsid Protein Lattice from Solid State NMR of Tubular Assemblies. J Am Chem Soc 2016; 138:8538-46. [PMID: 27298207 PMCID: PMC5550895 DOI: 10.1021/jacs.6b03983] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The HIV-1 capsid protein (CA) forms the capsid shell that encloses RNA within a mature HIV-1 virion. Previous studies by electron microscopy have shown that the capsid shell is primarily a triangular lattice of CA hexamers, with variable curvature that destroys the ideal symmetry of a planar lattice. The mature CA lattice depends on CA dimerization, which occurs through interactions between helix 9 segments of the C-terminal domain (CTD) of CA. Several high-resolution structures of the CTD-CTD dimerization interface have been reported, based on X-ray crystallography and multidimensional solution nuclear magnetic resonance (NMR), with significant differences in amino acid side chain conformations and helix 9-helix 9 orientations. In a structural model for tubular CA assemblies based on cryogenic electron microscopy (cryoEM) [Zhao et al. Nature, 2013, 497, 643-646], the dimerization interface is substantially disordered. The dimerization interface structure in noncrystalline CA assemblies and the extent to which this interface is structurally ordered within a curved lattice have therefore been unclear. Here we describe solid state NMR measurements on the dimerization interface in tubular CA assemblies, which contain the curved triangular lattice of a mature virion, including quantitative measurements of intermolecular and intramolecular distances using dipolar recoupling techniques, solid state NMR chemical shifts, and long-range side chain-side chain contacts. When combined with restraints on the distance and orientation between helix 9 segments from the cryoEM study, the solid state NMR data lead to a unique high-resolution structure for the dimerization interface in the noncrystalline lattice of CA tubes. These results demonstrate that CA lattice curvature is not dependent on disorder or variability in the dimerization interface. This work also demonstrates the feasibility of local structure determination within large noncrystalline assemblies formed by high-molecular-weight proteins, using modern solid state NMR methods.
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Affiliation(s)
- Marvin J. Bayro
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
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10
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Abstract
The HIV genome materials are encaged by a proteinaceous shell called the capsid, constructed from ∼1000-1500 copies of the capsid proteins. Because its stability and integrity are critical to the normal life cycle and infectivity of the virus, the HIV capsid is a promising antiviral drug target. In this paper, we review the studies shaping our understanding of the structure and dynamics of the capsid proteins and various forms of their assemblies, as well as the assembly mechanism.
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Affiliation(s)
- Bo Chen
- Department of Physics, University of Central Florida , Orlando, Florida 32816, United States
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11
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Lu JX, Bayro MJ, Tycko R. Major Variations in HIV-1 Capsid Assembly Morphologies Involve Minor Variations in Molecular Structures of Structurally Ordered Protein Segments. J Biol Chem 2016; 291:13098-112. [PMID: 27129282 DOI: 10.1074/jbc.m116.720557] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Indexed: 12/13/2022] Open
Abstract
We present the results of solid state nuclear magnetic resonance (NMR) experiments on HIV-1 capsid protein (CA) assemblies with three different morphologies, namely wild-type CA (WT-CA) tubes with 35-60 nm diameters, planar sheets formed by the Arg(18)-Leu mutant (R18L-CA), and R18L-CA spheres with 20-100 nm diameters. The experiments are intended to elucidate molecular structural variations that underlie these variations in CA assembly morphology. We find that multidimensional solid state NMR spectra of (15)N,(13)C-labeled CA assemblies are remarkably similar for the three morphologies, with only small differences in (15)N and (13)C chemical shifts, no significant differences in NMR line widths, and few differences in the number of detectable NMR cross-peaks. Thus, the pronounced differences in morphology do not involve major differences in the conformations and identities of structurally ordered protein segments. Instead, morphological variations are attributable to variations in conformational distributions within disordered segments, which do not contribute to the solid state NMR spectra. Variations in solid state NMR signals from certain amino acid side chains are also observed, suggesting differences in the intermolecular dimerization interface between curved and planar CA lattices, as well as possible differences in intramolecular helix-helix packing.
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Affiliation(s)
- Jun-Xia Lu
- From the Laboratory of Chemical Physics, NIDKK, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Marvin J Bayro
- From the Laboratory of Chemical Physics, NIDKK, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Robert Tycko
- From the Laboratory of Chemical Physics, NIDKK, National Institutes of Health, Bethesda, Maryland 20892-0520
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12
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Perilla JR, Gronenborn AM. Molecular Architecture of the Retroviral Capsid. Trends Biochem Sci 2016; 41:410-420. [PMID: 27039020 DOI: 10.1016/j.tibs.2016.02.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 02/21/2016] [Accepted: 02/26/2016] [Indexed: 12/13/2022]
Abstract
Retroviral capsid cores are proteinaceous containers that self-assemble to encase the viral genome and a handful of proteins that promote infection. Their function is to protect and aid in the delivery of viral genes to the nucleus of the host, and, in many cases, infection pathways are influenced by capsid-cellular interactions. From a mathematical perspective, capsid cores are polyhedral cages and, as such, follow well-defined geometric rules. However, marked morphological differences in shapes exist, depending on virus type. Given the specific roles of capsid in the viral life cycle, the availability of detailed molecular structures, particularly at assembly interfaces, opens novel avenues for targeted drug development against these pathogens. Here, we summarize recent advances in the structure and understanding of retroviral capsid, with particular emphasis on assemblies and the capsid cores.
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Affiliation(s)
- Juan R Perilla
- Beckman Institute for Advanced Science and Technology and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, and Pittsburgh Center for HIV Protein Interactions, Pittsburgh, PA 15260, USA.
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13
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Mattei S, Schur FK, Briggs JA. Retrovirus maturation-an extraordinary structural transformation. Curr Opin Virol 2016; 18:27-35. [PMID: 27010119 DOI: 10.1016/j.coviro.2016.02.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/13/2016] [Indexed: 10/22/2022]
Abstract
Retroviruses such as HIV-1 assemble and bud from infected cells in an immature, non-infectious form. Subsequently, a series of proteolytic cleavages catalysed by the viral protease leads to a spectacular structural rearrangement of the viral particle into a mature form that is competent to fuse with and infect a new cell. Maturation involves changes in the structures of protein domains, in the interactions between protein domains, and in the architecture of the viral components that are assembled by the proteins. Tight control of proteolytic cleavages at different sites is required for successful maturation, and the process is a major target of antiretroviral drugs. Here we will describe what is known about the structures of immature and mature retrovirus particles, and about the maturation process by which one transitions into the other. Despite a wealth of available data, fundamental questions about retroviral maturation remain unanswered.
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Affiliation(s)
- Simone Mattei
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Florian Km Schur
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - John Ag Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Molecular Medicine Partnership Unit, Heidelberg, Germany.
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14
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Schur FKM, Dick RA, Hagen WJH, Vogt VM, Briggs JAG. The Structure of Immature Virus-Like Rous Sarcoma Virus Gag Particles Reveals a Structural Role for the p10 Domain in Assembly. J Virol 2015; 89:10294-302. [PMID: 26223638 PMCID: PMC4580193 DOI: 10.1128/jvi.01502-15] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/24/2015] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED The polyprotein Gag is the primary structural component of retroviruses. Gag consists of independently folded domains connected by flexible linkers. Interactions between the conserved capsid (CA) domains of Gag mediate formation of hexameric protein lattices that drive assembly of immature virus particles. Proteolytic cleavage of Gag by the viral protease (PR) is required for maturation of retroviruses from an immature form into an infectious form. Within the assembled Gag lattices of HIV-1 and Mason-Pfizer monkey virus (M-PMV), the C-terminal domain of CA adopts similar quaternary arrangements, while the N-terminal domain of CA is packed in very different manners. Here, we have used cryo-electron tomography and subtomogram averaging to study in vitro-assembled, immature virus-like Rous sarcoma virus (RSV) Gag particles and have determined the structure of CA and the surrounding regions to a resolution of ∼8 Å. We found that the C-terminal domain of RSV CA is arranged similarly to HIV-1 and M-PMV, whereas the N-terminal domain of CA adopts a novel arrangement in which the upstream p10 domain folds back into the CA lattice. In this position the cleavage site between CA and p10 appears to be inaccessible to PR. Below CA, an extended density is consistent with the presence of a six-helix bundle formed by the spacer-peptide region. We have also assessed the affect of lattice assembly on proteolytic processing by exogenous PR. The cleavage between p10 and CA is indeed inhibited in the assembled lattice, a finding consistent with structural regulation of proteolytic maturation. IMPORTANCE Retroviruses first assemble into immature virus particles, requiring interactions between Gag proteins that form a protein layer under the viral membrane. Subsequently, Gag is cleaved by the viral protease enzyme into separate domains, leading to rearrangement of the virus into its infectious form. It is important to understand how Gag is arranged within immature retroviruses, in order to understand how virus assembly occurs, and how maturation takes place. We used the techniques cryo-electron tomography and subtomogram averaging to obtain a detailed structural picture of the CA domains in immature assembled Rous sarcoma virus Gag particles. We found that part of Gag next to CA, called p10, folds back and interacts with CA when Gag assembles. This arrangement is different from that seen in HIV-1 and Mason-Pfizer monkey virus, illustrating further structural diversity of retroviral structures. The structure provides new information on how the virus assembles and undergoes maturation.
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Affiliation(s)
- Florian K M Schur
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Robert A Dick
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Wim J H Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Volker M Vogt
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Molecular Medicine Partnership Unit, Heidelberg, Germany
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15
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Qiao X, Jeon J, Weber J, Zhu F, Chen B. Mechanism of polymorphism and curvature of HIV capsid assemblies probed by 3D simulations with a novel coarse grain model. Biochim Biophys Acta Gen Subj 2015; 1850:2353-67. [PMID: 26318016 DOI: 10.1016/j.bbagen.2015.08.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/17/2015] [Accepted: 08/19/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND During the maturation process, HIV capsid proteins self-assemble into polymorphic capsids. The strong polymorphism precludes high resolution structural characterization under in vivo conditions. In spite of the determination of structural models for various in vitro assemblies of HIV capsid proteins, the assembly mechanism is still not well-understood. METHODS We report 3D simulations of HIV capsid proteins by a novel coarse grain model that captures the backbone of the rigid segments in the protein accurately. The effects of protein dynamics on assembly are emulated by a static ensemble of subunits in conformations derived from molecular dynamics simulation. RESULTS We show that HIV capsid proteins robustly assemble into hexameric lattices in a range of conditions where trimers of dimeric subunits are the dominant oligomeric intermediates. Variations of hexameric lattice curvatures are observed in simulations with subunits of variable inter-domain orientations mimicking the conformation distribution in solution. Simulations with subunits based on pentameric structural models lead to assembly of sharp curved structures resembling the tips of authentic HIV capsids, along a distinct pathway populated by tetramers and pentamers with the characteristic quasi-equivalency of viral capsids. CONCLUSIONS Our results suggest that the polymorphism assembly is triggered by the inter-domain dynamics of HIV capsid proteins in solution. The assembly of highly curved structures arises from proteins in conformation with a highly specific inter-domain orientation. SIGNIFICANCE Our work proposes a mechanism of HIV capsid assembly based on available structural data, which can be readily verified. Our model can be applied to other large biomolecular assemblies.
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Affiliation(s)
- Xin Qiao
- Department of Physics, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA
| | - Jaekyun Jeon
- Department of Physics, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA
| | - Jeff Weber
- Department of Physics, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA
| | - Fangqiang Zhu
- Department of Physics, Indiana University - Purdue University Indianapolis, IN, USA
| | - Bo Chen
- Department of Physics, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.
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16
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Zhang W, Cao S, Martin JL, Mueller JD, Mansky LM. Morphology and ultrastructure of retrovirus particles. AIMS BIOPHYSICS 2015; 2:343-369. [PMID: 26448965 PMCID: PMC4593330 DOI: 10.3934/biophy.2015.3.343] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Retrovirus morphogenesis entails assembly of Gag proteins and the viral genome on the host plasma membrane, acquisition of the viral membrane and envelope proteins through budding, and formation of the core through the maturation process. Although in both immature and mature retroviruses, Gag and capsid proteins are organized as paracrystalline structures, the curvatures of these protein arrays are evidently not uniform within one or among all virus particles. The heterogeneity of retroviruses poses significant challenges to studying the protein contacts within the Gag and capsid lattices. This review focuses on current understanding of the molecular organization of retroviruses derived from the sub-nanometer structures of immature virus particles, helical capsid protein assemblies and soluble envelope protein complexes. These studies provide insight into the molecular elements that maintain the stability, flexibility and infectivity of virus particles. Also reviewed are morphological studies of retrovirus budding, maturation, infection and cell-cell transmission, which inform the structural transformation of the viruses and the cells during infection and viral transmission, and lead to better understanding of the interplay between the functioning viral proteins and the host cell.
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Affiliation(s)
- Wei Zhang
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA ; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA ; Characterization Facility, University of Minnesota, Minneapolis, MN, USA
| | - Sheng Cao
- Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, China
| | - Jessica L Martin
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA ; Pharmacology Graduate Program, University of Minnesota, Minneapolis, MN, USA
| | - Joachim D Mueller
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA ; School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA ; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA ; Pharmacology Graduate Program, University of Minnesota, Minneapolis, MN, USA ; Department of Microbiology, University of Minnesota, Minneapolis, MN, USA
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17
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Goh BC, Perilla JR, England MR, Heyrana KJ, Craven RC, Schulten K. Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis. Structure 2015; 23:1414-1425. [PMID: 26118533 PMCID: PMC4526393 DOI: 10.1016/j.str.2015.05.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/18/2015] [Accepted: 05/25/2015] [Indexed: 10/23/2022]
Abstract
Defining the molecular interaction between Gag proteins in an assembled hexagonal lattice of immature retrovirus particles is crucial for elucidating the mechanisms of virus assembly and maturation. Recent advances in cryo-electron microscopy have yielded subnanometer structural information on the morphology of immature Gag lattices, making computational modeling and simulations feasible for investigating the Gag-Gag interactions at the atomic level. We have examined the structure of Rous sarcoma virus (RSV) using all-atom molecular dynamics simulations and in vitro assembly, to create the first all-atom model of an immature retroviral lattice. Microseconds-long replica exchange molecular dynamics simulation of the spacer peptide (SP)-nucleocapsid (NC) subdomains results in a six-helix bundle with amphipathic properties. The resulting model of the RSV Gag lattice shows features and dynamics of the capsid protein with implications for the maturation process, and confirms the stabilizing role of the upstream and downstream regions of Gag, namely p10 and SP-NC.
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Affiliation(s)
- Boon Chong Goh
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Juan R Perilla
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Matthew R England
- Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Katrina J Heyrana
- Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Rebecca C Craven
- Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Klaus Schulten
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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18
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Affiliation(s)
- Di L. Bush
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Volker M. Vogt
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850;
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19
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Abstract
UNLABELLED Purified retroviral Gag proteins can assemble in vitro to form immature virus-like particles (VLPs). By cryoelectron tomography, Rous sarcoma virus VLPs show an organized hexameric lattice consisting chiefly of the capsid (CA) domain, with periodic stalk-like densities below the lattice. We hypothesize that the structure represented by these densities is formed by amino acid residues immediately downstream of the folded CA, namely, the short spacer peptide SP, along with a dozen flanking residues. These 24 residues comprise the SP assembly (SPA) domain, and we propose that neighboring SPA units in a Gag hexamer coalesce to form a six-helix bundle. Using in vitro assembly, alanine scanning mutagenesis, and biophysical analyses, we have further characterized the structure and function of SPA. Most of the amino acid residues in SPA could not be mutated individually without abrogating assembly, with the exception of a few residues near the N and C termini, as well as three hydrophilic residues within SPA. We interpret these results to mean that the amino acids that do not tolerate mutations contribute to higher-order structures in VLPs. Hydrogen-deuterium exchange analyses of unassembled Gag compared that of assembled VLPs showed strong protection at the SPA region, consistent with a higher-order structure. Circular dichroism revealed that a 29mer SPA peptide shifts from a random coil to a helix in a concentration-dependent manner. Analytical ultracentrifugation showed concentration-dependent self-association of the peptide into a hexamer. Taken together, these results provide strong evidence for the formation of a critical six-helix bundle in Gag assembly. IMPORTANCE The structure of a retrovirus like HIV is created by several thousand molecules of the viral Gag protein, which assemble to form the known hexagonal protein lattice in the virus particle. How the Gag proteins pack together in the lattice is incompletely understood. A short segment of Gag known to be critical for proper assembly has been hypothesized to form a six-helix bundle, which may be the nucleating event that leads to lattice formation. The experiments reported here, using the avian Rous sarcoma virus as a model system, further define the nature of this segment of Gag, show that it is in a higher-order structure in the virus particle, and provide the first direct evidence that it forms a six-helix bundle in retrovirus assembly. Such knowledge may provide underpinnings for the development of antiretroviral drugs that interfere with virus assembly.
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20
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Bayro MJ, Chen B, Yau WM, Tycko R. Site-specific structural variations accompanying tubular assembly of the HIV-1 capsid protein. J Mol Biol 2013; 426:1109-27. [PMID: 24370930 DOI: 10.1016/j.jmb.2013.12.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 10/25/2022]
Abstract
The 231-residue capsid (CA) protein of human immunodeficiency virus type 1 (HIV-1) spontaneously self-assembles into tubes with a hexagonal lattice that is believed to mimic the surface lattice of conical capsid cores within intact virions. We report the results of solid-state nuclear magnetic resonance (NMR) measurements on HIV-1 CA tubes that provide new information regarding changes in molecular structure that accompany CA self-assembly, local dynamics within CA tubes, and possible mechanisms for the generation of lattice curvature. This information is contained in site-specific assignments of signals in two- and three-dimensional solid-state NMR spectra, conformation-dependent (15)N and (13)C NMR chemical shifts, detection of highly dynamic residues under solution NMR conditions, measurements of local variations in transverse spin relaxation rates of amide (1)H nuclei, and quantitative measurements of site-specific (15)N-(15)N dipole-dipole couplings. Our data show that most of the CA sequence is conformationally ordered and relatively rigid in tubular assemblies and that structures of the N-terminal domain (NTD) and the C-terminal domain (CTD) observed in solution are largely retained. However, specific segments, including the N-terminal β-hairpin, the cyclophilin A binding loop, the inter-domain linker, segments involved in intermolecular NTD-CTD interactions, and the C-terminal tail, have substantial static or dynamical disorder in tubular assemblies. Other segments, including the 310-helical segment in CTD, undergo clear conformational changes. Structural variations associated with curvature of the CA lattice appear to be localized in the inter-domain linker and intermolecular NTD-CTD interface, while structural variations within NTD hexamers, around local 3-fold symmetry axes, and in CTD-CTD dimerization interfaces are less significant.
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Affiliation(s)
- Marvin J Bayro
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Bo Chen
- Department of Physics, University of Central Florida, Orlando, FL 32816, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
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21
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Sun ZYJ, Cheng Y, Kim M, Song L, Choi J, Kudahl UJ, Brusic V, Chowdhury B, Yu L, Seaman MS, Bellot G, Shih WM, Wagner G, Reinherz EL. Disruption of helix-capping residues 671 and 674 reveals a role in HIV-1 entry for a specialized hinge segment of the membrane proximal external region of gp41. J Mol Biol 2013; 426:1095-108. [PMID: 24075869 DOI: 10.1016/j.jmb.2013.09.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/18/2013] [Accepted: 09/20/2013] [Indexed: 11/30/2022]
Abstract
HIV-1 (human immunodeficiency virus type 1) uses its trimeric gp160 envelope (Env) protein consisting of non-covalently associated gp120 and gp41 subunits to mediate entry into human T lymphocytes. A facile virus fusion mechanism compensates for the sparse Env copy number observed on viral particles and includes a 22-amino-acid, lentivirus-specific adaptation at the gp41 base (amino acid residues 662-683), termed the membrane proximal external region (MPER). We show by NMR and EPR that the MPER consists of a structurally conserved pair of viral lipid-immersed helices separated by a hinge with tandem joints that can be locked by capping residues between helices. This design fosters efficient HIV-1 fusion via interconverting structures while, at the same time, affording immune escape. Disruption of both joints by double alanine mutations at Env positions 671 and 674 (AA) results in attenuation of Env-mediated cell-cell fusion and hemifusion, as well as viral infectivity mediated by both CD4-dependent and CD4-independent viruses. The potential mechanism of disruption was revealed by structural analysis of MPER conformational changes induced by AA mutation. A deeper acyl chain-buried MPER middle section and the elimination of cross-hinge rigid-body motion almost certainly impede requisite structural rearrangements during the fusion process, explaining the absence of MPER AA variants among all known naturally occurring HIV-1 viral sequences. Furthermore, those broadly neutralization antibodies directed against the HIV-1 MPER exploit the tandem joint architecture involving helix capping, thereby disrupting hinge function.
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Affiliation(s)
- Zhen-Yu J Sun
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yuxing Cheng
- Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Mikyung Kim
- Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Likai Song
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Jaewon Choi
- Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Ulrich J Kudahl
- Cancer Vaccine Center and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Vladimir Brusic
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Cancer Vaccine Center and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Barnali Chowdhury
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Lu Yu
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Michael S Seaman
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Gaëtan Bellot
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering at Harvard, Boston, MA 02115, USA
| | - William M Shih
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering at Harvard, Boston, MA 02115, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ellis L Reinherz
- Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
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22
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Jeong HS, Park HN, Kim JG, Hyun JK. Critical importance of the correction of contrast transfer function for
transmission electron microscopy-mediated structural biology. J Anal Sci Technol 2013. [DOI: 10.1186/2093-3371-4-14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstracts
Background
Transmission electron microscopy (TEM) is an excellent tool for studying
detailed biological structures. High-resolution structure determination is
now routinely performed using advanced sample preparation techniques and
image processing software. In particular, correction for contrast transfer
function (CTF) is crucial for extracting high-resolution information from
TEM image that is convoluted by imperfect imaging condition. Accurate
determination of defocus, one of the major elements constituting the CTF, is
mandatory for CTF correction.
Findings
To investigate the effect of correct estimation of image defocus and
subsequent CTF correction, we tested arbitrary CTF imposition onto the
images of two-dimensional crystals of Rous sarcoma virus capsid protein. The
morphology of the crystal in calculated projection maps from incorrect CTF
imposition was utterly distorted in comparison to an appropriately
CTF-corrected image.
Conclusion
This result demonstrates critical importance of CTF correction for producing
true representation of the specimen at high resolution.
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23
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Manocheewa S, Swain JV, Lanxon-Cookson E, Rolland M, Mullins JI. Fitness costs of mutations at the HIV-1 capsid hexamerization interface. PLoS One 2013; 8:e66065. [PMID: 23785468 PMCID: PMC3681919 DOI: 10.1371/journal.pone.0066065] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 05/03/2013] [Indexed: 12/24/2022] Open
Abstract
The recently available x-ray crystal structure of HIV-1 capsid hexamers has provided insight into the molecular interactions crucial for the virus's mature capsid formation. Amino acid changes at these interaction points are likely to have a strong impact on capsid functionality and, hence, viral infectivity and replication fitness. To test this hypothesis, we introduced the most frequently observed single amino acid substitution at 30 sites: 12 at the capsid hexamerization interface and 18 at non-interface sites. Mutations at the interface sites were more likely to be lethal (Fisher's exact test p = 0.027) and had greater negative impact on viral replication fitness (Wilcoxon rank sum test p = 0.040). Among the interface mutations studied, those located in the cluster of hydrophobic contacts at NTD-NTD interface and those that disrupted NTD-CTD inter-domain helix capping hydrogen bonds were the most detrimental, indicating that these interactions are particularly important for maintaining capsid structure and/or function. These functionally constrained sites provide potential targets for novel HIV drug development and vaccine immunogen design.
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Affiliation(s)
- Siriphan Manocheewa
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - J. Victor Swain
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Erinn Lanxon-Cookson
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Morgane Rolland
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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24
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Dalessio PM, Craven RC, Lokhandwala PM, Ropson IJ. Lethal mutations in the major homology region and their suppressors act by modulating the dimerization of the rous sarcoma virus capsid protein C-terminal domain. Proteins 2012; 81:316-25. [PMID: 23011855 DOI: 10.1002/prot.24188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 09/06/2012] [Accepted: 09/10/2012] [Indexed: 11/09/2022]
Abstract
An infective retrovirus requires a mature capsid shell around the viral replication complex. This shell is formed by about 1500 capsid protein monomers, organized into hexamer and pentamer rings that are linked to each other by the dimerization of the C-terminal domain (CTD). The major homology region (MHR), the most highly conserved protein sequence across retroviral genomes, is part of the CTD. Several mutations in the MHR appear to block infectivity by preventing capsid formation. Suppressor mutations have been identified that are distant in sequence and structure from the MHR and restore capsid formation. The effects of two lethal and two suppressor mutations on the stability and function of the CTD were examined. No correlation with infectivity was found for the stability of the lethal mutations (D155Y-CTD, F167Y-CTD) and suppressor mutations (R185W-CTD, I190V-CTD). The stabilities of three double mutant proteins (D155Y/R185W-CTD, F167Y/R185W-CTD, and F167Y/I190V-CTD) were additive. However, the dimerization affinity of the mutant proteins correlated strongly with biological function. The CTD proteins with lethal mutations did not dimerize, while those with suppressor mutations had greater dimerization affinity than WT-CTD. The suppressor mutations were able to partially correct the dimerization defect caused by the lethal MHR mutations in double mutant proteins. Despite their dramatic effects on dimerization, none of these residues participate directly in the proposed dimerization interface in a mature capsid. These findings suggest that the conserved sequence of the MHR has critical roles in the conformation(s) of the CTD that are required for dimerization and correct capsid maturation.
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Affiliation(s)
- Paula M Dalessio
- Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, USA
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25
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Grime JMA, Voth GA. Early stages of the HIV-1 capsid protein lattice formation. Biophys J 2012; 103:1774-83. [PMID: 23083721 DOI: 10.1016/j.bpj.2012.09.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/20/2012] [Accepted: 09/04/2012] [Indexed: 11/26/2022] Open
Abstract
The early stages in the formation of the HIV-1 capsid (CA) protein lattice are investigated. The underlying coarse-grained (CG) model is parameterized directly from experimental data and examined under various native contact interaction strengths, CA dimer interfacial configurations, and local surface curvatures. The mechanism of early contiguous mature-style CA p6 lattice formation is explored, and a trimer-of-dimers structure is found to be crucial for CA lattice production. Quasi-equivalent generation of both the pentamer and hexamer components of the HIV-1 viral CA is also demonstrated, and the formation of pentamers is shown to be highly sensitive to local curvature, supporting the view that such inclusions in high-curvature regions allow closure of the viral CA surface. The complicated behavior of CA lattice self-assembly is shown to be reducible to a relatively simple function of the trimer-of-dimers behavior.
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Affiliation(s)
- John M A Grime
- Department of Chemistry, University of Chicago, Chicago, Illinois, USA
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