1
|
In vitro investigation of protein assembly by combined microscopy and infrared spectroscopy at the nanometer scale. Proc Natl Acad Sci U S A 2022; 119:e2200019119. [PMID: 35914130 PMCID: PMC9371722 DOI: 10.1073/pnas.2200019119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The nanoscale structure and dynamics of proteins on surfaces has been extensively studied using various imaging techniques, such as transmission electron microscopy and atomic force microscopy (AFM) in liquid environments. These powerful imaging techniques, however, can potentially damage or perturb delicate biological material and do not provide chemical information, which prevents a fundamental understanding of the dynamic processes underlying their evolution under physiological conditions. Here, we use a platform developed in our laboratory that enables acquisition of infrared (IR) spectroscopy and AFM images of biological material in physiological liquids with nanometer resolution in a cell closed by atomically thin graphene membranes transparent to IR photons. In this work, we studied the self-assembly process of S-layer proteins at the graphene-aqueous solution interface. The graphene acts also as the membrane separating the solution containing the proteins and Ca2+ ions from the AFM tip, thus eliminating sample damage and contamination effects. The formation of S-layer protein lattices and their structural evolution was monitored by AFM and by recording the amide I and II IR absorption bands, which reveal the noncovalent interaction between proteins and their response to the environment, including ionic strength and solvation. Our measurement platform opens unique opportunities to study biological material and soft materials in general.
Collapse
|
2
|
Fló M, Carrión F, Olivero-Deibe N, Bianchi S, Portela M, Rammauro F, Alvarez B, Pritsch O. Kinetics of Bovine leukemia virus aspartic protease reveals its dimerization and conformational change. PLoS One 2022; 17:e0271671. [PMID: 35867649 PMCID: PMC9307154 DOI: 10.1371/journal.pone.0271671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 07/05/2022] [Indexed: 11/28/2022] Open
Abstract
The retropepsin (PR) of the Bovine leukemia virus (BLV) plays, as in other retroviruses, a crucial role in the transition from the non-infective viral particle to the infective virion by processing the polyprotein Gag. PR is expressed as an immature precursor associated with Gag, after an occasional −1 ribosomal frameshifting event. Self-hydrolysis of PR at specific N- and C-terminal sites releases the monomer that dimerizes giving rise to the active protease. We designed a strategy to express BLV PR in E. coli as a fusion protein with maltose binding protein, with a six-histidine tag at its N-terminal end, and bearing a tobacco etch virus protease hydrolysis site. This allowed us to obtain soluble and mature recombinant PR in relatively good yields, with exactly the same amino acid composition as the native protein. As PR presents relative promiscuity for the hydrolysis sites we designed four fluorogenic peptide substrates based on Förster resonance energy transfer (FRET) in order to characterize the activity of the recombinant enzyme. These substrates opened the way to perform kinetic studies, allowing us to characterize the dimer-monomer equilibrium. Furthermore, we obtained kinetic evidence for the existence of a conformational change that enables the interaction with the substrate. These results constitute a starting point for the elucidation of the kinetic properties of BLV-PR, and may be relevant not only to improve the chemical warfare against this virus but also to better understand other viral PRs.
Collapse
Affiliation(s)
- Martín Fló
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- * E-mail: (OP); (MF)
| | - Federico Carrión
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | | | - Sergio Bianchi
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Laboratorio de Biomarcadores Moleculares, Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Madelón Portela
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Facultad de Ciencias, Montevideo, Uruguay
| | - Florencia Rammauro
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Otto Pritsch
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- * E-mail: (OP); (MF)
| |
Collapse
|
3
|
Identification of 2-(4-N,N-Dimethylaminophenyl)-5-methyl-1-phenethyl-1H-benzimidazole targeting HIV-1 CA capsid protein and inhibiting HIV-1 replication in cellulo. BMC Pharmacol Toxicol 2022; 23:43. [PMID: 35765101 PMCID: PMC9241302 DOI: 10.1186/s40360-022-00581-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/30/2022] [Indexed: 11/29/2022] Open
Abstract
The capsid (CA) subunit of the HIV-1 Gag polyprotein is involved in several steps of the viral cycle, from the assembly of new viral particles to the protection of the viral genome until it enters into the nucleus of newly infected cells. As such, it represents an interesting therapeutic target to tackle HIV infection. In this study, we screened hundreds of compounds with a low cost of synthesis for their ability to interfere with Gag assembly in vitro. Representatives of the most promising families of compounds were then tested for their ability to inhibit HIV-1 replication in cellulo. From these molecules, a hit compound from the benzimidazole family with high metabolic stability and low toxicity, 2-(4-N,N-dimethylaminophenyl)-5-methyl-1-phenethyl-1H-benzimidazole (696), appeared to block HIV-1 replication with an IC50 of 3 µM. Quantitative PCR experiments demonstrated that 696 does not block HIV-1 infection before the end of reverse transcription, and molecular docking confirmed that 696 is likely to bind at the interface between two monomers of CA and interfere with capsid oligomerization. Altogether, 696 represents a promising lead molecule for the development of a new series of HIV-1 inhibitors.
Collapse
|
4
|
Structure of a Ty1 restriction factor reveals the molecular basis of transposition copy number control. Nat Commun 2021; 12:5590. [PMID: 34552077 PMCID: PMC8458377 DOI: 10.1038/s41467-021-25849-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 09/06/2021] [Indexed: 11/30/2022] Open
Abstract
Excessive replication of Saccharomyces cerevisiae Ty1 retrotransposons is regulated by Copy Number Control, a process requiring the p22/p18 protein produced from a sub-genomic transcript initiated within Ty1 GAG. In retrotransposition, Gag performs the capsid functions required for replication and re-integration. To minimize genomic damage, p22/p18 interrupts virus-like particle function by interaction with Gag. Here, we present structural, biophysical and genetic analyses of p18m, a minimal fragment of Gag that restricts transposition. The 2.8 Å crystal structure of p18m reveals an all α-helical protein related to mammalian and insect ARC proteins. p18m retains the capacity to dimerise in solution and the crystal structures reveal two exclusive dimer interfaces. We probe our findings through biophysical analysis of interface mutants as well as Ty1 transposition and p18m restriction in vivo. Our data provide insight into Ty1 Gag structure and suggest how p22/p18 might function in restriction through a blocking-of-assembly mechanism. In Saccharomyces cerevisiae, unchecked proliferation of Ty1 retrotransposons is controlled by the process of copy number control (CNC), which requires the p22/p18 protein, translated from an internal transcript within the Ty1 GAG gene. Here, the authors present the 2.8 Å crystal structure of a minimal p18 from Ty1-Gag that is able to restrict Ty1 transposition and identify two dimer interfaces in p18, whose roles were probed by mutagenesis both in vitro and in vivo. As p22/p18 contains only one of two conserved domains required for retroelement Gag assembly, they propose that p22/p18-Gag interactions block the Ty1 virus-like particle assembly pathway, resulting in defective particles incapable of supporting retrotransposition.
Collapse
|
5
|
A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly. Viruses 2021; 13:v13091853. [PMID: 34578434 PMCID: PMC8473085 DOI: 10.3390/v13091853] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 11/17/2022] Open
Abstract
The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 binding site in the immature Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice via a second IP6 binding site, and enhances core stability, creating a favorable environment for reverse transcription. IP6 also enhances assembly of other retroviruses, from both the Lentivirus and the Alpharetrovirus genera. These findings suggest that IP6 may have a conserved function throughout the family Retroviridae. Here, we discuss the different steps in the viral life cycle that are influenced by IP6, and describe in detail how IP6 interacts with the immature and mature lattices of different retroviruses.
Collapse
|
6
|
Crystal and solution structures reveal oligomerization of individual capsid homology domains of Drosophila Arc. PLoS One 2021; 16:e0251459. [PMID: 33989344 PMCID: PMC8121366 DOI: 10.1371/journal.pone.0251459] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/23/2021] [Indexed: 12/22/2022] Open
Abstract
Synaptic plasticity is vital for brain function and memory formation. One of the key proteins in long-term synaptic plasticity and memory is the activity-regulated cytoskeleton-associated protein (Arc). Mammalian Arc forms virus-like capsid structures in a process requiring the N-terminal domain and contains two C-terminal lobes that are structural homologues to retroviral capsids. Drosophila has two isoforms of Arc, dArc1 and dArc2, with low sequence similarity to mammalian Arc, but lacking a large N-terminal domain. Both dArc isoforms are related to the Ty3/gypsy retrotransposon capsid, consisting of N- and C-terminal lobes. Structures of dArc1, as well as capsids formed by both dArc isoforms, have been recently determined. We carried out structural characterization of the four individual dArc lobe domains. As opposed to the corresponding mammalian Arc lobe domains, which are monomeric, the dArc lobes were all oligomeric in solution, indicating a strong propensity for homophilic interactions. A truncated N-lobe from dArc2 formed a domain-swapped dimer in the crystal structure, resulting in a novel dimer interaction that could be relevant for capsid assembly or other dArc functions. This domain-swapped structure resembles the dimeric protein C of flavivirus capsids, as well as the structure of histones dimers, domain-swapped transcription factors, and membrane-interacting BAK domains. The strong oligomerization properties of the isolated dArc lobe domains explain the ability of dArc to form capsids in the absence of any large N-terminal domain, in contrast to the mammalian protein.
Collapse
|
7
|
Ni T, Gerard S, Zhao G, Dent K, Ning J, Zhou J, Shi J, Anderson-Daniels J, Li W, Jang S, Engelman AN, Aiken C, Zhang P. Intrinsic curvature of the HIV-1 CA hexamer underlies capsid topology and interaction with cyclophilin A. Nat Struct Mol Biol 2020; 27:855-862. [PMID: 32747784 DOI: 10.1038/s41594-020-0467-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/19/2020] [Indexed: 12/21/2022]
Abstract
The mature retrovirus capsid consists of a variably curved lattice of capsid protein (CA) hexamers and pentamers. High-resolution structures of the curved assembly, or in complex with host factors, have not been available. By devising cryo-EM methodologies for exceedingly flexible and pleomorphic assemblies, we have determined cryo-EM structures of apo-CA hexamers and in complex with cyclophilin A (CypA) at near-atomic resolutions. The CA hexamers are intrinsically curved, flexible and asymmetric, revealing the capsomere and not the previously touted dimer or trimer interfaces as the key contributor to capsid curvature. CypA recognizes specific geometries of the curved lattice, simultaneously interacting with three CA protomers from adjacent hexamers via two noncanonical interfaces, thus stabilizing the capsid. By determining multiple structures from various helical symmetries, we further revealed the essential plasticity of the CA molecule, which allows formation of continuously curved conical capsids and the mechanism of capsid pattern sensing by CypA.
Collapse
Affiliation(s)
- Tao Ni
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Samuel Gerard
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gongpu Zhao
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kyle Dent
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Jiying Ning
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jing Zhou
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jiong Shi
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jordan Anderson-Daniels
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wen Li
- Department of Medicine, Harvard Medical School, Boston, MA, USA.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sooin Jang
- Department of Medicine, Harvard Medical School, Boston, MA, USA.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alan N Engelman
- Department of Medicine, Harvard Medical School, Boston, MA, USA.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christopher Aiken
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. .,Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
| |
Collapse
|
8
|
Acton O, Grant T, Nicastro G, Ball NJ, Goldstone DC, Robertson LE, Sader K, Nans A, Ramos A, Stoye JP, Taylor IA, Rosenthal PB. Structural basis for Fullerene geometry in a human endogenous retrovirus capsid. Nat Commun 2019; 10:5822. [PMID: 31862888 PMCID: PMC6925226 DOI: 10.1038/s41467-019-13786-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/28/2019] [Indexed: 01/09/2023] Open
Abstract
The HML2 (HERV-K) group constitutes the most recently acquired family of human endogenous retroviruses, with many proviruses less than one million years old. Many maintain intact open reading frames and provirus expression together with HML2 particle formation are observed in early stage human embryo development and are associated with pluripotency as well as inflammatory disease, cancers and HIV-1 infection. Here, we reconstruct the core structural protein (CA) of an HML2 retrovirus, assemble particles in vitro and employ single particle cryogenic electron microscopy (cryo-EM) to determine structures of four classes of CA Fullerene shell assemblies. These icosahedral and capsular assemblies reveal at high-resolution the molecular interactions that allow CA to form both pentamers and hexamers and show how invariant pentamers and structurally plastic hexamers associate to form the unique polyhedral structures found in retroviral cores.
Collapse
Affiliation(s)
- Oliver Acton
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Tim Grant
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Giuseppe Nicastro
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Neil J Ball
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - David C Goldstone
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Laura E Robertson
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Kasim Sader
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Thermo Fisher Scientific Materials and Structural Analysis, Eindhoven, Netherlands
| | - Andrea Nans
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Andres Ramos
- Division of Molecular Structure, MRC National Institute for Medical Research, London, NW7 1AA, UK
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Jonathan P Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, 1 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, 1 Midland Road, London, NW1 1AT, UK.
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
Qualley DF, Cooper SE, Ross JL, Olson ED, Cantara WA, Musier-Forsyth K. Solution Conformation of Bovine Leukemia Virus Gag Suggests an Elongated Structure. J Mol Biol 2019; 431:1203-1216. [PMID: 30731090 PMCID: PMC6424597 DOI: 10.1016/j.jmb.2019.01.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 01/13/2023]
Abstract
Bovine leukemia virus (BLV) is a deltaretrovirus that infects domestic cattle. The structural protein Gag, found in all retroviruses, is a polyprotein comprising three major functional domains: matrix (MA), capsid (CA), and nucleocapsid (NC). Previous studies have shown that both mature BLV MA and NC are able to bind to nucleic acids; however, the viral assembly process and packaging of viral genomic RNA requires full-length Gag to produce infectious particles. Compared to lentiviruses, little is known about the structure of the Gag polyprotein of deltaretroviruses. In this work, structural models of full-length BLV Gag and Gag lacking the MA domain were generated based on previous structural data of individual domains, homology modeling, and flexible fitting to SAXS data using molecular dynamics. The models were used in molecular dynamic simulations to determine the relative mobility of the protein backbone. Functional annealing assays revealed the role of MA in the nucleic acid chaperone activity of BLV Gag. Our results show that full-length BLV Gag has an elongated rod-shaped structure that is relatively rigid, with the exception of the linker between the MA and CA domains. Deletion of the MA domain maintains the elongated structure but alters the rate of BLV Gag-facilitated annealing of two complementary nucleic acids. These data are consistent with a role for the MA domain of retroviral Gag proteins in modulating nucleic acid binding and chaperone activity. IMPORTANCE: BLV is a retrovirus that is found worldwide in domestic cattle. Since BLV infection has serious implications for agriculture, and given its similarities to human retroviruses such as HTLV-1, the development of an effective treatment would have numerous benefits. The Gag polyprotein exists in all retroviruses and is a key player in viral assembly. However, the full-length structure of Gag from any virus has yet to be elucidated at high resolution. This study provides structural data for BLV Gag and could be a starting point for modeling Gag-small molecule interactions with the ultimate goal of developing of a new class of pharmaceuticals.
Collapse
Affiliation(s)
- Dominic F Qualley
- Department of Chemistry and Biochemistry, and Center for One Health Studies, Berry College, Mt. Berry, GA 30149, USA.
| | - Sarah E Cooper
- Department of Chemistry and Biochemistry, and Center for One Health Studies, Berry College, Mt. Berry, GA 30149, USA
| | - James L Ross
- Department of Chemistry and Biochemistry, and Center for One Health Studies, Berry College, Mt. Berry, GA 30149, USA
| | - Erik D Olson
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA
| | - William A Cantara
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
12
|
Ngo VA, Fanning JK, Noskov SY. Comparative Analysis of Protein Hydration from MD simulations with Additive and Polarizable Force Fields. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800106] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Van A. Ngo
- Department of Biological SciencesCentre for Molecular Simulation and Biochemistry Research ClusterUniversity of Calgary Calgary Alberta T2N 1N4 Canada
| | - John Keenan Fanning
- Department of Biological SciencesCentre for Molecular Simulation and Biochemistry Research ClusterUniversity of Calgary Calgary Alberta T2N 1N4 Canada
| | - Sergei Yu Noskov
- Department of Biological SciencesCentre for Molecular Simulation and Biochemistry Research ClusterUniversity of Calgary Calgary Alberta T2N 1N4 Canada
| |
Collapse
|
13
|
Looking for Novel Capsid Protein Multimerization Inhibitors of Feline Immunodeficiency Virus. Pharmaceuticals (Basel) 2018; 11:ph11030067. [PMID: 29996481 PMCID: PMC6161179 DOI: 10.3390/ph11030067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 12/25/2022] Open
Abstract
Feline immunodeficiency virus (FIV) is a member of the retroviridae family of viruses. It causes acquired immunodeficiency syndrome (AIDS) in worldwide domestic and non-domestic cats and is a cause of an important veterinary issue. The genome organization of FIV and the clinical characteristics of the disease caused by FIV are similar to human immunodeficiency virus (HIV). Both viruses infect T lymphocytes, monocytes, and macrophages, with a similar replication cycle in infected cells. Thus, the infection of cats with FIV is also a useful tool for the study and development of novel drugs and vaccines against HIV. Anti-retroviral drugs studied extensively with regards to HIV infection have targeted different steps of the virus replication cycle: (1) disruption of the interaction with host cell surface receptors and co-receptors; (2) inhibition of fusion of the virus and cell membranes; (3) blocking of the reverse transcription of viral genomic RNA; (4) interruption of nuclear translocation and integration of viral DNA into host genomes; (5) prevention of viral transcript processing and nuclear export; and (6) inhibition of virion assembly and maturation. Despite the great success of anti-retroviral therapy in slowing HIV progression in humans, a similar therapy has not been thoroughly investigated for FIV infection in cats, mostly because of the little structural information available for FIV proteins. The FIV capsid protein (CA) drives the assembly of the viral particle, which is a critical step in the viral replication cycle. During this step, the CA protein oligomerizes to form a protective coat that surrounds the viral genome. In this work, we perform a large-scale screening of four hundred molecules from our in-house library using an in vitro assembly assay of p24, combined with microscale thermophoresis, to estimate binding affinity. This screening led to the discovery of around four novel hits that inhibited capsid assembly in vitro. These may provide new antiviral drugs against FIV.
Collapse
|
14
|
Corredor AP, González J, Baquero LA, Curtidor H, Olaya-Galán NN, Patarroyo MA, Gutiérrez MF. In silico and in vitro analysis of boAP3d1 protein interaction with bovine leukaemia virus gp51. PLoS One 2018; 13:e0199397. [PMID: 29928016 PMCID: PMC6013181 DOI: 10.1371/journal.pone.0199397] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/06/2018] [Indexed: 11/19/2022] Open
Abstract
The envelope glycoprotein 51 (gp51) is essential for bovine leukaemia virus (BLV) entry to bovine B-lymphocytes. Although the bovine adaptor protein 3 complex subunit delta-1 (boAP3D1) has been proposed as the potential receptor, the specific ligand-receptor interaction has not yet been completely defined and boAP3D1 receptor and gp51 3D structures have not been determined. This study was thus aimed at a functional annotation of boAP3D1 cellular adaptor protein and BLV gp51 and, proposing a reliable model for gp51-AP3D1 interaction using bioinformatics tools. The boAP3D1 receptor interaction patterns were calculated based on models of boAP3D1 receptor and gp51 complexes’ 3D structures, which were constructed using homology techniques and data-driven docking strategy. The results showed that the participation of 6 key amino acids (aa) on gp51 (Asn170, Trp127, His115, Ala97, Ser98 and Glu128) and 4 aa on AP3D1 (Lys925, Asp807, Asp695 and Arg800) was highly probable in the interaction between gp51 and BLVR domains. Three gp51 recombinant peptides were expressed and purified to validate these results: the complete domain (rgp51), the N-terminal portion (rNgp51) and the C-terminal fragment (rCgp51); and binding assays to Madin-Darby bovine kidney (MDBK) cells were then carried out with each recombinant. It was found that rNgp51 preferentially bound to MDBK cells, suggesting this domain’s functional role during invasion. The rNgp51-MDBK cell interaction was sensitive to trypsin (98% reduction) and chymotrypsin treatment (80% reduction). These results highlighted that the N-terminal portion of gp51 interacted in vitro with the AP3D1 receptor and provides a plausible in silico interaction model.
Collapse
Affiliation(s)
| | - Janneth González
- Nutrition and Biochemistry Department, Science Faculty, Universidad Javeriana, Bogotá DC, Colombia
- * E-mail: (MFG); (JG)
| | - Luis Alfredo Baquero
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá DC, Colombia
| | - Hernando Curtidor
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá DC, Colombia
- Basic Sciences Department, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá DC, Colombia
| | - Nury Nathalia Olaya-Galán
- Virology Laboratory, Universidad Javeriana, Bogotá DC, Colombia
- PhD Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá DC, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá DC, Colombia
- Basic Sciences Department, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá DC, Colombia
| | | |
Collapse
|
15
|
Retroviral restriction: nature's own solution. Curr Opin Infect Dis 2018; 29:609-614. [PMID: 27749368 DOI: 10.1097/qco.0000000000000322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW The present review will discuss recent advances in the development of anti-HIV therapies inspired by studies of the mechanisms of host restriction factor-mediated resistance to HIV infection. RECENT FINDINGS Manipulating the interplay between host cell restriction factors and viral accessory factors that overcome them can potentially be therapeutically useful. Preliminarily successful therapies - some of which are entering clinical trials - either inhibit the ability of virus to evade restriction factor-mediated immunity, or promote intracellular levels of restriction factors. These aims are achieved by multiple means, which are discussed. SUMMARY Many restriction factors appear to provide potentially useful targets for anti-HIV therapies, so time and interest should be invested in investigating ways to successfully therapeutically manipulate restriction factor-mediated immunity.
Collapse
|
16
|
Mattei S, Glass B, Hagen WJH, Kräusslich HG, Briggs JAG. The structure and flexibility of conical HIV-1 capsids determined within intact virions. Science 2017; 354:1434-1437. [PMID: 27980210 DOI: 10.1126/science.aah4972] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/18/2016] [Indexed: 12/30/2022]
Abstract
HIV-1 contains a cone-shaped capsid encasing the viral genome. This capsid is thought to follow fullerene geometry-a curved hexameric lattice of the capsid protein, CA, closed by incorporating 12 CA pentamers. Current models for core structure are based on crystallography of hexameric and cross-linked pentameric CA, electron microscopy of tubular CA arrays, and simulations. Here, we report subnanometer-resolution cryo-electron tomography structures of hexameric and pentameric CA within intact HIV-1 particles. Whereas the hexamer structure is compatible with crystallography studies, the pentamer forms using different interfaces. Determining multiple structures revealed how CA flexes to form the variably curved core shell. We show that HIV-1 CA assembles both aberrant and perfect fullerene cones, supporting models in which conical cores assemble de novo after maturation.
Collapse
Affiliation(s)
- Simone Mattei
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory-Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Bärbel Glass
- Department of Infectious Diseases, Virology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Wim J H Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory-Universitätsklinikum Heidelberg, Heidelberg, Germany.,Department of Infectious Diseases, Virology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. .,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory-Universitätsklinikum Heidelberg, Heidelberg, Germany
| |
Collapse
|
17
|
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.
Collapse
|
18
|
Taylor WR, Stoye JP, Taylor IA. A comparative analysis of the foamy and ortho virus capsid structures reveals an ancient domain duplication. BMC STRUCTURAL BIOLOGY 2017; 17:3. [PMID: 28372592 PMCID: PMC5379526 DOI: 10.1186/s12900-017-0073-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/10/2017] [Indexed: 01/28/2023]
Abstract
BACKGROUND The Spumaretrovirinae (foamy viruses) and the Orthoretrovirinae (e.g. HIV) share many similarities both in genome structure and the sequences of the core viral encoded proteins, such as the aspartyl protease and reverse transcriptase. Similarity in the gag region of the genome is less obvious at the sequence level but has been illuminated by the recent solution of the foamy virus capsid (CA) structure. This revealed a clear structural similarity to the orthoretrovirus capsids but with marked differences that left uncertainty in the relationship between the two domains that comprise the structure. METHODS We have applied protein structure comparison methods in order to try and resolve this ambiguous relationship. These included both the DALI method and the SAP method, with rigorous statistical tests applied to the results of both methods. For this, we employed collections of artificial fold 'decoys' (generated from the pair of native structures being compared) to provide a customised background distribution for each comparison, thus allowing significance levels to be estimated. RESULTS We have shown that the relationship of the two domains conforms to a simple linear correspondence rather than a domain transposition. These similarities suggest that the origin of both viral capsids was a common ancestor with a double domain structure. In addition, we show that there is also a significant structural similarity between the amino and carboxy domains in both the foamy and ortho viruses. CONCLUSIONS These results indicate that, as well as the duplication of the double domain capsid, there may have been an even more ancient gene-duplication that preceded the double domain structure. In addition, our structure comparison methodology demonstrates a general approach to problems where the components have a high intrinsic level of similarity.
Collapse
Affiliation(s)
- William R. Taylor
- Computational Cell and Molecular Biology Laboratory, Francis Crick Institute, Midland Road, London, NW1 1AT UK
| | - Jonathan P. Stoye
- Retrovirus-Host Interactions Laboratory, Francis Crick Institute, Midland Road, London, NW1 1AT UK
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, Francis Crick Institute, Midland Road, London, NW1 1AT UK
| |
Collapse
|
19
|
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
| |
Collapse
|
20
|
Ni R, Zhou J, Hossain N, Chau Y. Virus-inspired nucleic acid delivery system: Linking virus and viral mimicry. Adv Drug Deliv Rev 2016; 106:3-26. [PMID: 27473931 DOI: 10.1016/j.addr.2016.07.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 07/02/2016] [Accepted: 07/20/2016] [Indexed: 12/21/2022]
Abstract
Targeted delivery of nucleic acids into disease sites of human body has been attempted for decades, but both viral and non-viral vectors are yet to meet our expectations. Safety concerns and low delivery efficiency are the main limitations of viral and non-viral vectors, respectively. The structure of viruses is both ordered and dynamic, and is believed to be the key for effective transfection. Detailed understanding of the physical properties of viruses, their interaction with cellular components, and responses towards cellular environments leading to transfection would inspire the development of safe and effective non-viral vectors. To this goal, this review systematically summarizes distinctive features of viruses that are implied for efficient nucleic acid delivery but not yet fully explored in current non-viral vectors. The assembly and disassembly of viral structures, presentation of viral ligands, and the subcellular targeting of viruses are emphasized. Moreover, we describe the current development of cationic material-based viral mimicry (CVM) and structural viral mimicry (SVM) in these aspects. In light of the discrepancy, we identify future opportunities for rational design of viral mimics for the efficient delivery of DNA and RNA.
Collapse
Affiliation(s)
- Rong Ni
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Institute for Advanced Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Junli Zhou
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Naushad Hossain
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ying Chau
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
| |
Collapse
|
21
|
Li YL, Chandrasekaran V, Carter SD, Woodward CL, Christensen DE, Dryden KA, Pornillos O, Yeager M, Ganser-Pornillos BK, Jensen GJ, Sundquist WI. Primate TRIM5 proteins form hexagonal nets on HIV-1 capsids. eLife 2016; 5. [PMID: 27253068 PMCID: PMC4936896 DOI: 10.7554/elife.16269] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/19/2016] [Indexed: 12/04/2022] Open
Abstract
TRIM5 proteins are restriction factors that block retroviral infections by binding viral capsids and preventing reverse transcription. Capsid recognition is mediated by C-terminal domains on TRIM5α (SPRY) or TRIMCyp (cyclophilin A), which interact weakly with capsids. Efficient capsid recognition also requires the conserved N-terminal tripartite motifs (TRIM), which mediate oligomerization and create avidity effects. To characterize how TRIM5 proteins recognize viral capsids, we developed methods for isolating native recombinant TRIM5 proteins and purifying stable HIV-1 capsids. Biochemical and EM analyses revealed that TRIM5 proteins assembled into hexagonal nets, both alone and on capsid surfaces. These nets comprised open hexameric rings, with the SPRY domains centered on the edges and the B-box and RING domains at the vertices. Thus, the principles of hexagonal TRIM5 assembly and capsid pattern recognition are conserved across primates, allowing TRIM5 assemblies to maintain the conformational plasticity necessary to recognize divergent and pleomorphic retroviral capsids. DOI:http://dx.doi.org/10.7554/eLife.16269.001 After infecting a cell, a virus reproduces by forcing the cell to produce new copies of the virus, which then spread to other cells. However, cells have evolved ways to fight back against these infections. For example, many mammalian cells contain proteins called restriction factors that prevent the virus from multiplying. The TRIM5 proteins form one common set of restriction factors that act against a class of viruses called retroviruses. HIV-1 and related retroviruses have a protein shell known as a capsid that surrounds the genetic material of the virus. The capsid contains several hundred repeating units, each of which consists of a hexagonal ring of six CA proteins. Although this basic pattern is maintained across different retroviruses, the overall shape of the capsids can vary considerably. For instance, HIV-1 capsids are shaped like a cone, but other retroviruses can form cylinders or spheres. Soon after the retrovirus enters a mammalian cell, TRIM5 proteins bind to the capsid. This causes the capsid to be destroyed, which prevents viral replication. Previous research has shown that several TRIM5 proteins must link up with each other via a region of their structure called the B-box 2 domain in order to efficiently recognize capsids. How this assembly process occurs, and why it enables the TRIM5 proteins to recognize different capsids was not fully understood. Now, Li, Chandrasekaran et al. (and independently Wagner et al.) have investigated these questions. Using biochemical analyses and electron microscopy, Li, Chandrasekaran et al. found that TRIM5 proteins can bind directly to the surface of HIV-1 capsids. Several TRIM5 proteins link together to form large hexagonal nets, in which the B-box domains of the proteins are found at the points where three TRIM5 proteins meet. This arrangement mimics the pattern present in the HIV-1 capsid, and just a few TRIM5 rings can cover most of the capsid. Li, Chandrasekaran et al. then analysed TRIM5 proteins from several primates, including rhesus macaques, African green monkeys and chimpanzees. In all cases analyzed, the TRIM5 proteins assembled into hexagonal nets, although the individual units within the net did not have strictly regular shapes. These results suggest that TRIM5 proteins assemble a scaffold that can deform to match the pattern of the proteins in the capsid. Further work is now needed to understand how capsid recognition is linked to the processes that disable the virus. DOI:http://dx.doi.org/10.7554/eLife.16269.002
Collapse
Affiliation(s)
- Yen-Li Li
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | | | - Stephen D Carter
- Division of Biology, California Institute of Technology, Pasadena, United States
| | - Cora L Woodward
- Division of Biology, California Institute of Technology, Pasadena, United States
| | - Devin E Christensen
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - Kelly A Dryden
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, United States
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, United States
| | - Mark Yeager
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, United States.,Department of Medicine, Division of Cardiovascular Medicine, University of Virginia Health System, Charlottesville, United States
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, United States
| | - Grant J Jensen
- Division of Biology, California Institute of Technology, Pasadena, United States.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
| | - Wesley I Sundquist
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| |
Collapse
|
22
|
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.
Collapse
Affiliation(s)
- Bo Chen
- Department of Physics, University of Central Florida , Orlando, Florida 32816, United States
| |
Collapse
|
23
|
Khwaja A, Galilee M, Marx A, Alian A. Structure of FIV capsid C-terminal domain demonstrates lentiviral evasion of genetic fragility by coevolved substitutions. Sci Rep 2016; 6:24957. [PMID: 27102180 PMCID: PMC4840305 DOI: 10.1038/srep24957] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/08/2016] [Indexed: 12/22/2022] Open
Abstract
Viruses use a strategy of high mutational rates to adapt to environmental and therapeutic pressures, circumventing the deleterious effects of random single-point mutations by coevolved compensatory mutations, which restore protein fold, function or interactions damaged by initial ones. This mechanism has been identified as contributing to drug resistance in the HIV-1 Gag polyprotein and especially its capsid proteolytic product, which forms the viral capsid core and plays multifaceted roles in the viral life cycle. Here, we determined the X-ray crystal structure of C-terminal domain of the feline immunodeficiency virus (FIV) capsid and through interspecies analysis elucidate the structural basis of co-evolutionarily and spatially correlated substitutions in capsid sequences, which when otherwise uncoupled and individually substituted into HIV-1 capsid impair virion assembly and infectivity. The ability to circumvent the deleterious effects of single amino acid substitutions by cooperative secondary substitutions allows mutational flexibility that may afford viruses an important survival advantage. The potential of such interspecies structural analysis for preempting viral resistance by identifying such alternative but functionally equivalent patterns is discussed.
Collapse
Affiliation(s)
- Aya Khwaja
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Meytal Galilee
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Ailie Marx
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Akram Alian
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| |
Collapse
|
24
|
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.
Collapse
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.
| |
Collapse
|
25
|
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.
Collapse
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.
| |
Collapse
|
26
|
Pham S, Tabarin T, Garvey M, Pade C, Rossy J, Monaghan P, Hyatt A, Böcking T, Leis A, Gaus K, Mak J. Cryo-electron microscopy and single molecule fluorescent microscopy detect CD4 receptor induced HIV size expansion prior to cell entry. Virology 2015; 486:121-33. [PMID: 26432024 DOI: 10.1016/j.virol.2015.09.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 09/09/2015] [Accepted: 09/10/2015] [Indexed: 10/23/2022]
Abstract
Viruses are often thought to have static structure, and they only remodel after the viruses have entered target cells. Here, we detected a size expansion of virus particles prior to viral entry using cryo-electron microscopy (cryo-EM) and single molecule fluorescence imaging. HIV expanded both under cell-free conditions with soluble receptor CD4 (sCD4) targeting the CD4 binding site on the HIV-1 envelope protein (Env) and when HIV binds to receptor on cellular membrane. We have shown that the HIV Env is needed to facilitate receptor induced virus size expansions, showing that the 'lynchpin' for size expansion is highly specific. We demonstrate that the size expansion required maturation of HIV and an internal capsid core with wild type stability, suggesting that different HIV compartments are linked and are involved in remodelling. Our work reveals a previously unknown event in HIV entry, and we propose that this pre-entry priming process enables HIV particles to facilitate the subsequent steps in infection.
Collapse
Affiliation(s)
- Son Pham
- Deakin University, Victoria 3216, Australia; CSIRO Australian Animal Health Laboratory, Victoria 3220, Australia
| | - Thibault Tabarin
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, New South Wales 3220, Australia
| | - Megan Garvey
- Deakin University, Victoria 3216, Australia; CSIRO Australian Animal Health Laboratory, Victoria 3220, Australia
| | - Corinna Pade
- Deakin University, Victoria 3216, Australia; CSIRO Australian Animal Health Laboratory, Victoria 3220, Australia
| | - Jérémie Rossy
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, New South Wales 3220, Australia
| | - Paul Monaghan
- CSIRO Australian Animal Health Laboratory, Victoria 3220, Australia
| | - Alex Hyatt
- CSIRO Australian Animal Health Laboratory, Victoria 3220, Australia
| | - Till Böcking
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, New South Wales 3220, Australia
| | - Andrew Leis
- CSIRO Australian Animal Health Laboratory, Victoria 3220, Australia
| | - Katharina Gaus
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, New South Wales 3220, Australia.
| | - Johnson Mak
- Deakin University, Victoria 3216, Australia; CSIRO Australian Animal Health Laboratory, Victoria 3220, Australia.
| |
Collapse
|
27
|
Yu X, Mishra R, Holloway G, von Itzstein M, Coulson BS, Blanchard H. Substantial Receptor-induced Structural Rearrangement of Rotavirus VP8*: Potential Implications for Cross-Species Infection. Chembiochem 2015; 16:2176-81. [PMID: 26250751 DOI: 10.1002/cbic.201500360] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Indexed: 11/06/2022]
Abstract
Rotavirus-cell binding is the essential first step in rotavirus infection. This binding is a major determinant of rotavirus tropism, as host cell invasion is necessary to initiate infection. Initial rotavirus-cell interactions are mediated by carbohydrate-recognizing domain VP8* of the rotavirus capsid spike protein VP4. Here, we report the first observation of significant structural rearrangement of VP8* from human and animal rotavirus strains upon glycan receptor binding. The structural adaptability of rotavirus VP8* delivers important insights into how human and animal rotaviruses utilize the wider range of cellular glycans identified as VP8* binding partners. Furthermore, our studies on rotaviruses with atypical genetic makeup provide information expected to be critical for understanding the mechanisms of animal rotavirus gene emergence in humans and support implementation of epidemiologic surveillance of animal reservoirs as well as future vaccination schemes.
Collapse
Affiliation(s)
- Xing Yu
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, 4222, Australia.
| | - Rahul Mishra
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, 4222, Australia
| | - Gavan Holloway
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, 4222, Australia
| | - Barbara S Coulson
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Helen Blanchard
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, 4222, Australia.
| |
Collapse
|
28
|
Gres AT, Kirby KA, KewalRamani VN, Tanner JJ, Pornillos O, Sarafianos SG. STRUCTURAL VIROLOGY. X-ray crystal structures of native HIV-1 capsid protein reveal conformational variability. Science 2015; 349:99-103. [PMID: 26044298 DOI: 10.1126/science.aaa5936] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 05/27/2015] [Indexed: 12/19/2022]
Abstract
The detailed molecular interactions between native HIV-1 capsid protein (CA) hexamers that shield the viral genome and proteins have been elusive. We report crystal structures describing interactions between CA monomers related by sixfold symmetry within hexamers (intrahexamer) and threefold and twofold symmetry between neighboring hexamers (interhexamer). The structures describe how CA builds hexagonal lattices, the foundation of mature capsids. Lattice structure depends on an adaptable hydration layer modulating interactions among CA molecules. Disruption of this layer alters interhexamer interfaces, highlighting an inherent structural variability. A CA-targeting antiviral affects capsid stability by binding across CA molecules and subtly altering interhexamer interfaces remote to the ligand-binding site. Inherent structural plasticity, hydration layer rearrangement, and effector binding affect capsid stability and have functional implications for the retroviral life cycle.
Collapse
Affiliation(s)
- Anna T Gres
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA. Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
| | - Karen A Kirby
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA. Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65211, USA
| | - Vineet N KewalRamani
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - John J Tanner
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA. Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Stefan G Sarafianos
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA. Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65211, USA. Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
| |
Collapse
|