1
|
Liu Y, Zeng M, Liu S, Li C. Dynamics analysis of building block synthesis reactions for virus assembly in vitro. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:4082-4102. [PMID: 36899618 DOI: 10.3934/mbe.2023191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Virus assembly from structural protein monomers to virus shells is a key step of virus replication. Some drug targets were found in this process. It consists of two steps. Virus structural protein monomers firstly polymerize to building blocks, then these building blocks assemble into virus shells. So, these building block synthesis reactions in the first step are fundamental for virus assembly. Typically, virus building blocks are made up of less than six monomers. They are of five types, including dimer, trimer, tetramer, pentamer and hexamer. In this work, we develop five synthesis reaction dynamical models for these five types, respectively. Then, we prove the existence and uniqueness of the positive equilibrium solution for these dynamical models one by one. Subsequently, we also analyze the stability of the equilibrium states, respectively. We got the function of monomer and dimer concentrations for dimer building blocks in the equilibrium state. We also got the function of all intermediate polymers and monomers for trimer, tetramer, pentamer and hexamer building blocks in the equilibrium state, respectively. Based on our analysis, dimer building blocks in the equilibrium state will decrease as the ratio of the off-rate constant to the on-rate constant increases. Trimer building blocks in the equilibrium state will decrease with the increasing ratio of the off-rate constant to the on-rate constant of trimers. These results may provide further insight into the virus-building block synthesis dynamic property in vitro.
Collapse
Affiliation(s)
- Yuewu Liu
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China
| | - Mengfang Zeng
- Hunan Federation of Social Sciences, Changsha 410000, China
| | - Shengyong Liu
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China
| | - Chun Li
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Lau D, Walsh JC, Peng W, Shah VB, Turville S, Jacques DA, Böcking T. Fluorescence Biosensor for Real-Time Interaction Dynamics of Host Proteins with HIV-1 Capsid Tubes. ACS APPLIED MATERIALS & INTERFACES 2019; 11:34586-34594. [PMID: 31483592 DOI: 10.1021/acsami.9b08521] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The human immunodeficiency virus 1 (HIV-1) capsid serves as a binding platform for proteins and small molecules from the host cell that regulate various steps in the virus life cycle. However, there are currently no quantitative methods that use assembled capsid lattices to measure host-pathogen interaction dynamics. Here we developed a single-molecule fluorescence biosensor using self-assembled capsid tubes as biorecognition elements and imaged capsid binders using total internal reflection fluorescence microscopy in a microfluidic setup. The method is highly sensitive in its ability to observe and quantify binding, to obtain dissociation constants, and to extract kinetics with an extended application of using more complex analytes that can accelerate characterization of novel capsid binders.
Collapse
|
4
|
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
|
5
|
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
|
6
|
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
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Suiter CL, Quinn CM, Lu M, Hou G, Zhang H, Polenova T. MAS NMR of HIV-1 protein assemblies. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:10-22. [PMID: 25797001 PMCID: PMC4432874 DOI: 10.1016/j.jmr.2014.12.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/08/2014] [Accepted: 12/17/2014] [Indexed: 06/04/2023]
Abstract
The negative global impact of the AIDS pandemic is well known. In this perspective article, the utility of magic angle spinning (MAS) NMR spectroscopy to answer pressing questions related to the structure and dynamics of HIV-1 protein assemblies is examined. In recent years, MAS NMR has undergone major technological developments enabling studies of large viral assemblies. We discuss some of these evolving methods and technologies and provide a perspective on the current state of MAS NMR as applied to the investigations into structure and dynamics of HIV-1 assemblies of CA capsid protein and of Gag maturation intermediates.
Collapse
Affiliation(s)
- Christopher L Suiter
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Manman Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Huilan Zhang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| |
Collapse
|
9
|
Kang BS, Eom CY, Kim W, Kim PI, Ju SY, Ryu J, Han GH, Oh JI, Cho H, Baek SH, Kim G, Kim M, Hyun J, Jin E, Kim SW. Construction of target-specific virus-like particles for the delivery of algicidal compounds to harmful algae. Environ Microbiol 2014; 17:1463-74. [DOI: 10.1111/1462-2920.12650] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 09/23/2014] [Accepted: 09/26/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Beom Sik Kang
- School of Life Science and Biotechnology; Kyungpook National University; Daegu 702-701 Korea
| | - Chi-Yong Eom
- NanoBio Convergence Research Team; Western Seoul Center; Korea Basic Science Institute; Seoul 120-750 Korea
| | - Wonduck Kim
- Department of Environmental Engineering and Pioneer Research Center for Controlling of Harmful Algal Bloom; Chosun University; Gwangju 501-759 Korea
| | - Pyoung il Kim
- Department of Environmental Engineering and Pioneer Research Center for Controlling of Harmful Algal Bloom; Chosun University; Gwangju 501-759 Korea
| | - Sun Yi Ju
- Department of Environmental Engineering and Pioneer Research Center for Controlling of Harmful Algal Bloom; Chosun University; Gwangju 501-759 Korea
| | - Jaewon Ryu
- Department of Environmental Engineering and Pioneer Research Center for Controlling of Harmful Algal Bloom; Chosun University; Gwangju 501-759 Korea
| | - Gui Hwan Han
- Department of Environmental Engineering and Pioneer Research Center for Controlling of Harmful Algal Bloom; Chosun University; Gwangju 501-759 Korea
| | - Jeong-Il Oh
- Department of Microbiology; Pusan University; Pusan 609-735 Korea
| | - Hoon Cho
- Department of Polymer Science and Engineering; Chosun University; Gwangju 501-759 Korea
| | - Seung Ho Baek
- South Sea Institute; Korea Ocean Research and Development Institute; Geoje 656-830 Korea
| | - Gueeda Kim
- Department of Life Science and Research Institute for Natural Sciences; Hanyang University; Seoul 133-791 Korea
| | - Minju Kim
- Department of Life Science and Research Institute for Natural Sciences; Hanyang University; Seoul 133-791 Korea
| | - Jaekyung Hyun
- Division of Electron Microscopic Research; Korea Basic Science Institute; Daejeon 305-333 Korea
| | - EonSeon Jin
- Department of Life Science and Research Institute for Natural Sciences; Hanyang University; Seoul 133-791 Korea
| | - Si Wouk Kim
- Department of Environmental Engineering and Pioneer Research Center for Controlling of Harmful Algal Bloom; Chosun University; Gwangju 501-759 Korea
| |
Collapse
|
10
|
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;
| |
Collapse
|
11
|
Abstract
UNLABELLED During virion maturation, the Rous sarcoma virus (RSV) capsid protein is cleaved from the Gag protein as the proteolytic intermediate CA-SP. Further trimming at two C-terminal sites removes the spacer peptide (SP), producing the mature capsid proteins CA and CA-S. Abundant genetic and structural evidence shows that the SP plays a critical role in stabilizing hexameric Gag interactions that form immature particles. Freeing of CA-SP from Gag breaks immature interfaces and initiates the formation of mature capsids. The transient persistence of CA-SP in maturing virions and the identification of second-site mutations in SP that restore infectivity to maturation-defective mutant viruses led us to hypothesize that SP may play an important role in promoting the assembly of mature capsids. This study presents a biophysical and biochemical characterization of CA-SP and its assembly behavior. Our results confirm cryo-electron microscopy (cryo-EM) structures reported previously by Keller et al. (J. Virol. 87:13655-13664, 2013, doi:10.1128/JVI.01408-13) showing that monomeric CA-SP is fully capable of assembling into capsid-like structures identical to those formed by CA. Furthermore, SP confers aggressive assembly kinetics, which is suggestive of higher-affinity CA-SP interactions than observed with either of the mature capsid proteins. This aggressive assembly is largely independent of the SP amino acid sequence, but the formation of well-ordered particles is sensitive to the presence of the N-terminal β-hairpin. Additionally, CA-SP can nucleate the assembly of CA and CA-S. These results suggest a model in which CA-SP, once separated from the Gag lattice, can actively promote the interactions that form mature capsids and provide a nucleation point for mature capsid assembly. IMPORTANCE The spacer peptide is a documented target for antiretroviral therapy. This study examines the biochemical and biophysical properties of CA-SP, an intermediate form of the retrovirus capsid protein. The results demonstrate a previously unrecognized activity of SP in promoting capsid assembly during maturation.
Collapse
|
12
|
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.
Collapse
|
13
|
Andersen KB. The retrovirus MA and PreTM proteins follow immature MLV cores. Virus Res 2013; 175:134-42. [PMID: 23643491 DOI: 10.1016/j.virusres.2013.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/17/2013] [Accepted: 04/17/2013] [Indexed: 10/26/2022]
Abstract
We have used mild detergent to analyze the core of Moloney Murine Leukemia Virus (MoMLV) and core-like complexes in infected cells. The immature core consists of the Gag polyprotein (PrGag) and viral RNA (vRNA). It is known to be detergent-resistant, in contrast to the mature Gag core. The core matures by cleavage of PrGag into MA (matrix), p12, CA (capsid) and NC (nucleocapsid) protein. We found that mature Gag proteins were bound to the PrGag cores. The degree of binding differed widely. No (<0.1%) p12 bound, low amount of CA (3-5%), and higher amount of MA (13-20%) bound. Varying NC was bound (5-15%). NC could be released by RNase A in agreement with its binding to viral RNA. The TM (transmembrane) protein was also examined. A low amount of TM was bound to the PrGag core (approximately 5%), whereas a very high amount (65%) of the PreTM (TM with the cytoplasmic R peptide tail) bound. The binding in the PrGag core appears to occur by direct protein-protein interactions as only minute amounts of lipids including raft lipids were observed after detergent treatment.
Collapse
Affiliation(s)
- Klaus B Andersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK2100 Copenhagen, Denmark.
| |
Collapse
|
14
|
Biophysical characterization of the feline immunodeficiency virus p24 capsid protein conformation and in vitro capsid assembly. PLoS One 2013; 8:e56424. [PMID: 23457565 PMCID: PMC3574121 DOI: 10.1371/journal.pone.0056424] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 01/10/2013] [Indexed: 12/27/2022] Open
Abstract
The Feline Immunodeficiency Virus (FIV) capsid protein p24 oligomerizes to form a closed capsid that protects the viral genome. Because of its crucial role in the virion, FIV p24 is an interesting target for the development of therapeutic strategies, although little is known about its structure and assembly. We defined and optimized a protocol to overexpress recombinant FIV capsid protein in a bacterial system. Circular dichroism and isothermal titration calorimetry experiments showed that the structure of the purified FIV p24 protein was comprised mainly of α-helices. Dynamic light scattering (DLS) and cross-linking experiments demonstrated that p24 was monomeric at low concentration and dimeric at high concentration. We developed a protocol for the in vitro assembly of the FIV capsid. As with HIV, an increased ionic strength resulted in FIV p24 assembly in vitro. Assembly appeared to be dependent on temperature, salt concentration, and protein concentration. The FIV p24 assembly kinetics was monitored by DLS. A limit end-point diameter suggested assembly into objects of definite shapes. This was confirmed by electron microscopy, where FIV p24 assembled into spherical particles. Comparison of FIV p24 with other retroviral capsid proteins showed that FIV assembly is particular and requires further specific study.
Collapse
|
15
|
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.
Collapse
Affiliation(s)
- Paula M Dalessio
- Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, USA
| | | | | | | |
Collapse
|
16
|
Tsiang M, Niedziela-Majka A, Hung M, Jin D, Hu E, Yant S, Samuel D, Liu X, Sakowicz R. A trimer of dimers is the basic building block for human immunodeficiency virus-1 capsid assembly. Biochemistry 2012; 51:4416-28. [PMID: 22564075 DOI: 10.1021/bi300052h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Human immunodeficiency virus-1 (HIV-1) capsid protein (CA) has become a target of antiviral drug design in recent years. The recognition that binding of small molecules to the CA protein can result in the perturbation of capsid assembly or disassembly has led to mathematical modeling of the process. Although a number of capsid assembly models have been developed using biophysical parameters of the CA protein obtained experimentally, there is currently no model of CA polymerization that can be practically used to analyze in vitro CA polymerization data to facilitate drug discovery. Herein, we describe an equilibrium model of CA polymerization for the kinetic analysis of in vitro assembly of CA into polymer tubes. This new mathematical model has been used to assess whether a triangular trimer of dimers rather than a hexagonal hexamer can be the basic capsomere building block of CA polymer. The model allowed us to quantify for the first time the affinity for each of the four crucial interfaces involved in the polymerization process and indicated that the trimerization of CA dimers is a relatively slow step in CA polymerization in vitro. For wild-type CA, these four interfaces include the interface between two monomers of a CA dimer (K(D) = 6.6 μM), the interface between any two dimers within a CA trimer of dimers (K(D) = 32 nM), and two types of interfaces between neighboring trimers of dimers, either within the same ring around the perimeter of the polymer tube (K(D) = 438 nM) or from two adjacent rings (K(D) = 147 nM). A comparative analysis of the interface dissociation constants between wild-type and two mutant CA proteins, cross-linked hexamer (A14C/E45C/W184A/M185A) and A14C/E45C, yielded results that are consistent with the trimer of dimers with a triangular geometry being the capsomere building block involved in CA polymer growth. This work provides additional insights into the mechanism of HIV-1 CA assembly and may prove useful in elucidating how small molecule CA binding agents may disturb this essential step in the HIV-1 life cycle.
Collapse
Affiliation(s)
- Manuel Tsiang
- Gilead Sciences, Foster City, California 94404, United States.
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Byeon IJL, Hou G, Han Y, Suiter CL, Ahn J, Jung J, Byeon CH, Gronenborn AM, Polenova T. Motions on the millisecond time scale and multiple conformations of HIV-1 capsid protein: implications for structural polymorphism of CA assemblies. J Am Chem Soc 2012; 134:6455-66. [PMID: 22428579 PMCID: PMC3325613 DOI: 10.1021/ja300937v] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The capsid protein (CA) of human immunodeficiency virus 1 (HIV-1) assembles into a cone-like structure that encloses the viral RNA genome. Interestingly, significant heterogeneity in shape and organization of capsids can be observed in mature HIV-1 virions. In vitro, CA also exhibits structural polymorphism and can assemble into various morphologies, such as cones, tubes, and spheres. Many intermolecular contacts that are critical for CA assembly are formed by its C-terminal domain (CTD), a dimerization domain, which was found to adopt different orientations in several X-ray and NMR structures of the CTD dimer and full-length CA proteins. Tyr145 (Y145), residue two in our CTD construct used for NMR structure determination, but not present in the crystallographic constructs, was found to be crucial for infectivity and engaged in numerous interactions at the CTD dimer interface. Here we investigate the origin of CA structural plasticity using solid-state NMR and solution NMR spectroscopy. In the solid state, the hinge region connecting the NTD and CTD is flexible on the millisecond time scale, as evidenced by the backbone motions of Y145 in CA conical assemblies and in two CTD constructs (137-231 and 142-231), allowing the protein to access multiple conformations essential for pleimorphic capsid assemblies. In solution, the CTD dimer exists as two major conformers, whose relative populations differ for the different CTD constructs. In the longer CTD (144-231) construct that contains the hinge region between the NTD and CTD, the populations of the two conformers are likely determined by the protonation state of the E175 side chain that is located at the dimer interface and within hydrogen-bonding distance of the W184 side chain on the other monomer. At pH 6.5, the major conformer exhibits the same dimer interface as full-length CA. In the short CTD (150-231) construct, no pH-dependent conformational shift is observed. These findings suggest that the presence of structural plasticity at the CTD dimer interface permits pleiotropic HIV-1 capsid assembly, resulting in varied capsid morphologies.
Collapse
Affiliation(s)
- In-Ja L. Byeon
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Guangjin Hou
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Yun Han
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Christopher L. Suiter
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Jinwoo Ahn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Jinwon Jung
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Chang-Hyeock Byeon
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Tatyana Polenova
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| |
Collapse
|
18
|
A Structural Model for the Generation of Continuous Curvature on the Surface of a Retroviral Capsid. J Mol Biol 2012; 417:212-23. [DOI: 10.1016/j.jmb.2012.01.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 12/25/2011] [Accepted: 01/13/2012] [Indexed: 01/06/2023]
|
19
|
Ganser-Pornillos BK, Yeager M, Pornillos O. Assembly and architecture of HIV. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:441-65. [PMID: 22297526 PMCID: PMC6743068 DOI: 10.1007/978-1-4614-0980-9_20] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
HIV forms spherical, membrane-enveloped, pleomorphic virions, 1,000-1,500 Å in diameter, which contain two copies of its single-stranded, positive-sense RNA genome. Virus particles initially bud from host cells in a noninfectious or immature form, in which the genome is further encapsulated inside a spherical protein shell composed of around 2,500 copies of the virally encoded Gag polyprotein. The Gag molecules are radially arranged, adherent to the inner leaflet of the viral membrane, and closely associated as a hexagonal, paracrystalline lattice. Gag comprises three major structural domains called MA, CA, and NC. For immature virions to become infectious, they must undergo a maturation process that is initiated by proteolytic processing of Gag by the viral protease. The new Gag-derived proteins undergo dramatic rearrangements to form the mature virus. The mature MA protein forms a "matrix" layer and remains attached to the viral envelope, NC condenses with the genome, and approximately 1,500 copies of CA assemble into a new cone-shaped protein shell, called the mature capsid, which surrounds the genomic ribonucleoprotein complex. The HIV capsid conforms to the mathematical principles of a fullerene shell, in which the CA subunits form about 250 CA hexamers arrayed on a variably curved hexagonal lattice, which is closed by incorporation of exactly 12 pentamers, seven pentamers at the wide end and five at the narrow end of the cone. This chapter describes our current understanding of HIV's virion architecture and its dynamic transformations: the process of virion assembly as orchestrated by Gag, the architecture of the immature virion, the virus maturation process, and the structure of the mature capsid.
Collapse
Affiliation(s)
- Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
| | | | | |
Collapse
|
20
|
Yeager M. Design of in vitro symmetric complexes and analysis by hybrid methods reveal mechanisms of HIV capsid assembly. J Mol Biol 2011; 410:534-52. [PMID: 21762799 DOI: 10.1016/j.jmb.2011.04.073] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 04/28/2011] [Accepted: 04/28/2011] [Indexed: 12/26/2022]
Abstract
Unlike the capsids of icosahedral viruses, retroviral capsids are pleomorphic, with variably curved, closed fullerene shells composed of ∼250 hexamers and exactly 12 pentamers of the viral CA protein. Structures of CA oligomers have been difficult to obtain because the subunit-subunit interactions are inherently weak, and CA tends to spontaneously assemble into capsid-like particles. Guided by a cryoEM-based model of the hexagonal lattice of HIV-1 CA, we used a two-step biochemical strategy to obtain soluble CA hexamers and pentamers for crystallization. First, each oligomer was stabilized by engineering disulfide cross-links between the N-terminal domains of adjacent subunits. Second, the cross-linked oligomers were prevented from polymerizing into hyperstable, capsid-like structures by mutations that weakened the dimeric association between the C-terminal domains that link adjacent oligomers. The X-ray structures revealed that the oligomers are comprised of a fairly rigid, central symmetric ring of N-terminal domains encircled by mobile C-terminal domains. Assembly of the quasi-equivalent oligomers requires remarkably subtle rearrangements in inter-subunit quaternary bonding interactions, and appears to be controlled by an electrostatic switch that favors hexamers over pentamers. An atomic model of the complete HIV-1 capsid was then built using the fullerene cone as a template. Rigid-body rotations around two assembly interfaces are sufficient to generate the full range of continuously varying lattice curvature in the fullerene cone. The steps in determining this HIV-1 capsid atomic model exemplify the synergy of hybrid methods in structural biology, a powerful approach for exploring the structure of pleomorphic macromolecular complexes.
Collapse
Affiliation(s)
- Mark Yeager
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
| |
Collapse
|
21
|
Abstract
The mature capsids of human immunodeficiency virus type 1 (HIV-1) and other retroviruses are fullerene shells, composed of the viral CA protein, that enclose the viral genome and facilitate its delivery into new host cells1. Retroviral CA proteins contain independently-folded N-terminal and C-terminal domains (NTD and CTD) that are connected by a flexible linker2–4. The NTD forms either hexameric or pentameric rings, whereas the CTD forms symmetric homodimers that connect the rings into a hexagonal lattice3,5–13. We previously used a disulfide crosslinking strategy to enable isolation and crystallization of soluble HIV-1 CA hexamers11,14. By the same approach, we have now determined the X-ray structure of the HIV-1 CA pentamer at 2.5 Å resolution. Two mutant CA proteins with engineered disulfides at different positions (P17C/T19C and N21C/A22C) converged onto the same quaternary structure, indicating that the disulfide-crosslinked proteins recapitulate the structure of the native pentamer. Assembly of the quasi-equivalent hexamers and pentamers requires remarkably subtle rearrangements in subunit interactions, and appears to be controlled by an electrostatic switch that favors hexamers over pentamers. This study completes the gallery of sub-structures describing the components of the HIV-1 capsid and enables atomic level modeling of the complete capsid. Rigid-body rotations around two assembly interfaces appear sufficient to generate the full range of continuously varying lattice curvature in the fullerene cone.
Collapse
|