1
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Macleod SL, Super EH, Batt LJ, Yates E, Jones ST. Plate-Based High-Throughput Fluorescence Assay for Assessing Enveloped Virus Integrity. Biomacromolecules 2024; 25:4925-4933. [PMID: 39040021 PMCID: PMC11323024 DOI: 10.1021/acs.biomac.4c00358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/26/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024]
Abstract
Viruses are a considerable threat to global health and place major burdens on economies worldwide. Manufactured viruses are also being widely used as delivery agents to treat (gene therapies) or prevent diseases (vaccines). Therefore, it is vital to study and fully understand the infectious state of viruses. Current techniques used to study viruses are often slow or nonexistent, making the development of new techniques of paramount importance. Here we present a high-throughput and robust, cell-free plate-based assay (FAIRY: Fluorescence Assay for vIRal IntegritY), capable of differentiating intact from nonintact enveloped viruses, i.e, infectious from noninfectious. Using a thiazole orange-terminated polymer, a 99% increase in fluorescence was observed between treated (heat or virucide) and nontreated. The FAIRY assay allowed for the rapid determination of the infectivity of a range of enveloped viruses, highlighting its potential as a valuable tool for the study of viruses and interventions against them.
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Affiliation(s)
- Shannan-Leigh Macleod
- Department
of Materials and Henry Royce Institute, University of Manchester, Manchester M13 9PL, UK
| | - Elana H. Super
- Department
of Materials and Henry Royce Institute, University of Manchester, Manchester M13 9PL, UK
| | - Lauren J. Batt
- Department
of Materials and Henry Royce Institute, University of Manchester, Manchester M13 9PL, UK
| | - Eleanor Yates
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Samuel T. Jones
- Department
of Materials and Henry Royce Institute, University of Manchester, Manchester M13 9PL, UK
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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2
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Ye X, Hu Y, Qiu H, Li N. Probe capsid structure stability and dynamics of adeno-associated virus as an important viral vector for gene therapy by hydrogen-deuterium exchange-mass spectrometry. Protein Sci 2024; 33:e5074. [PMID: 38888268 PMCID: PMC11184576 DOI: 10.1002/pro.5074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/14/2024] [Accepted: 05/25/2024] [Indexed: 06/20/2024]
Abstract
Adeno-associated virus (AAV), a widely used gene therapy vector, is a small, nonenveloped virus that contains a single-stranded DNA genome with a maximum length of 4.7 kb. Despite extensive biophysical and structural characterization, many aspects of AAV functions remain elusive. This knowledge gap is primarily due to a lack of structurally resolved dynamic information and the absence of structural coverage of functionally critical segments on the AAV capsid. Here, we developed a protocol to study AAV structural dynamics by hydrogen-deuterium exchange mass spectrometry (HDX-MS), a powerful method for monitoring protein structure stability and dynamics in solution. We performed HDX-MS measurements on AAVs without or with different DNA payloads of different sizes, and obtained detailed dynamic information on the entire AAV sequence including the two functionally important segments not previously structurally characterized. The unique N terminus of the capsid protein VP1 (VP1u) was found to adopt a highly dynamic and unstable conformation with low HDX protection across the entire region, whereas the presence of a DNA payload increased its protection. The VP1 and VP2 shared region (VP1/2) showed no measurable protection, with or without DNA. Differential HDX between empty and full capsid samples allowed us to identify potential new DNA-capsid interaction sites located primarily around the five-fold channel, which differ from the three-fold pocket binding site previously identified. Our HDX-MS method for characterizing AAV structural dynamics opens a new way for future efforts to understand AAV structure-function relationships and engineer next-generation AAV vectors with improved gene delivery properties.
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Affiliation(s)
- Xiang Ye
- Regeneron Pharmaceuticals, Inc.TarrytownNew YorkUSA
| | - Yunli Hu
- Regeneron Pharmaceuticals, Inc.TarrytownNew YorkUSA
| | - Haibo Qiu
- Regeneron Pharmaceuticals, Inc.TarrytownNew YorkUSA
| | - Ning Li
- Regeneron Pharmaceuticals, Inc.TarrytownNew YorkUSA
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3
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Ikeda T, Yamaguchi Y, Oyama H, Matsushita A, Tsunaka Y, Fukuhara M, Torisu T, Uchiyama S. Higher-Order Structure of Adeno-Associated Virus Serotype 8 by Hydrogen/Deuterium Exchange Mass Spectrometry. Viruses 2024; 16:585. [PMID: 38675928 PMCID: PMC11053801 DOI: 10.3390/v16040585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/29/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
The higher-order structure (HOS) is a critical quality attribute of recombinant adeno-associated viruses (rAAVs). Evaluating the HOS of the entire rAAV capsid is challenging because of the flexibility and/or less folded nature of the VP1 unique (VP1u) and VP1/VP2 common regions, which are structural features essential for these regions to exert their functions following viral infection. In this study, hydrogen/deuterium exchange mass spectrometry (HDX-MS) was used for the structural analysis of full and empty rAAV8 capsids. We obtained 486 peptides representing 85% sequence coverage. Surprisingly, the VP1u region showed rapid deuterium uptake even though this region contains the phospholipase A2 domain composed primarily of α-helices. The comparison of deuterium uptake between full and empty capsids showed significant protection from hydrogen/deuterium exchange in the full capsid at the channel structure of the 5-fold symmetry axis. This corresponds to cryo-electron microscopy studies in which the extended densities were observed only in the full capsid. In addition, deuterium uptake was reduced in the VP1u region of the full capsid, suggesting the folding and/or interaction of this region with the encapsidated genome. This study demonstrated HDX-MS as a powerful method for probing the structure of the entire rAAV capsid.
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Affiliation(s)
- Tomohiko Ikeda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (T.I.); (Y.Y.); (H.O.); (A.M.); (Y.T.); (M.F.); (T.T.)
| | - Yuki Yamaguchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (T.I.); (Y.Y.); (H.O.); (A.M.); (Y.T.); (M.F.); (T.T.)
| | - Hiroaki Oyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (T.I.); (Y.Y.); (H.O.); (A.M.); (Y.T.); (M.F.); (T.T.)
| | - Aoba Matsushita
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (T.I.); (Y.Y.); (H.O.); (A.M.); (Y.T.); (M.F.); (T.T.)
| | - Yasuo Tsunaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (T.I.); (Y.Y.); (H.O.); (A.M.); (Y.T.); (M.F.); (T.T.)
| | - Mitsuko Fukuhara
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (T.I.); (Y.Y.); (H.O.); (A.M.); (Y.T.); (M.F.); (T.T.)
| | - Tetsuo Torisu
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (T.I.); (Y.Y.); (H.O.); (A.M.); (Y.T.); (M.F.); (T.T.)
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (T.I.); (Y.Y.); (H.O.); (A.M.); (Y.T.); (M.F.); (T.T.)
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
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4
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Kant R, Mishra N, Gross ML. Antibody Binding Captures High Energy State of an Antigen: The Case of Nsp1 SARS-CoV-2 as Revealed by Hydrogen-Deuterium Exchange Mass Spectrometry. Int J Mol Sci 2023; 24:17342. [PMID: 38139170 PMCID: PMC10743928 DOI: 10.3390/ijms242417342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
We describe an investigation using structural mass spectrometry (MS) of the impact of two antibodies, 15497 and 15498, binding the highly flexible SARS-CoV-2 Nsp1 protein. We determined the epitopes and paratopes involved in the antibody-protein interactions by using hydrogen-deuterium exchange MS (HDX-MS). Notably, the Fab (Fragment antigen binding) for antibody 15498 captured a high energy form of the antigen exhibiting significant conformational changes that added flexibility over most of the Nsp1 protein. The Fab for antibody 15497, however, showed usual antigen binding behavior, revealing local changes presumably including the binding site. These findings illustrate an unusual antibody effect on an antigen and are consistent with the dynamic nature of the Nsp1 protein. Our studies suggest that this interaction capitalizes on the high flexibility of Nsp1 to undergo conformational change and be trapped in a higher energy state by binding with a specific antibody.
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Affiliation(s)
- Ravi Kant
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA;
| | - Nawneet Mishra
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA;
| | - Michael L. Gross
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA;
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5
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Luque D, Ortega-Esteban A, Valbuena A, Luis Vilas J, Rodríguez-Huete A, Mateu MG, Castón JR. Equilibrium Dynamics of a Biomolecular Complex Analyzed at Single-amino Acid Resolution by Cryo-electron Microscopy. J Mol Biol 2023; 435:168024. [PMID: 36828271 DOI: 10.1016/j.jmb.2023.168024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
The biological function of macromolecular complexes depends not only on large-scale transitions between conformations, but also on small-scale conformational fluctuations at equilibrium. Information on the equilibrium dynamics of biomolecular complexes could, in principle, be obtained from local resolution (LR) data in cryo-electron microscopy (cryo-EM) maps. However, this possibility had not been validated by comparing, for a same biomolecular complex, LR data with quantitative information on equilibrium dynamics obtained by an established solution technique. In this study we determined the cryo-EM structure of the minute virus of mice (MVM) capsid as a model biomolecular complex. The LR values obtained correlated with crystallographic B factors and with hydrogen/deuterium exchange (HDX) rates obtained by mass spectrometry (HDX-MS), a gold standard for determining equilibrium dynamics in solution. This result validated a LR-based cryo-EM approach to investigate, with high spatial resolution, the equilibrium dynamics of biomolecular complexes. As an application of this approach, we determined the cryo-EM structure of two mutant MVM capsids and compared their equilibrium dynamics with that of the wild-type MVM capsid. The results supported a previously suggested linkage between mechanical stiffening and impaired equilibrium dynamics of a virus particle. Cryo-EM is emerging as a powerful approach for simultaneously acquiring information on the atomic structure and local equilibrium dynamics of biomolecular complexes.
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Affiliation(s)
- Daniel Luque
- Spanish National Microbiology Centre, Institute of Health Carlos III, Madrid, Spain
| | - Alvaro Ortega-Esteban
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Jose Luis Vilas
- Biocomputing Unit, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
| | - José R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain.
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6
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Strobl K, Mateu MG, de Pablo PJ. Exploring nucleic acid condensation and release from individual parvovirus particles with different physicochemical cues. Virology 2023; 581:1-7. [PMID: 36842268 DOI: 10.1016/j.virol.2023.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/12/2023] [Indexed: 02/16/2023]
Abstract
In the infection cycle, viruses release their genome in the host cell during uncoating. Here we use a variety of physicochemical procedures to induce and monitor the in vitro uncoating of ssDNA from individual Minute Virus of Mice (MVM) particles. Our experiments revealed two pathways of genome release: i) filamentous ssDNA appearing around intact virus particles when using gradual mechanical fatigue and heating at moderate temperature (50 °C). ii) thick structures of condensed ssDNA appearing when the virus particle is disrupted by mechanical nanoindentations, denaturing agent guanidinium chloride and high temperature (70 °C). We propose that in the case of filamentous ssDNA, when the capsid integrity is conserved, the genome is externalized through one channel of the capsid pores. However, the disruption of virus particles revealed a native structure of condensed genome. The mechanical analysis of intact particles after DNA strands ejection confirm the stabilization role of ssDNA in MVM.
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Affiliation(s)
- K Strobl
- Department of Condensed Matter Physics Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - M G Mateu
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Pedro J de Pablo
- Department of Condensed Matter Physics Universidad Autónoma de Madrid, 28049, Madrid, Spain; Instituto de Física de la Materia Condensada (IFIMAC) Universidad Autónoma de Madrid, 28049, Madrid, Spain.
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7
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Pathak AK, Bandyopadhyay T. Heat-induced transitions of an empty minute virus of mice capsid in explicit water: all-atom MD simulation. J Biomol Struct Dyn 2022; 40:11900-11913. [PMID: 34459706 DOI: 10.1080/07391102.2021.1969283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The capsid-like structure of the virus-based protein nanoparticles (NPs) can serve as bionanomaterials, with applications in biomedicines and nanotechnology. Release of packaged material from these nanocontainers is associated with subtle conformational changes of the NP structure, which in vitro, is readily accomplished by heating. Characterizing the structural changes as a function of temperature may provide fresh insights into nanomaterial/antiviral strategies. Here, we have calculated heat induced changes in the properties of an empty minute virus of mice particle using large-scale ≈ 3.0 × 106 all-atom molecular dynamics simulations. We focus on two heat induced structural changes of the NP, namely, dynamical transition (DT) and breathing transition (BT), both characterized by sudden and sharp change of measured parameters at temperatures, TDT and TBT, respectively. While DT is assessed by mean-square fluctuation of hydrogen atoms of the NP, BT is monitored through internal volume and permeation rate of water molecules through the NP. Both the transitions, resulting primarily from collective atomistic motion, are found to occur at temperatures widely separated from one another (TBT>TDT). The breathing motions, responsible for the translocation events of the packaged materials through the NP to kick off, are further probed by computing atomic resolution stresses from NVE simulations. Distribution of equilibrium atomistic stresses on the NP reveals a largely asymmetric nature and suggests structural breathing may actually represent large dynamic changes in the hotspot regions, far from the NP pores, which is in remarkable resemblance with recently conducted hydrogen-deuterium exchange coupled to mass spectrometry experiment. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arup Kumar Pathak
- Theoretical Chemistry Section, Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section, Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
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8
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Sae-Ueng U, Bhunchoth A, Phironrit N, Treetong A, Sapcharoenkun C, Chatchawankanphanich O, Leartsakulpanich U, Chitnumsub P. Thermoresponsive C22 phage stiffness modulates the phage infectivity. Sci Rep 2022; 12:13001. [PMID: 35906255 PMCID: PMC9338302 DOI: 10.1038/s41598-022-16795-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/15/2022] [Indexed: 12/01/2022] Open
Abstract
Bacteriophages offer a sustainable alternative for controlling crop disease. However, the lack of knowledge on phage infection mechanisms makes phage-based biological control varying and ineffective. In this work, we interrogated the temperature dependence of the infection and thermo-responsive behavior of the C22 phage. This soilborne podovirus is capable of lysing Ralstonia solanacearum, causing bacterial wilt disease. We revealed that the C22 phage could better infect the pathogenic host cell when incubated at low temperatures (25, 30 °C) than at high temperatures (35, 40 °C). Measurement of the C22 phage stiffness revealed that the phage stiffness at low temperatures was 2–3 times larger than at high temperatures. In addition, the imaging results showed that more C22 phage particles were attached to the cell surface at low temperatures than at high temperatures, associating the phage stiffness and the phage attachment. The result suggests that the structure and stiffness modulation in response to temperature change improve infection, providing mechanistic insight into the C22 phage lytic cycle. Our study signifies the need to understand phage responses to the fluctuating environment for effective phage-based biocontrol implementation.
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Affiliation(s)
- Udom Sae-Ueng
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Anjana Bhunchoth
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Namthip Phironrit
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Alongkot Treetong
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Chaweewan Sapcharoenkun
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Orawan Chatchawankanphanich
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
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9
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Thompson EJ, Paul A, Iavarone AT, Klinman JP. Identification of Thermal Conduits That Link the Protein-Water Interface to the Active Site Loop and Catalytic Base in Enolase. J Am Chem Soc 2021; 143:785-797. [PMID: 33395523 DOI: 10.1021/jacs.0c09423] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We report here on the salient role of protein mobility in accessing conformational landscapes that enable efficient enzyme catalysis. We are focused on yeast enolase, a highly conserved lyase with a TIM barrel domain and catalytic loop, as part of a larger study of the relationship of site selective protein motions to chemical reactivity within superfamilies. Enthalpically hindered variants were developed by replacement of a conserved hydrophobic side chain (Leu 343) with smaller side chains. Leu343 is proximal to the active site base in enolase, and comparative pH rate profiles for the valine and alanine variants indicate a role for side chain hydrophobicity in tuning the pKa of the catalytic base. However, the magnitude of a substrate deuterium isotope effect is almost identical for wild-type (WT) and Leu343Ala, supporting an unchanged rate-determining proton abstraction step. The introduced hydrophobic side chains at position 343 lead to a discontinuous break in both activity and activation energy as a function of side chain volume. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments were performed as a function of time and temperature for WT and Leu343Ala, and provide a spatially resolved map of changes in protein flexibility following mutation. Impacts on protein flexibility are localized to specific networks that arise at the protein-solvent interface and terminate in a loop that has been shown by X-ray crystallography to close over the active site. These interrelated effects are discussed in the context of long-range, solvent-accessible and thermally activated networks that play key roles in tuning the precise distances and interactions among reactants.
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Affiliation(s)
- Emily J Thompson
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Adhayana Paul
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Anthony T Iavarone
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
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10
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Affiliation(s)
- Tobias
P. Wörner
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Tatiana M. Shamorkina
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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11
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Bruinsma RF, Wuite GJL, Roos WH. Physics of viral dynamics. NATURE REVIEWS. PHYSICS 2021; 3:76-91. [PMID: 33728406 PMCID: PMC7802615 DOI: 10.1038/s42254-020-00267-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 05/12/2023]
Abstract
Viral capsids are often regarded as inert structural units, but in actuality they display fascinating dynamics during different stages of their life cycle. With the advent of single-particle approaches and high-resolution techniques, it is now possible to scrutinize viral dynamics during and after their assembly and during the subsequent development pathway into infectious viruses. In this Review, the focus is on the dynamical properties of viruses, the different physical virology techniques that are being used to study them, and the physical concepts that have been developed to describe viral dynamics.
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Affiliation(s)
- Robijn F. Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California, USA
| | - Gijs J. L. Wuite
- Fysica van levende systemen, Vrije Universiteit, Amsterdam, the Netherlands
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
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12
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Lesne J, Locard-Paulet M, Parra J, Zivković D, Menneteau T, Bousquet MP, Burlet-Schiltz O, Marcoux J. Conformational maps of human 20S proteasomes reveal PA28- and immuno-dependent inter-ring crosstalks. Nat Commun 2020; 11:6140. [PMID: 33262340 PMCID: PMC7708635 DOI: 10.1038/s41467-020-19934-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 11/06/2020] [Indexed: 01/17/2023] Open
Abstract
Hydrogen-Deuterium eXchange coupled to Mass Spectrometry (HDX-MS) is now common practice in structural biology. However, it is most of the time applied to rather small oligomeric complexes. Here, we report on the use of HDX-MS to investigate conformational differences between the human standard 20S (std20S) and immuno 20S (i20s) proteasomes alone or in complex with PA28αβ or PA28γ activators. Their solvent accessibility is analyzed through a dedicated bioinformatic pipeline including stringent statistical analysis and 3D visualization. These data confirm the existence of allosteric differences between the std20S and i20S at the surface of the α-ring triggered from inside the catalytic β-ring. Additionally, binding of the PA28 regulators to the 20S proteasomes modify solvent accessibility due to conformational changes of the β-rings. This work is not only a proof-of-concept that HDX-MS can be used to get structural insights on large multi-protein complexes in solution, it also demonstrates that the binding of the std20S or i20S subtype to any of its PA28 activator triggers allosteric changes that are specific to this 20S/PA28 pair.
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Affiliation(s)
- Jean Lesne
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
- Centre de Biologie Structurale, CNRS, Université de Montpellier, INSERM, 34090, Montpellier, France
| | - Marie Locard-Paulet
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Julien Parra
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Dušan Zivković
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Thomas Menneteau
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Marie-Pierre Bousquet
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.
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13
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Tajoddin NN, Konermann L. Analysis of Temperature-Dependent H/D Exchange Mass Spectrometry Experiments. Anal Chem 2020; 92:10058-10067. [DOI: 10.1021/acs.analchem.0c01828] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nastaran N. Tajoddin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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14
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Schrad JR, Abrahão JS, Cortines JR, Parent KN. Structural and Proteomic Characterization of the Initiation of Giant Virus Infection. Cell 2020; 181:1046-1061.e6. [PMID: 32392465 DOI: 10.1016/j.cell.2020.04.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/07/2020] [Accepted: 04/17/2020] [Indexed: 12/26/2022]
Abstract
Since their discovery, giant viruses have expanded our understanding of the principles of virology. Due to their gargantuan size and complexity, little is known about the life cycles of these viruses. To answer outstanding questions regarding giant virus infection mechanisms, we set out to determine biomolecular conditions that promote giant virus genome release. We generated four infection intermediates in Samba virus (Mimivirus genus, lineage A) as visualized by cryoelectron microscopy (cryo-EM), cryoelectron tomography (cryo-ET), and scanning electron microscopy (SEM). Each of these four intermediates reflects similar morphology to a stage that occurs in vivo. We show that these genome release stages are conserved in other mimiviruses. Finally, we identified proteins that are released from Samba and newly discovered Tupanvirus through differential mass spectrometry. Our work revealed the molecular forces that trigger infection are conserved among disparate giant viruses. This study is also the first to identify specific proteins released during the initial stages of giant virus infection.
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Affiliation(s)
- Jason R Schrad
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jônatas S Abrahão
- Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Juliana R Cortines
- Department of Virology, Institute of Microbiology Paulo de Goes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil.
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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15
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Bradshaw RT, Marinelli F, Faraldo-Gómez JD, Forrest LR. Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles. Biophys J 2020; 118:1649-1664. [PMID: 32105651 PMCID: PMC7136279 DOI: 10.1016/j.bpj.2020.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/28/2020] [Accepted: 02/05/2020] [Indexed: 01/12/2023] Open
Abstract
Hydrogen-deuterium exchange combined with mass spectrometry (HDX-MS) is a widely applied biophysical technique that probes the structure and dynamics of biomolecules without the need for site-directed modifications or bio-orthogonal labels. The mechanistic interpretation of HDX data, however, is often qualitative and subjective, owing to a lack of quantitative methods to rigorously translate observed deuteration levels into atomistic structural information. To help address this problem, we have developed a methodology to generate structural ensembles that faithfully reproduce HDX-MS measurements. In this approach, an ensemble of protein conformations is first generated, typically using molecular dynamics simulations. A maximum-entropy bias is then applied post hoc to the resulting ensemble such that averaged peptide-deuteration levels, as predicted by an empirical model, agree with target values within a given level of uncertainty. We evaluate this approach, referred to as HDX ensemble reweighting (HDXer), for artificial target data reflecting the two major conformational states of a binding protein. We demonstrate that the information provided by HDX-MS experiments and by the model of exchange are sufficient to recover correctly weighted structural ensembles from simulations, even when the relevant conformations are rarely observed. Degrading the information content of the target data—e.g., by reducing sequence coverage, by averaging exchange levels over longer peptide segments, or by incorporating different sources of uncertainty—reduces the structural accuracy of the reweighted ensemble but still allows for useful insights into the distinctive structural features reflected by the target data. Finally, we describe a quantitative metric to rank candidate structural ensembles according to their correspondence with target data and illustrate the use of HDXer to describe changes in the conformational ensemble of the membrane protein LeuT. In summary, HDXer is designed to facilitate objective structural interpretations of HDX-MS data and to inform experimental approaches and further developments of theoretical exchange models.
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Affiliation(s)
- Richard T Bradshaw
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Fabrizio Marinelli
- Theoretical Molecular Biophysics Unit, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Unit, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland.
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16
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Zheng SJ, Zheng J, Xiong CF, Xiao HM, Liu SJ, Feng YQ. Hydrogen–Deuterium Scrambling Based on Chemical Isotope Labeling Coupled with LC–MS: Application to Amine Metabolite Identification in Untargeted Metabolomics. Anal Chem 2020; 92:2043-2051. [DOI: 10.1021/acs.analchem.9b04512] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Shu-Jian Zheng
- Frontier Science Center for Immunology and Metabolism, Department of Chemistry, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Jie Zheng
- Frontier Science Center for Immunology and Metabolism, Department of Chemistry, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Cai-Feng Xiong
- Frontier Science Center for Immunology and Metabolism, Department of Chemistry, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Hua-Ming Xiao
- Frontier Science Center for Immunology and Metabolism, Department of Chemistry, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Shi-Jie Liu
- Frontier Science Center for Immunology and Metabolism, Department of Chemistry, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Yu-Qi Feng
- Frontier Science Center for Immunology and Metabolism, Department of Chemistry, Wuhan University, Wuhan 430072, People’s Republic of China
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17
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Dülfer J, Kadek A, Kopicki JD, Krichel B, Uetrecht C. Structural mass spectrometry goes viral. Adv Virus Res 2019; 105:189-238. [PMID: 31522705 DOI: 10.1016/bs.aivir.2019.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Over the last 20 years, mass spectrometry (MS), with its ability to analyze small sample amounts with high speed and sensitivity, has more and more entered the field of structural virology, aiming to investigate the structure and dynamics of viral proteins as close to their native environment as possible. The use of non-perturbing labels in hydrogen-deuterium exchange MS allows for the analysis of interactions between viral proteins and host cell factors as well as their dynamic responses to the environment. Cross-linking MS, on the other hand, can analyze interactions in viral protein complexes and identify virus-host interactions in cells. Native MS allows transferring viral proteins, complexes and capsids into the gas phase and has broken boundaries to overcome size limitations, so that now even the analysis of intact virions is possible. Different MS approaches not only inform about size, stability, interactions and dynamics of virus assemblies, but also bridge the gap to other biophysical techniques, providing valuable constraints for integrative structural modeling of viral complex assemblies that are often inaccessible by single technique approaches. In this review, recent advances are highlighted, clearly showing that structural MS approaches in virology are moving towards systems biology and ever more experiments are performed on cellular level.
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Affiliation(s)
- Jasmin Dülfer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Alan Kadek
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany.
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18
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Masson GR, Burke JE, Ahn NG, Anand GS, Borchers C, Brier S, Bou-Assaf GM, Engen JR, Englander SW, Faber J, Garlish R, Griffin PR, Gross ML, Guttman M, Hamuro Y, Heck AJR, Houde D, Iacob RE, Jørgensen TJD, Kaltashov IA, Klinman JP, Konermann L, Man P, Mayne L, Pascal BD, Reichmann D, Skehel M, Snijder J, Strutzenberg TS, Underbakke ES, Wagner C, Wales TE, Walters BT, Weis DD, Wilson DJ, Wintrode PL, Zhang Z, Zheng J, Schriemer DC, Rand KD. Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat Methods 2019; 16:595-602. [PMID: 31249422 PMCID: PMC6614034 DOI: 10.1038/s41592-019-0459-y] [Citation(s) in RCA: 395] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/23/2019] [Indexed: 12/20/2022]
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful biophysical technique being increasingly applied to a wide variety of problems. As the HDX-MS community continues to grow, adoption of best practices in data collection, analysis, presentation and interpretation will greatly enhance the accessibility of this technique to nonspecialists. Here we provide recommendations arising from community discussions emerging out of the first International Conference on Hydrogen-Exchange Mass Spectrometry (IC-HDX; 2017). It is meant to represent both a consensus viewpoint and an opportunity to stimulate further additions and refinements as the field advances.
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Affiliation(s)
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
| | - Natalie G Ahn
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Ganesh S Anand
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - Christoph Borchers
- Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Sébastien Brier
- Institut Pasteur, Chemistry and Structural Biology Department, Paris, France
| | | | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - S Walter Englander
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Patrick R Griffin
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Yoshitomo Hamuro
- Johnson & Johnson Pharmaeutical Research and Development, Jersey City, NJ, USA
| | - Albert J R Heck
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | | | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej, Odense, Denmark
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, Canada
| | - Petr Man
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Leland Mayne
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Dana Reichmann
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Joost Snijder
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Timothy S Strutzenberg
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - Eric S Underbakke
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | | | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Benjamin T Walters
- Department of Early Stage Pharmaceutical Development, Genentech, Inc., South San Francisco, CA, USA
| | - David D Weis
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, ON, Canada
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | | | - Jie Zheng
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB, Canada.
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
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19
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Kondylis P, Schlicksup CJ, Zlotnick A, Jacobson SC. Analytical Techniques to Characterize the Structure, Properties, and Assembly of Virus Capsids. Anal Chem 2019; 91:622-636. [PMID: 30383361 PMCID: PMC6472978 DOI: 10.1021/acs.analchem.8b04824] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Panagiotis Kondylis
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Christopher J. Schlicksup
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Stephen C. Jacobson
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
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20
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Systematic analysis of biological roles of charged amino acid residues located throughout the structured inner wall of a virus capsid. Sci Rep 2018; 8:9543. [PMID: 29934575 PMCID: PMC6015035 DOI: 10.1038/s41598-018-27749-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 06/01/2018] [Indexed: 12/31/2022] Open
Abstract
Structure-based mutational analysis of viruses is providing many insights into the relationship between structure and biological function of macromolecular complexes. We have systematically investigated the individual biological roles of charged residues located throughout the structured capsid inner wall (outside disordered peptide segments) of a model spherical virus, the minute virus of mice (MVM). The functional effects of point mutations that altered the electrical charge at 16 different positions at the capsid inner wall were analyzed. The results revealed that MVM capsid self-assembly is rather tolerant to point mutations that alter the number and distribution of charged residues at the capsid inner wall. However, mutations that either increased or decreased the number of positive charges around capsid-bound DNA segments reduced the thermal resistance of the virion. Moreover, mutations that either removed or changed the positions of negatively charged carboxylates in rings of acidic residues around capsid pores were deleterious by precluding a capsid conformational transition associated to through-pore translocation events. The results suggest that number, distribution and specific position of electrically charged residues across the inner wall of a spherical virus may have been selected through evolution as a compromise between several different biological requirements.
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21
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Changes in the stability and biomechanics of P22 bacteriophage capsid during maturation. Biochim Biophys Acta Gen Subj 2018; 1862:1492-1504. [PMID: 29550430 DOI: 10.1016/j.bbagen.2018.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 02/11/2018] [Accepted: 03/04/2018] [Indexed: 12/21/2022]
Abstract
The capsid of P22 bacteriophage undergoes a series of structural transitions during maturation that guide it from spherical to icosahedral morphology. The transitions include the release of scaffold proteins and capsid expansion. Although P22 maturation has been investigated for decades, a unified model that incorporates thermodynamic and biophysical analyses is not available. A general and specific model of icosahedral capsid maturation is of significant interest to theoreticians searching for fundamental principles as well as virologists and material scientists seeking to alter maturation to their advantage. To address this challenge, we have combined the results from orthogonal biophysical techniques including differential scanning fluorimetry, atomic force microscopy, circular dichroism, and hydrogen-deuterium exchange mass spectrometry. By integrating these results from single particle and population measurements, an energy landscape of P22 maturation from procapsid through expanded shell to wiffle ball emerged, highlighting the role of metastable structures and the thermodynamics guiding maturation. The propagation of weak quaternary interactions across symmetric elements of the capsid is a key component for stability in P22. A surprising finding is that the progression to wiffle ball, which lacks pentamers, shows that chemical and thermal stability can be uncoupled from mechanical rigidity, elegantly demonstrating the complexity inherent in capsid protein interactions and the emergent properties that can arise from icosahedral symmetry. On a broader scale, this work demonstrates the power of applying orthogonal biophysical techniques to elucidate assembly mechanisms for supramolecular complexes and provides a framework within which other viral systems can be compared.
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22
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Valbuena A, Rodríguez-Huete A, Mateu MG. Mechanical stiffening of human rhinovirus by cavity-filling antiviral drugs. NANOSCALE 2018; 10:1440-1452. [PMID: 29302674 DOI: 10.1039/c7nr08704g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Emerging studies at the nanoscale on the relationships between the structure, mechanical properties and infectivity of virus particles are revealing important physics-based foundations of virus biology that may have biomedical and nanotechnological applications. Human rhinovirus (HRV) is the major causative agent of common colds leading to important economic losses, and is also associated with more severe diseases. There is renewed interest in developing effective anti-HRV drugs, but none have been approved so far. We have chosen HRV to explore a possible link between virus mechanics and infectivity and the antiviral effect of certain drugs. In particular, we have investigated a suggestion that the antiviral action of drugs that bind to capsid cavities (pockets) may be related to changes in virus stiffness. Mechanical analysis using atomic force microscopy shows that filling the pockets with drugs or genetically introducing bulkier amino acid side chains into the pockets stiffen HRV virions to different extents. Drug-mediated stiffening affected some regions distant from the pockets and involved in genome uncoating, and may be caused by a subtle structural rearrangement of the virus particle. The results also revealed for HRV a quantitative, logarithmic relationship between mechanical stiffening, achieved either by drug binding or introducing bulkier amino acid side chains into the pockets, and reduced infectivity. From a fundamental physics perspective, these drugs may exert their biological effect by decreasing the deformability of the virion, thus impairing its equilibrium dynamics. The results encourage the design of novel antiviral drugs that inhibit infection by mechanically stiffening the viral particles.
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Affiliation(s)
- Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid 28049, Spain.
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23
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Guerra P, Valbuena A, Querol-Audí J, Silva C, Castellanos M, Rodríguez-Huete A, Garriga D, Mateu MG, Verdaguer N. Structural basis for biologically relevant mechanical stiffening of a virus capsid by cavity-creating or spacefilling mutations. Sci Rep 2017; 7:4101. [PMID: 28642465 PMCID: PMC5481337 DOI: 10.1038/s41598-017-04345-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 05/12/2017] [Indexed: 11/26/2022] Open
Abstract
Recent studies reveal that the mechanical properties of virus particles may have been shaped by evolution to facilitate virus survival. Manipulation of the mechanical behavior of virus capsids is leading to a better understanding of viral infection, and to the development of virus-based nanoparticles with improved mechanical properties for nanotechnological applications. In the minute virus of mice (MVM), deleterious mutations around capsid pores involved in infection-related translocation events invariably increased local mechanical stiffness and interfered with pore-associated dynamics. To provide atomic-resolution insights into biologically relevant changes in virus capsid mechanics, we have determined by X-ray crystallography the structural effects of deleterious, mechanically stiffening mutations around the capsid pores. Data show that the cavity-creating N170A mutation at the pore wall does not induce any dramatic structural change around the pores, but instead generates subtle rearrangements that propagate throughout the capsid, resulting in a more compact, less flexible structure. Analysis of the spacefilling L172W mutation revealed the same relationship between increased stiffness and compacted capsid structure. Implications for understanding connections between virus mechanics, structure, dynamics and infectivity, and for engineering modified virus-based nanoparticles, are discussed.
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Affiliation(s)
- Pablo Guerra
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Jordi Querol-Audí
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain
| | - Cristina Silva
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain
| | - Milagros Castellanos
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Damià Garriga
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain.
| | - Nuria Verdaguer
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain.
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