1
|
Wei WS, Trubiano A, Sigl C, Paquay S, Dietz H, Hagan MF, Fraden S. Hierarchical assembly is more robust than egalitarian assembly in synthetic capsids. Proc Natl Acad Sci U S A 2024; 121:e2312775121. [PMID: 38324570 PMCID: PMC10873614 DOI: 10.1073/pnas.2312775121] [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: 07/25/2023] [Accepted: 12/07/2023] [Indexed: 02/09/2024] Open
Abstract
Self-assembly of complex and functional materials remains a grand challenge in soft material science. Efficient assembly depends on a delicate balance between thermodynamic and kinetic effects, requiring fine-tuning affinities and concentrations of subunits. By contrast, we introduce an assembly paradigm that allows large error-tolerance in the subunit affinity and helps avoid kinetic traps. Our combined experimental and computational approach uses a model system of triangular subunits programmed to assemble into T = 3 icosahedral capsids comprising 60 units. The experimental platform uses DNA origami to create monodisperse colloids whose three-dimensional geometry is controlled to nanometer precision, with two distinct bonds whose affinities are controlled to kBT precision, quantified in situ by static light scattering. The computational model uses a coarse-grained representation of subunits, short-ranged potentials, and Langevin dynamics. Experimental observations and modeling reveal that when the bond affinities are unequal, two distinct hierarchical assembly pathways occur, in which the subunits first form dimers in one case and pentamers in another. These hierarchical pathways produce complete capsids faster and are more robust against affinity variation than egalitarian pathways, in which all binding sites have equal strengths. This finding suggests that hierarchical assembly may be a general engineering principle for optimizing self-assembly of complex target structures.
Collapse
Affiliation(s)
- Wei-Shao Wei
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Anthony Trubiano
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Christian Sigl
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Garching85748, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Garching85748, Germany
| | - Stefan Paquay
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Hendrik Dietz
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Garching85748, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Garching85748, Germany
| | - Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Seth Fraden
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| |
Collapse
|
2
|
Valbuena A, Strobl K, Gil-Redondo JC, Valiente L, de Pablo PJ, Mateu MG. Single-Molecule Analysis of Genome Uncoating from Individual Human Rhinovirus Particles, and Modulation by Antiviral Drugs. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2304722. [PMID: 37806749 DOI: 10.1002/smll.202304722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/26/2023] [Indexed: 10/10/2023]
Abstract
Infection of humans by many viruses is typically initiated by the internalization of a single virion in each of a few susceptible cells. Thus, the outcome of the infection process may depend on stochastic single-molecule events. A crucial process for viral infection, and thus a target for developing antiviral drugs, is the uncoating of the viral genome. Here a force spectroscopy procedure using an atomic force microscope is implemented to study uncoating for individual human rhinovirus particles. Application of an increasing mechanical force on a virion led to a high force-induced structural transition that facilitated extrusion of the viral RNA molecule without loss of capsid integrity. Application of force to virions that h ad previously extruded the RNA, or to RNA-free capsids, led to a lower force-induced event associated with capsid disruption. The kinetic parameters are determined for each reaction. The high-force event is a stochastic process governed by a moderate free energy barrier (≈20 kcal mol-1 ), which results in a heterogeneous population of structurally weakened virions in which different fractions of the RNA molecule are externalized. The effects of antiviral compounds or capsid mutation on the kinetics of this reaction reveal a correlation between the reaction rate and virus infectivity.
Collapse
Affiliation(s)
- Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Klara Strobl
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Juan Carlos Gil-Redondo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Luis Valiente
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Pedro J de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Instituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| |
Collapse
|
3
|
Martín-Bravo M, Gomez Llorente JM, Hernández-Rojas J. Virtual indentation of the empty capsid of the minute virus of mice using a minimal coarse-grained model. Phys Rev E 2024; 109:024402. [PMID: 38491620 DOI: 10.1103/physreve.109.024402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/02/2024] [Indexed: 03/18/2024]
Abstract
A minimal coarse-grained model for T=1 viral capsids assembled from 20 protein rigid trimers has been designed by extending a previously proposed form of the interaction energy written as a sum of anisotropic pairwise interactions between the trimeric capsomers. The extension of the model has been performed to properly account for the coupling between two internal coordinates: the one that measures the intercapsomer distance and the other that gives the intercapsomer dihedral angle. The model has been able to fit with less than a 10% error the atomic force microscopy (AFM) indentation experimental data for the empty capsid of the minute virus of mice (MVM), providing in this way an admissible picture of the main mechanisms behind the capsid deformations. In this scenario, the bending of the intercapsomer dihedral angle is the angular internal coordinate that can support larger deformations away from its equilibrium values, determining important features of the AFM indentation experiments as the elastic constants along the three symmetry axes of the capsid and the critical indentations. From the value of one of the parameters of our model, we conclude that trimers in the MVM must be quite oblate tops, in excellent agreement with their known structure. The transition from the linear to the nonlinear regimes sampled in the indentation process appears to be an interesting topic for future research in physical virology.
Collapse
Affiliation(s)
- Manuel Martín-Bravo
- Departamento de Física and IUdEA, Universidad de La Laguna, 38200 Tenerife, Spain
| | | | | |
Collapse
|
4
|
Hoffmann MD, Zdechlik AC, He Y, Nedrud D, Aslanidi G, Gordon W, Schmidt D. Multiparametric domain insertional profiling of adeno-associated virus VP1. Mol Ther Methods Clin Dev 2023; 31:101143. [PMID: 38027057 PMCID: PMC10661864 DOI: 10.1016/j.omtm.2023.101143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 10/21/2023] [Indexed: 12/01/2023]
Abstract
Several evolved properties of adeno-associated virus (AAV), such as broad tropism and immunogenicity in humans, are barriers to AAV-based gene therapy. Most efforts to re-engineer these properties have focused on variable regions near AAV's 3-fold protrusions and capsid protein termini. To comprehensively survey AAV capsids for engineerable hotspots, we determined multiple AAV fitness phenotypes upon insertion of six structured protein domains into the entire AAV-DJ capsid protein VP1. This is the largest and most comprehensive AAV domain insertion dataset to date. Our data revealed a surprising robustness of AAV capsids to accommodate large domain insertions. Insertion permissibility depended strongly on insertion position, domain type, and measured fitness phenotype, which clustered into contiguous structural units that we could link to distinct roles in AAV assembly, stability, and infectivity. We also identified engineerable hotspots of AAV that facilitate the covalent attachment of binding scaffolds, which may represent an alternative approach to re-direct AAV tropism.
Collapse
Affiliation(s)
- Mareike D. Hoffmann
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alina C. Zdechlik
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yungui He
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Nedrud
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Wendy Gordon
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel Schmidt
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|
5
|
Fuertes MA, López Mateos D, Valiente L, Rodríguez Huete A, Valbuena A, Mateu MG. Electrostatic Screening, Acidic pH and Macromolecular Crowding Increase the Self-Assembly Efficiency of the Minute Virus of Mice Capsid In Vitro. Viruses 2023; 15:v15051054. [PMID: 37243141 DOI: 10.3390/v15051054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/14/2023] [Accepted: 04/22/2023] [Indexed: 05/28/2023] Open
Abstract
The hollow protein capsids from a number of different viruses are being considered for multiple biomedical or nanotechnological applications. In order to improve the applied potential of a given viral capsid as a nanocarrier or nanocontainer, specific conditions must be found for achieving its faithful and efficient assembly in vitro. The small size, adequate physical properties and specialized biological functions of the capsids of parvoviruses such as the minute virus of mice (MVM) make them excellent choices as nanocarriers and nanocontainers. In this study we analyzed the effects of protein concentration, macromolecular crowding, temperature, pH, ionic strength, or a combination of some of those variables on the fidelity and efficiency of self-assembly of the MVM capsid in vitro. The results revealed that the in vitro reassembly of the MVM capsid is an efficient and faithful process. Under some conditions, up to ~40% of the starting virus capsids were reassembled in vitro as free, non aggregated, correctly assembled particles. These results open up the possibility of encapsidating different compounds in VP2-only capsids of MVM during its reassembly in vitro, and encourage the use of virus-like particles of MVM as nanocontainers.
Collapse
Affiliation(s)
- Miguel Angel Fuertes
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Diego López Mateos
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Luis Valiente
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Alicia Rodríguez Huete
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
6
|
Hoffmann MD, Zdechlik AC, He Y, Nedrud D, Aslanidi G, Gordon W, Schmidt D. Multiparametric domain insertional profiling of Adeno-Associated Virus VP1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537549. [PMID: 37131661 PMCID: PMC10153220 DOI: 10.1101/2023.04.19.537549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Evolved properties of Adeno-Associated Virus (AAV), such as broad tropism and immunogenicity in humans, are barriers to AAV-based gene therapy. Previous efforts to re-engineer these properties have focused on variable regions near AAV’s 3-fold protrusions and capsid protein termini. To comprehensively survey AAV capsids for engineerable hotspots, we determined multiple AAV fitness phenotypes upon insertion of large, structured protein domains into the entire AAV-DJ capsid protein VP1. This is the largest and most comprehensive AAV domain insertion dataset to date. Our data revealed a surprising robustness of AAV capsids to accommodate large domain insertions. There was strong positional, domain-type, and fitness phenotype dependence of insertion permissibility, which clustered into correlated structural units that we could link to distinct roles in AAV assembly, stability, and infectivity. We also identified new engineerable hotspots of AAV that facilitate the covalent attachment of binding scaffolds, which may represent an alternative approach to re-direct AAV tropism.
Collapse
|
7
|
Xu Z, Wei D, Zeng Q, Zhang H, Sun Y, Demongeot J. More or less deadly? A mathematical model that predicts SARS-CoV-2 evolutionary direction. Comput Biol Med 2023; 153:106510. [PMID: 36630829 PMCID: PMC9816089 DOI: 10.1016/j.compbiomed.2022.106510] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/18/2022] [Accepted: 12/31/2022] [Indexed: 01/09/2023]
Abstract
SARS-CoV-2 has caused tremendous deaths globally. It is of great value to predict the evolutionary direction of SARS-CoV-2. In this paper, we proposed a novel mathematical model that could predict the evolutionary trend of SARS-CoV-2. We focus on the mutational effects on viral assembly capacity. A robust coarse-grained mathematical model is constructed to simulate the virus dynamics in the host body. Both virulence and transmissibility can be quantified in this model. A delicate equilibrium point that optimizes the transmissibility can be numerically obtained. Based on this model, the virulence of SARS-CoV-2 might further decrease, accompanied by an enhancement of transmissibility. However, this trend is not continuous; its virulence will not disappear but remains at a relatively stable range. A virus assembly model which simulates the virus packing process is also proposed. It can be explained why a few mutations would lead to a significant divergence in clinical performance, both in the overall particle formation quantity and virulence. This research provides a novel mathematical attempt to elucidate the evolutionary driving force in RNA virus evolution.
Collapse
Affiliation(s)
- Zhaobin Xu
- Department of Life Science, Dezhou University, Dezhou, 253023, China.
| | - Dongqing Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Qiangcheng Zeng
- Department of Life Science, Dezhou University, Dezhou, 253023, China
| | - Hongmei Zhang
- Department of Life Science, Dezhou University, Dezhou, 253023, China
| | - Yinghui Sun
- Department of Life Science, Dezhou University, Dezhou, 253023, China
| | - Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, Faculty of Medicine, University Grenoble Alpes (UGA), 38700, La Tronche, France.
| |
Collapse
|
8
|
Chen NC, Wang CH, Yoshimura M, Yeh YQ, Guan HH, Chuankhayan P, Lin CC, Lin PJ, Huang YC, Wakatsuki S, Ho MC, Chen CJ. Structures of honeybee-infecting Lake Sinai virus reveal domain functions and capsid assembly with dynamic motions. Nat Commun 2023; 14:545. [PMID: 36726015 PMCID: PMC9892032 DOI: 10.1038/s41467-023-36235-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/18/2023] [Indexed: 02/03/2023] Open
Abstract
Understanding the structural diversity of honeybee-infecting viruses is critical to maintain pollinator health and manage the spread of diseases in ecology and agriculture. We determine cryo-EM structures of T = 4 and T = 3 capsids of virus-like particles (VLPs) of Lake Sinai virus (LSV) 2 and delta-N48 LSV1, belonging to tetraviruses, at resolutions of 2.3-2.6 Å in various pH environments. Structural analysis shows that the LSV2 capsid protein (CP) structural features, particularly the protruding domain and C-arm, differ from those of other tetraviruses. The anchor loop on the central β-barrel domain interacts with the neighboring subunit to stabilize homo-trimeric capsomeres during assembly. Delta-N48 LSV1 CP interacts with ssRNA via the rigid helix α1', α1'-α1 loop, β-barrel domain, and C-arm. Cryo-EM reconstructions, combined with X-ray crystallographic and small-angle scattering analyses, indicate that pH affects capsid conformations by regulating reversible dynamic particle motions and sizes of LSV2 VLPs. C-arms exist in all LSV2 and delta-N48 LSV1 VLPs across varied pH conditions, indicating that autoproteolysis cleavage is not required for LSV maturation. The observed linear domino-scaffold structures of various lengths, made up of trapezoid-shape capsomeres, provide a basis for icosahedral T = 4 and T = 3 architecture assemblies. These findings advance understanding of honeybee-infecting viruses that can cause Colony Collapse Disorder.
Collapse
Affiliation(s)
- Nai-Chi Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan, ROC
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan, ROC
| | - Masato Yoshimura
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan, ROC
| | - Yi-Qi Yeh
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan, ROC
| | - Hong-Hsiang Guan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan, ROC
| | - Phimonphan Chuankhayan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan, ROC
| | - Chien-Chih Lin
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan, ROC
| | - Pei-Ju Lin
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan, ROC.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30043, Taiwan, ROC
| | - Yen-Chieh Huang
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan, ROC
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University, Stanford, CA, 94305, USA.,SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Structural Molecular Biology, Menlo Park, CA, 94025, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan, ROC.
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan, ROC. .,Department of Physics, National Tsing Hua University, Hsinchu, 30043, Taiwan, ROC. .,Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, ROC. .,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC.
| |
Collapse
|
9
|
Mizrahi I, Bruinsma R, Rudnick J. Spanning tree model and the assembly kinetics of RNA viruses. Phys Rev E 2022; 106:044405. [PMID: 36397584 DOI: 10.1103/physreve.106.044405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 05/17/2022] [Indexed: 06/16/2023]
Abstract
Single-stranded RNA (ssRNA) viruses self-assemble spontaneously in solutions that contain the viral RNA genome molecules and viral capsid proteins. The self-assembly of empty capsids can be understood on the basis of free energy minimization. However, during the self-assembly of complete viral particles in the cytoplasm of an infected cell, the viral genome molecules must be selected from a large pool of very similar host messenger RNA molecules and it is not known whether this also can be understood by free energy minimization. We address this question using a simple mathematical model, the spanning tree model, that was recently proposed for the assembly of small ssRNA viruses. We present a statistical physics analysis of the properties of this model. RNA selection takes place via a kinetic mechanism that operates during the formation of the nucleation complex and that is related to Hopfield kinetic proofreading.
Collapse
Affiliation(s)
- Inbal Mizrahi
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
| | - Robijn Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Joseph Rudnick
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
| |
Collapse
|
10
|
Hennecker CD, Lachance-Brais C, Sleiman H, Mittermaier A. Using transient equilibria (TREQ) to measure the thermodynamics of slowly assembling supramolecular systems. SCIENCE ADVANCES 2022; 8:eabm8455. [PMID: 35385301 PMCID: PMC8985918 DOI: 10.1126/sciadv.abm8455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Supramolecular chemistry involves the noncovalent assembly of monomers into materials with unique properties and wide-ranging applications. Thermal analysis is a key analytical tool in this field, as it provides quantitative thermodynamic information on both the structural stability and nature of the underlying molecular interactions. However, there exist many supramolecular systems whose kinetics are so slow that the thermodynamic methods currently applied are unreliable or fail completely. We have developed a simple and rapid spectroscopic method for extracting accurate thermodynamic parameters from these systems. It is based on repeatedly raising and lowering the temperature during assembly and identifying the points of transient equilibrium as they are passed on the up- and down-scans. In a proof-of-principle application to the coassembly of polydeoxyadenosine (polyA) containing 15 adenosines and cyanuric acid (CA), we found that roughly 30% of the CA binding sites on the polyA chains were unoccupied, with implications for high-valence systems.
Collapse
|
11
|
Mizrahi I, Bruinsma R, Rudnick J. Packaging contests between viral RNA molecules and kinetic selectivity. PLoS Comput Biol 2022; 18:e1009913. [PMID: 35363785 PMCID: PMC9022832 DOI: 10.1371/journal.pcbi.1009913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 04/21/2022] [Accepted: 02/09/2022] [Indexed: 11/18/2022] Open
Abstract
The paper presents a statistical-mechanics model for the kinetic selection of viral RNA molecules by packaging signals during the nucleation stage of the assembly of small RNA viruses. The effects of the RNA secondary structure and folding geometry of the packaging signals on the assembly activation energy barrier are encoded by a pair of characteristics: the wrapping number and the maximum ladder distance. Kinetic selection is found to be optimal when assembly takes place under conditions of supersaturation and also when the concentration ratio of capsid protein and viral RNA concentrations equals the stoichiometric ratio of assembled viral particles. As a function of the height of the activation energy barrier, there is a form of order-disorder transition such that for sufficiently low activation energy barriers, kinetic selectivity is erased by entropic effects associated with the number of assembly pathways.
Collapse
Affiliation(s)
- Inbal Mizrahi
- Department of Physics and Astronomy, University of California, Los Angeles, California, United States of America
| | - Robijn Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California, United States of America
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, United States of America
- * E-mail:
| | - Joseph Rudnick
- Department of Physics and Astronomy, University of California, Los Angeles, California, United States of America
| |
Collapse
|
12
|
|
13
|
Kobayashi R, Inaba H, Matsuura K. Fluorescence Correlation Spectroscopy Analysis of Effect of Molecular Crowding on Self-Assembly of β-Annulus Peptide into Artificial Viral Capsid. Int J Mol Sci 2021; 22:ijms22094754. [PMID: 33946174 PMCID: PMC8125178 DOI: 10.3390/ijms22094754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Recent progress in the de novo design of self-assembling peptides has enabled the construction of peptide-based viral capsids. Previously, we demonstrated that 24-mer β-annulus peptides from tomato bushy stunt virus spontaneously self-assemble into an artificial viral capsid. Here we propose to use the artificial viral capsid through the self-assembly of β-annulus peptide as a simple model to analyze the effect of molecular crowding environment on the formation process of viral capsid. Artificial viral capsids formed by co-assembly of fluorescent-labelled and unmodified β-annulus peptides in dilute aqueous solutions and under molecular crowding conditions were analyzed using fluorescence correlation spectroscopy (FCS). The apparent particle size and the dissociation constant (Kd) of the assemblies decreased with increasing concentration of the molecular crowding agent, i.e., polyethylene glycol (PEG). This is the first successful in situ analysis of self-assembling process of artificial viral capsid under molecular crowding conditions.
Collapse
Affiliation(s)
- Risako Kobayashi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan; (R.K.); (H.I.)
| | - Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan; (R.K.); (H.I.)
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan; (R.K.); (H.I.)
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
- Correspondence: ; Tel.: +81-857-31-5262
| |
Collapse
|
14
|
Le DT, Müller KM. In Vitro Assembly of Virus-Like Particles and Their Applications. Life (Basel) 2021; 11:334. [PMID: 33920215 PMCID: PMC8069851 DOI: 10.3390/life11040334] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Virus-like particles (VLPs) are increasingly used for vaccine development and drug delivery. Assembly of VLPs from purified monomers in a chemically defined reaction is advantageous compared to in vivo assembly, because it avoids encapsidation of host-derived components and enables loading with added cargoes. This review provides an overview of ex cella VLP production methods focusing on capsid protein production, factors that impact the in vitro assembly, and approaches to characterize in vitro VLPs. The uses of in vitro produced VLPs as vaccines and for therapeutic delivery are also reported.
Collapse
Affiliation(s)
| | - Kristian M. Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Valbuena A, Maity S, Mateu MG, Roos WH. Visualization of Single Molecules Building a Viral Capsid Protein Lattice through Stochastic Pathways. ACS NANO 2020; 14:8724-8734. [PMID: 32633498 PMCID: PMC7392527 DOI: 10.1021/acsnano.0c03207] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/26/2020] [Indexed: 05/20/2023]
Abstract
Direct visualization of pathways followed by single molecules while they spontaneously self-assemble into supramolecular biological machines may provide fundamental knowledge to guide molecular therapeutics and the bottom-up design of nanomaterials and nanodevices. Here, high-speed atomic force microscopy is used to visualize self-assembly of the bidimensional lattice of protein molecules that constitutes the framework of the mature human immunodeficiency virus capsid. By real-time imaging of the assembly reaction, individual transient intermediates and reaction pathways followed by single molecules could be revealed. As when assembling a jigsaw puzzle, the capsid protein lattice is randomly built. Lattice patches grow independently from separate nucleation events whereby individual molecules follow different paths. Protein subunits can be added individually, while others form oligomers before joining a lattice or are occasionally removed from the latter. Direct real-time imaging of supramolecular self-assembly has revealed a complex, chaotic process involving multiple routes followed by individual molecules that are inaccessible to bulk (averaging) techniques.
Collapse
Affiliation(s)
- Alejandro Valbuena
- Centro
de Biología Molecular “Severo Ochoa”, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Sourav Maity
- Moleculaire
Biofysica, Zernike Instituut, Rijksuniversiteit
Groningen, 9712 CP Groningen, The Netherlands
| | - Mauricio G. Mateu
- Centro
de Biología Molecular “Severo Ochoa”, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Wouter H. Roos
- Moleculaire
Biofysica, Zernike Instituut, Rijksuniversiteit
Groningen, 9712 CP Groningen, The Netherlands
| |
Collapse
|
17
|
Martín‐Arroyo M, Prado A, Chamorro R, Bilbao N, González‐Rodríguez D. Elucidating Noncovalent Reaction Mechanisms: G‐Quartet as an Intermediate in G‐Quadruplex Assembly. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Miguel Martín‐Arroyo
- Nanostructured Molecular Systems and Materials (MSMn) Group Departamento de Química Orgánica Facultad de Ciencias Universidad Autónoma de Madrid 28049 Madrid Spain
| | - Anselmo Prado
- Nanostructured Molecular Systems and Materials (MSMn) Group Departamento de Química Orgánica Facultad de Ciencias Universidad Autónoma de Madrid 28049 Madrid Spain
| | - Raquel Chamorro
- Nanostructured Molecular Systems and Materials (MSMn) Group Departamento de Química Orgánica Facultad de Ciencias Universidad Autónoma de Madrid 28049 Madrid Spain
| | - Nerea Bilbao
- Nanostructured Molecular Systems and Materials (MSMn) Group Departamento de Química Orgánica Facultad de Ciencias Universidad Autónoma de Madrid 28049 Madrid Spain
| | - David González‐Rodríguez
- Nanostructured Molecular Systems and Materials (MSMn) Group Departamento de Química Orgánica Facultad de Ciencias Universidad Autónoma de Madrid 28049 Madrid Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem) Universidad Autónoma de Madrid 28049 Madrid Spain
| |
Collapse
|
18
|
Martín-Arroyo M, Del Prado A, Chamorro R, Bilbao N, González-Rodríguez D. Elucidating Noncovalent Reaction Mechanisms: G-Quartet as an Intermediate in G-Quadruplex Assembly. Angew Chem Int Ed Engl 2020; 59:9041-9046. [PMID: 32125063 DOI: 10.1002/anie.201916261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/17/2020] [Indexed: 12/20/2022]
Abstract
In analogy to covalent reactions, the understanding of noncovalent association pathways is fundamental to influence and control any supramolecular process. Following an approach that is reminiscent of covalent methodologies, we study here, for the first time, the mechanism of G-quadruplex formation in organic solvents. Our results support a reaction pathway in which the cation shifts the equilibrium towards a G-quartet transient intermediate, which then acts as a template in the formation of the G-quadruplex product.
Collapse
Affiliation(s)
- Miguel Martín-Arroyo
- Nanostructured Molecular Systems and Materials (MSMn) Group, Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Anselmo Del Prado
- Nanostructured Molecular Systems and Materials (MSMn) Group, Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Raquel Chamorro
- Nanostructured Molecular Systems and Materials (MSMn) Group, Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Nerea Bilbao
- Nanostructured Molecular Systems and Materials (MSMn) Group, Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - David González-Rodríguez
- Nanostructured Molecular Systems and Materials (MSMn) Group, Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| |
Collapse
|
19
|
Buzón P, Maity S, Roos WH. Physical virology: From virus self-assembly to particle mechanics. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 12:e1613. [PMID: 31960585 PMCID: PMC7317356 DOI: 10.1002/wnan.1613] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/01/2019] [Accepted: 12/11/2019] [Indexed: 12/19/2022]
Abstract
Viruses are highly ordered supramolecular complexes that have evolved to propagate by hijacking the host cell's machinery. Although viruses are very diverse, spreading through cells of all kingdoms of life, they share common functions and properties. Next to the general interest in virology, fundamental viral mechanisms are of growing importance in other disciplines such as biomedicine and (bio)nanotechnology. However, in order to optimally make use of viruses and virus-like particles, for instance as vehicle for targeted drug delivery or as building blocks in electronics, it is essential to understand their basic chemical and physical properties and characteristics. In this context, the number of studies addressing the mechanisms governing viral properties and processes has recently grown drastically. This review summarizes a specific part of these scientific achievements, particularly addressing physical virology approaches aimed to understand the self-assembly of viruses and the mechanical properties of viral particles. Using a physicochemical perspective, we have focused on fundamental studies providing an overview of the molecular basis governing these key aspects of viral systems. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
Collapse
Affiliation(s)
- Pedro Buzón
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| |
Collapse
|
20
|
Le DT, Radukic MT, Müller KM. Adeno-associated virus capsid protein expression in Escherichia coli and chemically defined capsid assembly. Sci Rep 2019; 9:18631. [PMID: 31819093 PMCID: PMC6901487 DOI: 10.1038/s41598-019-54928-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/20/2019] [Indexed: 01/17/2023] Open
Abstract
Research and clinical applications of recombinant adeno-associated virus (rAAV) significantly increased in recent years alongside regulatory approvals of rAAV gene therapy products. To date, all rAAV vectors as well as AAV empty capsids are produced in eukaryotic cells. We explored a new route to generate AAV capsids with the aim to analyze capsid assembly in a chemically defined setting and pave the way for new production methods and applications based on AAV virus-like particles (VLPs). We generated these empty capsids by bacterial expression and subsequent concomitant protein refolding and VLP formation. AAV serotype 2 structural protein VP3 was expressed in Escherichia coli. VLPs formed as demonstrated by dynamic light scattering, atomic force microscopy, and ELISA. Furthermore, VLPs internalized into human HeLa cells. To extend the application range of the VLPs, we tested peptide insertions, at the genetic level, in a surface loop (amino acid position 587) or at the C-terminus of VP3 and these variants also formed VLPs. VLPs developed without assembly-activating protein (AAP), but adding purified recombinant AAP to the refolding process increased capsid yield. Our findings offer a new route to understand AAV assembly biology and open a toolbox for AAV production strategies that might enable capsid display for vaccination and matching of capsids with cargoes at large scale and low cost.
Collapse
Affiliation(s)
- Dinh To Le
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Marco T Radukic
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Kristian M Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Bielefeld, Germany.
| |
Collapse
|
21
|
Marchetti M, Kamsma D, Cazares Vargas E, Hernandez García A, van der Schoot P, de Vries R, Wuite GJL, Roos WH. Real-Time Assembly of Viruslike Nucleocapsids Elucidated at the Single-Particle Level. NANO LETTERS 2019; 19:5746-5753. [PMID: 31368710 PMCID: PMC6696885 DOI: 10.1021/acs.nanolett.9b02376] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/24/2019] [Indexed: 05/20/2023]
Abstract
While the structure of a multitude of viral particles has been resolved to atomistic detail, their assembly pathways remain largely elusive. Key unresolved issues are particle nucleation, particle growth, and the mode of genome compaction. These issues are difficult to address in bulk approaches and are effectively only accessible by the real-time tracking of assembly dynamics of individual particles. This we do here by studying the assembly into rod-shaped viruslike particles (VLPs) of artificial capsid polypeptides. Using fluorescence optical tweezers, we establish that small oligomers perform one-dimensional diffusion along the DNA. Larger oligomers are immobile and nucleate VLP growth. A multiplexed acoustic force spectroscopy approach reveals that DNA is compacted in regular steps, suggesting packaging via helical wrapping into a nucleocapsid. By reporting how real-time assembly tracking elucidates viral nucleation and growth principles, our work opens the door to a fundamental understanding of the complex assembly pathways of both VLPs and naturally evolved viruses.
Collapse
Affiliation(s)
- Margherita Marchetti
- Department
of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Moleculaire
Biofysica, Zernike Instituut, Rijksuniversiteit
Groningen, 9712 CP Groningen, The Netherlands
| | - Douwe Kamsma
- Department
of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Ernesto Cazares Vargas
- Institute
of Chemistry, Department of Chemistry of Biomacromolecules, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Armando Hernandez García
- Institute
of Chemistry, Department of Chemistry of Biomacromolecules, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Paul van der Schoot
- Institute
for Theoretical Physics, Utrecht University, 3512 JE Utrecht, The Netherlands
- Department
of Applied Physics, Eindhoven University
of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Renko de Vries
- Laboratory
of Physical Chemistry and Colloid Science, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Gijs J. L. Wuite
- Department
of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- E-mail:
| | - Wouter H. Roos
- Moleculaire
Biofysica, Zernike Instituut, Rijksuniversiteit
Groningen, 9712 CP Groningen, The Netherlands
- E-mail:
| |
Collapse
|
22
|
Medrano M, Valbuena A, Rodríguez-Huete A, Mateu MG. Structural determinants of mechanical resistance against breakage of a virus-based protein nanoparticle at a resolution of single amino acids. NANOSCALE 2019; 11:9369-9383. [PMID: 31041970 DOI: 10.1039/c9nr01935a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Virus particles and other protein-based supramolecular complexes have a vast nanotechnological potential. However, protein nanostructures are "soft" materials prone to disruption by force. Whereas some non-biological nanoparticles (NPs) may be stronger, for certain applications protein- and virus-based NPs have potential advantages related to their structure, self-assembly, production, engineering, and/or inbuilt functions. Thus, it may be desirable to acquire the knowledge needed to engineer protein-based nanomaterials with a higher strength against mechanical breakage. Here we have used the capsid of the minute virus of mice to experimentally identify individual chemical groups that determine breakage-related properties of a virus particle. Individual amino acid side chains that establish interactions between building blocks in the viral particle were truncated using protein engineering. Indentation experiments using atomic force microscopy were carried out to investigate the role of each targeted side chain in determining capsid strength and brittleness, by comparing the maximum force and deformation each modified capsid withstood before breaking apart. Side chains with major roles in determining capsid strength against breakage included polar groups located in solvent-exposed positions, and did not generally correspond with those previously identified as determinants of mechanical stiffness. In contrast, apolar side chains buried along the intersubunit interfaces that generally determined capsid stiffness had, at most, a minor influence on strength against disruption. Whereas no correlated variations between strength and either stiffness or brittleness were found, brittleness and stiffness were quantitatively correlated. Implications for developing robust protein-based NPs and for acquiring a deeper physics-based perspective of viruses are discussed.
Collapse
Affiliation(s)
- María Medrano
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | | | | | | |
Collapse
|
23
|
Chen MY, Butler SS, Chen W, Suh J. Physical, chemical, and synthetic virology: Reprogramming viruses as controllable nanodevices. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 11:e1545. [PMID: 30411529 PMCID: PMC6461522 DOI: 10.1002/wnan.1545] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/03/2018] [Accepted: 10/04/2018] [Indexed: 01/24/2023]
Abstract
The fields of physical, chemical, and synthetic virology work in partnership to reprogram viruses as controllable nanodevices. Physical virology provides the fundamental biophysical understanding of how virus capsids assemble, disassemble, display metastability, and assume various configurations. Chemical virology considers the virus capsid as a chemically addressable structure, providing chemical pathways to modify the capsid exterior, interior, and subunit interfaces. Synthetic virology takes an engineering approach, modifying the virus capsid through rational, combinatorial, and bioinformatics-driven design strategies. Advances in these three subfields of virology aim to develop virus-based materials and tools that can be applied to solve critical problems in biomedicine and biotechnology, including applications in gene therapy and drug delivery, diagnostics, and immunotherapy. Examples discussed include mammalian viruses, such as adeno-associated virus (AAV), plant viruses, such as cowpea mosaic virus (CPMV), and bacterial viruses, such as Qβ bacteriophage. Importantly, research efforts in physical, chemical, and synthetic virology have further unraveled the design principles foundational to the form and function of viruses. This article is categorized under: Diagnostic Tools > Diagnostic Nanodevices Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
Collapse
Affiliation(s)
| | - Susan S Butler
- Department of Bioengineering, Rice University, Houston, Texas
| | - Weitong Chen
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas
| | - Junghae Suh
- Department of Bioengineering, Rice University, Houston, Texas
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, Texas
| |
Collapse
|
24
|
Lin Y, Penna M, Thomas MR, Wojciechowski JP, Leonardo V, Wang Y, Pashuck ET, Yarovsky I, Stevens MM. Residue-Specific Solvation-Directed Thermodynamic and Kinetic Control over Peptide Self-Assembly with 1D/2D Structure Selection. ACS NANO 2019; 13:1900-1909. [PMID: 30673202 PMCID: PMC6396410 DOI: 10.1021/acsnano.8b08117] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/16/2019] [Indexed: 05/18/2023]
Abstract
Understanding the self-organization and structural transformations of molecular ensembles is important to explore the complexity of biological systems. Here, we illustrate the crucial role of cosolvents and solvation effects in thermodynamic and kinetic control over peptide association into ultrathin Janus nanosheets, elongated nanobelts, and amyloid-like fibrils. We gained further insight into the solvation-directed self-assembly (SDSA) by investigating residue-specific peptide solvation using molecular dynamics modeling. We proposed the preferential solvation of the aromatic and alkyl domains on the peptide backbone and protofibril surface, which results in volume exclusion effects and restricts the peptide association between hydrophobic walls. We explored the SDSA phenomenon in a library of cosolvents (protic and aprotic), where less polar cosolvents were found to exert a stronger influence on the energetic balance at play during peptide propagation. By tailoring cosolvent polarity, we were able to achieve precise control of the peptide nanostructures with 1D/2D shape selection. We also illustrated the complexity of the SDSA system with pathway-dependent peptide aggregation, where two self-assembly states ( i.e., thermodynamic equilibrium state and kinetically trapped state) from different sample preparation methods were obtained.
Collapse
Affiliation(s)
- Yiyang Lin
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Matthew Penna
- School
of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
| | - Michael R. Thomas
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Jonathan P. Wojciechowski
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Vincent Leonardo
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Ye Wang
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - E. Thomas Pashuck
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Irene Yarovsky
- School
of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
- E-mail:
| | - Molly M. Stevens
- School
of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
- E-mail:
| |
Collapse
|
25
|
Harkness V RW, Avakyan N, Sleiman HF, Mittermaier AK. Mapping the energy landscapes of supramolecular assembly by thermal hysteresis. Nat Commun 2018; 9:3152. [PMID: 30089867 PMCID: PMC6082911 DOI: 10.1038/s41467-018-05502-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/02/2018] [Indexed: 01/28/2023] Open
Abstract
Understanding how biological macromolecules assemble into higher-order structures is critical to explaining their function in living organisms and engineered biomaterials. Transient, partly-structured intermediates are essential in many assembly processes and pathway selection, but are challenging to characterize. Here we present a simple thermal hysteresis method based on rapid, non-equilibrium melting and annealing measurements that maps the rate of supramolecular assembly as a function of temperature and concentration. A straightforward analysis of these surfaces provides detailed information on the natures of assembly pathways, offering temperature resolution beyond that accessible with conventional techniques. Validating the approach using a tetrameric guanine quadruplex, we obtain strikingly good agreement with previous kinetics measurements and reveal temperature-dependent changes to the assembly pathway. In an application to the recently discovered co-assembly of polydeoxyadenosine (poly(A)) and cyanuric acid, we show that fiber elongation is initiated when an unstable complex containing three poly(A) monomers acquires a fourth strand. Complex assembly pathways often involve transient, partly-formed intermediates that are challenging to characterize. Here, the authors present a simple and rapid spectroscopic thermal hysteresis method for mapping the energy landscapes of supramolecular assembly.
Collapse
Affiliation(s)
- Robert W Harkness V
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal Quebec, H3A 0B8, Canada
| | - Nicole Avakyan
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal Quebec, H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal Quebec, H3A 0B8, Canada
| | - Anthony K Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal Quebec, H3A 0B8, Canada.
| |
Collapse
|
26
|
Nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging genome or polyelectrolyte. Nat Commun 2018; 9:3071. [PMID: 30082710 PMCID: PMC6078970 DOI: 10.1038/s41467-018-05426-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 07/05/2018] [Indexed: 11/20/2022] Open
Abstract
The survival of viruses partly relies on their ability to self-assemble inside host cells. Although coarse-grained simulations have identified different pathways leading to assembled virions from their components, experimental evidence is severely lacking. Here, we use time-resolved small-angle X-ray scattering to uncover the nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging their full RNA genome. We reveal the formation of amorphous complexes via an en masse pathway and their relaxation into virions via a synchronous pathway. The binding energy of capsid subunits on the genome is moderate (~7kBT0, with kB the Boltzmann constant and T0 = 298 K, the room temperature), while the energy barrier separating the complexes and the virions is high (~ 20kBT0). A synthetic polyelectrolyte can lower this barrier so that filled capsids are formed in conditions where virions cannot build up. We propose a representation of the dynamics on a free energy landscape. The mechanism by which virus capsules assemble around RNA to package their genetic material is not clear. Here, the authors observed the assembly of the cowpea chlorotic mottle virus capsid around viral RNA or poly(styrene sulfonic acid) using time-resolved small-angle X-ray scattering measurements.
Collapse
|
27
|
Molecular dynamics study of T = 3 capsid assembly. J Biol Phys 2018; 44:147-162. [PMID: 29607454 DOI: 10.1007/s10867-018-9486-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/16/2018] [Indexed: 02/08/2023] Open
Abstract
Molecular dynamics simulation is used to model the self-assembly of polyhedral shells containing 180 trapezoidal particles that correspond to the T = 3 virus capsid. Three kinds of particle, differing only slightly in shape, are used to account for the effect of quasi-equivalence. Bond formation between particles is reversible and an explicit atomistic solvent is included. Under suitable conditions the simulations are able to produce complete shells, with the majority of unused particles remaining as monomers, and practically no other clusters. There are also no incorrectly assembled clusters. The simulations reveal details of intermediate structures along the growth pathway, information that is relevant for interpreting experiment.
Collapse
|
28
|
Matsuura K. Synthetic approaches to construct viral capsid-like spherical nanomaterials. Chem Commun (Camb) 2018; 54:8944-8959. [DOI: 10.1039/c8cc03844a] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This feature article describes recent progress in synthetic strategies to construct viral capsid-like spherical nanomaterials using the self-assembly of peptides and/or proteins.
Collapse
Affiliation(s)
- Kazunori Matsuura
- Department of Chemistry and Biotechnology
- Graduate School of Engineering
- Tottori University
- Tottori 680-8552
- Japan
| |
Collapse
|
29
|
Angelescu DG. Role of polyion length in the co-assembly of stoichiometric viral-like nanoparticles. JOURNAL OF POLYMER RESEARCH 2017. [DOI: 10.1007/s10965-017-1416-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
30
|
Chen J, Chevreuil M, Combet S, Lansac Y, Tresset G. Investigating the thermal dissociation of viral capsid by lattice model. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:474001. [PMID: 29098985 PMCID: PMC7104912 DOI: 10.1088/1361-648x/aa8d88] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/08/2017] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
The dissociation of icosahedral viral capsids was investigated by a homogeneous and a heterogeneous lattice model. In thermal dissociation experiments with cowpea chlorotic mottle virus and probed by small-angle neutron scattering, we observed a slight shrinkage of viral capsids, which can be related to the strengthening of the hydrophobic interaction between subunits at increasing temperature. By considering the temperature dependence of hydrophobic interaction in the homogeneous lattice model, we were able to give a better estimate of the effective charge. In the heterogeneous lattice model, two sets of lattice sites represented different capsid subunits with asymmetric interaction strengths. In that case, the dissociation of capsids was found to shift from a sharp one-step transition to a gradual two-step transition by weakening the hydrophobic interaction between AB and CC subunits. We anticipate that such lattice models will shed further light on the statistical mechanics underlying virus assembly and disassembly.
Collapse
Affiliation(s)
- Jingzhi Chen
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Maelenn Chevreuil
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Sophie Combet
- Laboratoire Léon Brillouin (LLB), UMR 12 CEA-CNRS, CEA-Saclay, F-91191 Gif-sur-Yvette Cedex, France
| | - Yves Lansac
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
- GREMAN, CNRS, Université François Rabelais, 73200 Tours, France
| | - Guillaume Tresset
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
| |
Collapse
|
31
|
Carrillo PJP, Medrano M, Valbuena A, Rodríguez-Huete A, Castellanos M, Pérez R, Mateu MG. Amino Acid Side Chains Buried along Intersubunit Interfaces in a Viral Capsid Preserve Low Mechanical Stiffness Associated with Virus Infectivity. ACS NANO 2017; 11:2194-2208. [PMID: 28117975 DOI: 10.1021/acsnano.6b08549] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Single-molecule experimental techniques and theoretical approaches reveal that important aspects of virus biology can be understood in biomechanical terms at the nanoscale. A detailed knowledge of the relationship in virus capsids between small structural changes caused by single-point mutations and changes in mechanical properties may provide further physics-based insights into virus function; it may also facilitate the engineering of viral nanoparticles with improved mechanical behavior. Here, we used the minute virus of mice to undertake a systematic experimental study on the contribution to capsid stiffness of amino acid side chains at interprotein interfaces and the specific noncovalent interactions they establish. Selected side chains were individually truncated by introducing point mutations to alanine, and the effects on local and global capsid stiffness were determined using atomic force microscopy. The results revealed that, in the natural virus capsid, multiple, mostly hydrophobic, side chains buried along the interfaces between subunits preserve a comparatively low stiffness of most (S2 and S3) regions. Virtually no point mutation tested substantially reduced stiffness, whereas most mutations increased stiffness of the S2/S3 regions. This stiffening was invariably associated with reduced virus yields during cell infection. The experimental evidence suggests that a comparatively low stiffness at S3/S2 capsid regions may have been biologically selected because it facilitates capsid assembly, increasing infectious virus yields. This study demonstrated also that knowledge of individual amino acid side chains and biological pressures that determine the physical behavior of a protein nanoparticle may be used for engineering its mechanical properties.
Collapse
Affiliation(s)
- Pablo José P Carrillo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - María Medrano
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Milagros Castellanos
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Rebeca Pérez
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|