1
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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.
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Affiliation(s)
- Manuel Martín-Bravo
- Departamento de Física and IUdEA, Universidad de La Laguna, 38200 Tenerife, Spain
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2
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Teunissen AJP, Burnett ME, Prévot G, Klein ED, Bivona D, Mulder WJM. Embracing nanomaterials' interactions with the innate immune system. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 13:e1719. [PMID: 33847441 PMCID: PMC8511354 DOI: 10.1002/wnan.1719] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/12/2021] [Accepted: 03/21/2021] [Indexed: 12/17/2022]
Abstract
Immunotherapy has firmly established itself as a compelling avenue for treating disease. Although many clinically approved immunotherapeutics engage the adaptive immune system, therapeutically targeting the innate immune system remains much less explored. Nanomedicine offers a compelling opportunity for innate immune system engagement, as many nanomaterials inherently interact with myeloid cells (e.g., monocytes, macrophages, neutrophils, and dendritic cells) or can be functionalized to target their cell-surface receptors. Here, we provide a perspective on exploiting nanomaterials for innate immune system regulation. We focus on specific nanomaterial design parameters, including size, form, rigidity, charge, and surface decoration. Furthermore, we examine the potential of high-throughput screening and machine learning, while also providing recommendations for advancing the field. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Diagnostic Tools > In Vivo Nanodiagnostics and Imaging Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease.
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Affiliation(s)
- Abraham J. P. Teunissen
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Marianne E. Burnett
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Geoffrey Prévot
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emma D. Klein
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Daniel Bivona
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Willem J. M. Mulder
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
- Laboratory of Chemical Biology, Department of Biochemical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
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3
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Li S, Matoz-Fernandez DA, Olvera de la Cruz M. Effect of Mechanical Properties on Multicomponent Shell Patterning. ACS NANO 2021; 15:14804-14812. [PMID: 34402621 DOI: 10.1021/acsnano.1c04795] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Self-organized shells are fundamental in biological compartmentalization. They protect genomic material or enclose enzymes to aid the metabolic process. Studies of crystalline shells have shown the importance of the mechanical properties of building units in the shell morphology. However, the mechanism underlying the morphology of multicomponent assemblies is still poorly understood. Here, we analyze multicomponent closed shells that have different mechanical properties. By minimizing elastic energy, we show that heterogeneous bending rigidities regulate the surface pattern into circular, spikes, and ridge shapes. Interestingly, our continuum elasticity model recovers the patterns that have been proposed in bacterial microcompartments (BMCs), which are self-organized protein shells that aid the breakdown of complex molecules and allow bacteria to survive in hostile environments. In addition, our work elucidates the principles of pattern formation that can be used to design and engineer multicomponent microcompartments with a specific surface distribution of the components.
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Affiliation(s)
- Siyu Li
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, United States
| | - Daniel A Matoz-Fernandez
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, United States
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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4
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Kiss B, Mudra D, Török G, Mártonfalvi Z, Csík G, Herényi L, Kellermayer M. Single-particle virology. Biophys Rev 2020; 12:1141-1154. [PMID: 32880826 PMCID: PMC7471434 DOI: 10.1007/s12551-020-00747-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/18/2020] [Indexed: 01/02/2023] Open
Abstract
The development of advanced experimental methodologies, such as optical tweezers, scanning-probe and super-resolved optical microscopies, has led to the evolution of single-molecule biophysics, a field of science that allows direct access to the mechanistic detail of biomolecular structure and function. The extension of single-molecule methods to the investigation of particles such as viruses permits unprecedented insights into the behavior of supramolecular assemblies. Here we address the scope of viral exploration at the level of individual particles. In an era of increased awareness towards virology, single-particle approaches are expected to facilitate the in-depth understanding, and hence combating, of viral diseases.
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Affiliation(s)
- Bálint Kiss
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Dorottya Mudra
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - György Török
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Zsolt Mártonfalvi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Gabriella Csík
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Levente Herényi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Miklós Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
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5
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Indelicato G, Cermelli P, Twarock R. Surface stresses in complex viral capsids and non-quasi-equivalent viral architectures. J R Soc Interface 2020; 17:20200455. [PMID: 32752992 PMCID: PMC7482553 DOI: 10.1098/rsif.2020.0455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/14/2020] [Indexed: 12/02/2022] Open
Abstract
Many larger and more complex viruses deviate from the capsid layouts predicted in the seminal Caspar-Klug theory of icosahedral viruses. Instead of being built from one type of capsid protein (CP), they code for multiple distinct structural proteins that either break the local symmetry of the CP building blocks (capsomers) in specific positions or exhibit auxiliary proteins that stabilize the capsid shell. We investigate here the hypothesis that this occurs as a response to mechanical stress. For this, we construct a coarse-grained model of a viral capsid, derived from the experimentally determined atomistic positions of the CPs, that represents the basic features of protein organization in the viral capsid as described in Caspar-Klug theory. We focus here on viruses in the PRD1-adenovirus lineage. For T = 28 viruses in this lineage, which have capsids formed from two distinct structural proteins, we show that the tangential shear stress in the viral capsid concentrates at the sites of local symmetry breaking. In the T = 21, 25 and 27 capsids, we show that stabilizing proteins decrease the tangential stress. These results suggest that mechanical properties can act as selective pressures on the evolution of capsid components, offsetting the coding cost imposed by the need for such additional protein components.
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Affiliation(s)
| | - Paolo Cermelli
- Dipartimento di Matematica, Università di Torino, Torino, Italy
| | - Reidun Twarock
- Department of Mathematics, University of York, York, UK
- Department of Biology, University of York, York, UK
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6
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Martín-Bravo M, Gomez Llorente JM, Hernández-Rojas J. A minimal coarse-grained model for the low-frequency normal mode analysis of icosahedral viral capsids. SOFT MATTER 2020; 16:3443-3455. [PMID: 32196061 DOI: 10.1039/d0sm00299b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The main goal of this work is the design of a coarse-grained theoretical model of minimal resolution for the study of the physical properties of icosahedral virus capsids within the linear-response regime. In this model the capsid is represented as an interacting many-body system whose composing elements are capsid subunits (capsomers), which are treated as three-dimensional rigid bodies. The total interaction potential energy is written as a sum of pairwise capsomer-capsomer interactions. Based on previous work [Gomez Llorente et al., Soft Matter, 2014, 10, 3560], a minimal and complete anisotropic binary interaction that includes a full Hessian matrix of independent force constants is proposed. In this interaction model, capsomers have rotational symmetry around an axis of order n > 2. The full coarse-grained model is applied to analyse the low-frequency normal-mode spectrum of icosahedral T = 1 capsids. The model performance is evaluated by fitting its predicted spectrum to the full-atom results for the Satellite Tobacco Necrosis Virus (STNV) capsid [Dykeman and Sankey, Phys. Rev. Lett., 2008, 100, 028101]. Two capsomer choices that are compatible with the capsid icosahedral symmetry are checked, namely pentamers (n = 5) and trimers (n = 3). Both subunit types provide fair fits, from which the magnitude of the coarse-grained force constants for a real virus is obtained. The model is able to uncover latent instabilities whose analysis is fully consistent with the current knowledge about the STNV capsid, which does not self-assemble in the absence of RNA and is thermally unstable. The straightforward generalisability of the model beyond the linear regime and its completeness make it a promising tool to theoretically interpret many experimental data such as those provided by the atomic force microscopy or even to better understand processes far from equilibrium such as the capsid self-assembly.
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Affiliation(s)
- M Martín-Bravo
- Departamento de Física and IUdEA, Universidad de La Laguna, 38200 Tenerife, Spain.
| | - J M Gomez Llorente
- Departamento de Física and IUdEA, Universidad de La Laguna, 38200 Tenerife, Spain.
| | - J Hernández-Rojas
- Departamento de Física and IUdEA, Universidad de La Laguna, 38200 Tenerife, Spain.
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7
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Hadi-Alijanvand H. Soft regions of protein surface are potent for stable dimer formation. J Biomol Struct Dyn 2019; 38:3587-3598. [PMID: 31476974 DOI: 10.1080/07391102.2019.1662328] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
By having knowledge about the characteristics of protein interaction interfaces, we will be able to manipulate protein complexes for therapies. Dimer state is considered as the primary alphabet of the most proteins' quaternary structure. The properties of binding interface between subunits and of noninterface region define the specificity and stability of the intended protein complex. Considering some topological properties and amino acids' affinity for binding in interfaces of protein dimers, we construct the interface-specific recurrence plots. The data obtained from recurrence quantitative analysis, and accessibility-related metrics help us to classify the protein dimers into four distinct classes. Some mechanical properties of binding interfaces are computed for each predefined class of the dimers. The computed mechanical characteristics of binding patch region are compared with those of nonbinding region of proteins. Our observations indicate that the mechanical properties of protein binding sites have a decisive impact on determining the dimer stability. We introduce a new concept in analyzing protein structure by considering mechanical properties of protein structure. We conclude that the interface region between subunits of stable dimers is usually mechanically softer than the interface of unstable protein dimers. AbbreviationsAABaverage affinity for bindingANManisotropic network modelAPCaffinity propagation clusteringASAaccessible surface areaCCDinter residues distanceCSCcomplex stability codeDMdistance matrixΔGdissPISA-computed dissociation free energyGNMGaussian normal mode analysisNMAnormal mode analysisPBPprotein binding patchPISAproteins, interfaces, structures and assembliesrASArelative accessible area in respect to unfolded state of residuesRMrecurrence matrixrPrelative protrusionRPrecurrence plotRQArecurrence quantitative analysisSEMstandard error of meanCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hamid Hadi-Alijanvand
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
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8
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Lošdorfer Božič A, Šiber A. Electrostatics-Driven Inflation of Elastic Icosahedral Shells as a Model for Swelling of Viruses. Biophys J 2018; 115:822-829. [PMID: 30139522 DOI: 10.1016/j.bpj.2018.07.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/20/2018] [Accepted: 07/30/2018] [Indexed: 01/13/2023] Open
Abstract
We develop a clear theoretical description of radial swelling in virus-like particles that delineates the importance of electrostatic contributions to swelling in the absence of any conformational changes. The model couples the elastic parameters of the capsid-represented as a continuous elastic shell-to the electrostatic pressure acting on it. We show that different modifications of the electrostatic interactions brought about by, for instance, changes in pH or solution ionic strength are often sufficient to achieve the experimentally observed swelling (∼10% of the capsid radius). Additionally, we derive analytical expressions for the electrostatics-driven radial swelling of virus-like particles that enable one to quickly estimate the magnitudes of physical quantities involved.
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9
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Lin S, Xie YM, Li Q, Huang X, Zhang Z, Ma G, Zhou S. Shell buckling: from morphogenesis of soft matter to prospective applications. BIOINSPIRATION & BIOMIMETICS 2018; 13:051001. [PMID: 29923834 DOI: 10.1088/1748-3190/aacdd1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Being one of the commonest deformation modes for soft matter, shell buckling is the primary reason for the growth and nastic movement of many plants, as well as the formation of complex natural morphology. On-demand regulation of buckling-induced deformation associated with wrinkling, ruffling, folding, creasing and delaminating has profound implications for diverse scopes, which can be seen in its broad applications in microfabrication, 4D printing, actuator and drug delivery. This paper reviews the recent remarkable developments in the shell buckling of soft matter to explain the most representative natural morphogenesis from the perspectives of theoretical analysis in continuum mechanics, finite element analysis, and experimental validations. Imitation of buckling-induced shape transformation and its applications are also discussed for the innovations of sophisticated materials and devices in future.
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Affiliation(s)
- Sen Lin
- School of Civil and Transportation Engineering, Hebei University of Technology, 5340 Xiping Road, Beichen District, Tianjin 300401, People's Republic of China
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10
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Aznar M, Roca-Bonet S, Reguera D. Viral nanomechanics with a virtual atomic force microscope. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:264001. [PMID: 29769436 PMCID: PMC7104910 DOI: 10.1088/1361-648x/aac57a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 05/07/2018] [Accepted: 05/15/2018] [Indexed: 05/22/2023]
Abstract
One of the most important components of a virus is the protein shell or capsid that encloses its genetic material. The main role of the capsid is to protect the viral genome against external aggressions, facilitating its safe and efficient encapsulation and delivery. As a consequence, viral capsids have developed astonishing mechanical properties that are crucial for viral function. These remarkable properties have started to be unveiled in single-virus nanoindentation experiments, and are opening the door to the use of viral-derived artificial nanocages for promising bio- and nano-technological applications. However, the interpretation of nanoindentation experiments is often difficult, requiring the support of theoretical and simulation analysis. Here we present a 'Virtual AFM' (VAFM), a Brownian Dynamics simulation of a coarse-grained model of virus aimed to mimic the standard setup of atomic force microscopy (AFM) nanoindentation experiments. Despite the heavy level of coarse-graining, these simulations provide valuable information which is not accessible in experiments. Rather than focusing on a specific virus, the VAFM will be used to analyze how the mechanical response and breaking of viruses depend on different parameters controlling the effective interactions between capsid's structural units. In particular, we will discuss the influence of adsorption, the tip radius, and the rigidity and shape of the shell on its mechanical response.
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Affiliation(s)
- María Aznar
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Sergi Roca-Bonet
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - David Reguera
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- University of Barcelona Institute of Complex Systems (UBICS), Martí i Franquès 1, 08028 Barcelona, Spain
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11
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Zhang L, Ru CQ. Post-buckling of a pressured biopolymer spherical shell with the mode interaction. Proc Math Phys Eng Sci 2018; 474:20170834. [PMID: 29662343 DOI: 10.1098/rspa.2017.0834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/05/2018] [Indexed: 12/20/2022] Open
Abstract
Imperfection sensitivity is essential for mechanical behaviour of biopolymer shells characterized by high geometric heterogeneity. The present work studies initial post-buckling and imperfection sensitivity of a pressured biopolymer spherical shell based on non-axisymmetric buckling modes and associated mode interaction. Our results indicate that for biopolymer spherical shells with moderate radius-to-thickness ratio (say, less than 30) and smaller effective bending thickness (say, less than 0.2 times average shell thickness), the imperfection sensitivity predicted based on the axisymmetric mode without the mode interaction is close to the present results based on non-axisymmetric modes with the mode interaction with a small (typically, less than 10%) relative errors. However, for biopolymer spherical shells with larger effective bending thickness, the maximum load an imperfect shell can sustain predicted by the present non-axisymmetric analysis can be significantly (typically, around 30%) lower than those predicted based on the axisymmetric mode without the mode interaction. In such cases, a more accurate non-axisymmetric analysis with the mode interaction, as given in the present work, is required for imperfection sensitivity of pressured buckling of biopolymer spherical shells. Finally, the implications of the present study to two specific types of biopolymer spherical shells (viral capsids and ultrasound contrast agents) are discussed.
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Affiliation(s)
- Lei Zhang
- Department of Mechanical Engineering, University of Alberta, Edmonton, CanadaT6G 2G8
| | - C Q Ru
- Department of Mechanical Engineering, University of Alberta, Edmonton, CanadaT6G 2G8
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12
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Normal mode analysis of Zika virus. Comput Biol Chem 2018; 72:53-61. [PMID: 29414097 DOI: 10.1016/j.compbiolchem.2018.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/04/2018] [Accepted: 01/12/2018] [Indexed: 02/06/2023]
Abstract
In recent years, Zika virus (ZIKV) caused a new pandemic due to its rapid spread and close relationship with microcephaly. As a result, ZIKV has become an obvious global health concern. Information about the fundamental viral features or the biological process of infection remains limited, despite considerable efforts. Meanwhile, the icosahedral shell structure of the mature ZIKV was recently revealed by cryo-electron microscopy. This structural information enabled us to simulate ZIKV. In this study, we analyzed the dynamic properties of ZIKV through simulation from the mechanical viewpoint. We performed normal mode analysis (NMA) for a dimeric structure of ZIKV consisting of the envelope proteins and the membrane proteins as a unit structure. By analyzing low-frequency normal modes, we captured intrinsic vibrational motions and defined basic vibrational properties of the unit structure. Moreover, we also simulated the entire shell structure of ZIKV at the reduced computational cost, similar to the case of the unit structure, by utilizing its icosahedral symmetry. From the NMA results, we can not only comprehend the putative dynamic fluctuations of ZIKV but also verify previous inference such that highly mobile glycosylation sites would play an important role in ZIKV. Consequently, this theoretical study is expected to give us an insight on the underlying biological functions and infection mechanism of ZIKV.
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13
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Vörös Z, Csík G, Herényi L, Kellermayer MSZ. Stepwise reversible nanomechanical buckling in a viral capsid. NANOSCALE 2017; 9:1136-1143. [PMID: 28009879 DOI: 10.1039/c6nr06598h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Viruses are nanoscale infectious agents constructed of a proteinaceous capsid that protects the packaged genomic material. Nanoindentation experiments using atomic force microscopy have, in recent years, provided unprecedented insight into the elastic properties, structural stability and maturation-dependent mechanical changes in viruses. However, the dynamics of capsid behavior are still unresolved. Here we used high-resolution nanoindentation experiments on mature, DNA-filled T7 bacteriophage particles. The elastic regime of the nanoindentation force trace contained discrete, stepwise transitions that cause buckling of the T7 capsid with magnitudes that are integer multiples of ∼0.6 nm. Remarkably, the transitions are reversible and contribute to the rapid consolidation of the capsid structure against a force during cantilever retraction. The stepwise transitions were present even following the removal of the genomic DNA by heat treatment, indicating that they are related to the structure and dynamics of the capsomeric proteins. Dynamic force spectroscopy experiments revealed that the thermally activated consolidation step is ∼104 times faster than spontaneous buckling, suggesting that the capsid stability is under strong dynamic control. Capsid structural dynamics may play an important role in protecting the genomic material from harsh environmental impacts. The nanomechanics approach employed here may be used to investigate the structural dynamics of other viruses and nanoscale containers as well.
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Affiliation(s)
- Zsuzsanna Vörös
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47., Budapest H-1094, Hungary.
| | - Gabriella Csík
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47., Budapest H-1094, Hungary.
| | - Levente Herényi
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47., Budapest H-1094, Hungary.
| | - Miklós S Z Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47., Budapest H-1094, Hungary. and MTA-SE Molecular Biophysics Research Group, Semmelweis University, Tűzoltó u. 37-47., Budapest H-1094, Hungary
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14
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Zhang L, Ru CQ. Imperfection sensitivity of pressured buckling of biopolymer spherical shells. Phys Rev E 2016; 93:062403. [PMID: 27415294 DOI: 10.1103/physreve.93.062403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Indexed: 12/18/2022]
Abstract
Imperfection sensitivity is essential for mechanical behavior of biopolymer shells [such as ultrasound contrast agents (UCAs) and spherical viruses] characterized by high geometric heterogeneity. In this work, an imperfection sensitivity analysis is conducted based on a refined shell model recently developed for spherical biopolymer shells of high structural heterogeneity and thickness nonuniformity. The influence of related parameters (including the ratio of radius to average shell thickness, the ratio of transverse shear modulus to in-plane shear modulus, and the ratio of effective bending thickness to average shell thickness) on imperfection sensitivity is examined for pressured buckling. Our results show that the ratio of effective bending thickness to average shell thickness has a major effect on the imperfection sensitivity, while the effect of the ratio of transverse shear modulus to in-plane shear modulus is usually negligible. For example, with physically realistic parameters for typical imperfect spherical biopolymer shells, the present model predicts that actual maximum external pressure could be reduced to as low as 60% of that of a perfect UCA spherical shell or 55%-65% of that of a perfect spherical virus shell, respectively. The moderate imperfection sensitivity of spherical biopolymer shells with physically realistic imperfection is largely attributed to the fact that biopolymer shells are relatively thicker (defined by smaller radius-to-thickness ratio) and therefore practically realistic imperfection amplitude normalized by thickness is very small as compared to that of classical elastic thin shells which have much larger radius-to-thickness ratio.
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Affiliation(s)
- Lei Zhang
- Department of Mechanical Engineering, University of Alberta, Edmonton, Canada T6G 2G8
| | - C Q Ru
- Department of Mechanical Engineering, University of Alberta, Edmonton, Canada T6G 2G8
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15
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Moerman P, van der Schoot P, Kegel W. Kinetics versus Thermodynamics in Virus Capsid Polymorphism. J Phys Chem B 2016; 120:6003-9. [PMID: 27027925 DOI: 10.1021/acs.jpcb.6b01953] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Virus coat proteins spontaneously self-assemble into empty shells in aqueous solution under the appropriate physicochemical conditions, driven by an interaction free energy per bond on the order of 2-5 times the thermal energy kBT. For this seemingly modest interaction strength, each protein building block nonetheless gains a very large binding free energy, between 10 and 20 kBT. Because of this, there is debate about whether the assembly process is reversible or irreversible. Here we discuss capsid polymorphism observed in in vitro experiments from the perspective of nucleation theory and of the thermodynamics of mass action. We specifically consider the potential contribution of a curvature free energy term to the effective interaction potential between the proteins. From these models, we propose experiments that may conclusively reveal whether virus capsid assembly into a mixture of polymorphs is a reversible or an irreversible process.
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Affiliation(s)
| | - Paul van der Schoot
- Department of Applied Physics, Eindhoven University of Technology , 612 AZ Eindhoven, The Netherlands
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16
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Aggarwal A, May ER, Brooks CL, Klug WS. Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature. Phys Rev E 2016; 93:012417. [PMID: 26871111 DOI: 10.1103/physreve.93.012417] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Indexed: 06/05/2023]
Abstract
Many experimental and theoretical methods have been developed to calculate the coarse-grained continuum elastic properties of macromolecules. However, all of those methods assume uniform elastic properties. Following the continuum mechanics framework, we present a systematic way of calculating the nonuniform effective elastic properties from atomic thermal fluctuations obtained from molecular dynamics simulation at any coarse-grained scale using a potential of the mean-force approach. We present the results for a mutant of Sesbania mosaic virus capsid, where we calculate the elastic moduli at different scales and observe an apparent problem with the chosen reference configuration in some cases. We present a possible explanation using an elastic network model, where inducing random prestrain results in a similar behavior. This phenomenon provides a novel insight into the continuum nature of macromolecules and defines the limits on details that the elasticity theory can capture. Further investigation into prestrains could elucidate important aspects of conformational dynamics of macromolecules.
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Affiliation(s)
- Ankush Aggarwal
- Zienkiewicz Centre for Computational Engineering, Swansea University, Swansea SA1 8EN, United Kigdom
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Charles L Brooks
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - William S Klug
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, California 90095, USA
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17
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Hickman SJ, Ross JF, Paci E. Prediction of stability changes upon mutation in an icosahedral capsid. Proteins 2015; 83:1733-41. [PMID: 26178267 PMCID: PMC4737204 DOI: 10.1002/prot.24859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 06/24/2015] [Accepted: 07/04/2015] [Indexed: 11/08/2022]
Abstract
Identifying the contributions to thermodynamic stability of capsids is of fundamental and practical importance. Here we use simulation to assess how mutations affect the stability of lumazine synthase from the hyperthermophile Aquifex aeolicus, a T = 1 icosahedral capsid; in the simulations the icosahedral symmetry of the capsid is preserved by simulating a single pentamer and imposing crystal symmetry, in effect simulating an infinite cubic lattice of icosahedral capsids. The stability is assessed by estimating the free energy of association using an empirical method previously proposed to identify biological units in crystal structures. We investigate the effect on capsid formation of seven mutations, for which it has been experimentally assessed whether they disrupt capsid formation or not. With one exception, our approach predicts the effect of the mutations on the capsid stability. The method allows the identification of interaction networks, which drive capsid assembly, and highlights the plasticity of the interfaces between subunits in the capsid. Proteins 2015; 83:1733–1741. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc
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Affiliation(s)
- Samuel J Hickman
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - James F Ross
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Emanuele Paci
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
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18
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Rahimi A, Varano AC, Demmert AC, Melanson LA, McDonald SM, Kelly DF. A Non-Symmetric Reconstruction Technique for Transcriptionally-Active Viral Assemblies. ACTA ACUST UNITED AC 2015; 2. [PMID: 27819069 PMCID: PMC5094455 DOI: 10.13188/2474-1914.1000004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The molecular mechanisms by which RNA viruses coordinate their transcriptional activities are not fully understood. For rotavirus, an important pediatric gastroenteric pathogen, transcription occurs within a double-layered particle that encloses the viral genome. To date, there remains very little structural information available for actively-transcribing rotavirus double-layered particles, which could provide new insights for antiviral development. To improve our vision of these viral assemblies, we developed a new combinatorial strategy that utilizes currently available high-resolution image processing tools. First, we employed a 3D classification routine that allowed us to sort transcriptionally-active rotavirus assemblies on the basis of their internal density. Next, we implemented an additional 3D refinement procedure using the most active class of DLPs. For comparison, the refined structures were computed in parallel by (1) enforcing icosahedral symmetry, and by (2) using no symmetry operators. Comparing the resulting structures, we were able to visualize the continuum that exists between viral capsid proteins and the viral RNA for the first time.
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Affiliation(s)
- Amina Rahimi
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA
| | | | - Andrew C Demmert
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA; Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | | | - Sarah M McDonald
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA; Virginia Tech Carilion School of Medicine, Roanoke, VA, USA; Department of Biomedical Sciences and Pathology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Deborah F Kelly
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA; Virginia Tech Carilion School of Medicine, Roanoke, VA, USA; Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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19
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Boyd KJ, Bansal P, Feng J, May ER. Stability of Norwalk Virus Capsid Protein Interfaces Evaluated by in Silico Nanoindentation. Front Bioeng Biotechnol 2015; 3:103. [PMID: 26284238 PMCID: PMC4520240 DOI: 10.3389/fbioe.2015.00103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/10/2015] [Indexed: 01/17/2023] Open
Abstract
Norwalk virus causes severe gastroenteritis for which there is currently no specific anti-viral therapy. A stage of the infection process is uncoating of the protein capsid to expose the viral genome and allow for viral replication. A mechanical characterization of the Norwalk virus may provide important information relating to the mechanism of uncoating. The mechanical strength of the Norwalk virus has previously been investigated using atomic force microscopy (AFM) nanoindentation experiments. Those experiments cannot resolve specific molecular interactions, and therefore, we have employed a molecular modeling approach to gain insights into the potential uncoating mechanism of the Norwalk capsid. In this study, we perform simulated nanoindentation using a coarse-grained structure-based model, which provides an estimate of the spring constant in good agreement with the experimentally determined value. We further analyze the fracture mechanisms and determine weak interfaces in the capsid structure, which are potential sites to inhibit uncoating by stabilization of these weak interfaces. We conclude by identifying potential target sites at the junction of a weak protein–protein interface.
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Affiliation(s)
- Kevin J Boyd
- Department of Molecular and Cell Biology, University of Connecticut , Storrs, CT , USA
| | - Prakhar Bansal
- Department of Molecular and Cell Biology, University of Connecticut , Storrs, CT , USA
| | - Jun Feng
- Department of Chemistry, West Virginia University , Morgantown, WV , USA
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut , Storrs, CT , USA
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20
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Abstract
I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to molecular dynamics simulations, and I give an overview of some of the important conclusions about virus assembly that have resulted from these modeling efforts. Topics include the assembly of empty viral shells, assembly around single-stranded nucleic acids to form viral particles, and assembly around synthetic polymers or charged nanoparticles for nanotechnology or biomedical applications. I present some examples in which modeling efforts have promoted experimental breakthroughs, as well as directions in which the connection between modeling and experiment can be strengthened.
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21
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Hirsh AD, Perkins NC. DNA buckling in bacteriophage cavities as a mechanism to aid virus assembly. J Struct Biol 2015; 189:251-8. [PMID: 25613203 DOI: 10.1016/j.jsb.2015.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 01/09/2015] [Accepted: 01/10/2015] [Indexed: 01/03/2023]
Abstract
While relatively simple biologically, bacteriophages are sophisticated biochemical machines that execute a precise sequence of events during virus assembly, DNA packaging, and ejection. These stages of the viral life cycle require intricate coordination of viral components whose structures are being revealed by single molecule experiments and high resolution (cryo-electron microscopy) reconstructions. For example, during packaging, bacteriophages employ some of the strongest known molecular motors to package DNA against increasing pressure within the viral capsid shell. Located upstream of the motor is an elaborate portal system through which DNA is threaded. A high resolution reconstruction of the portal system for bacteriophage ϕ29 reveals that DNA buckles inside a small cavity under large compressive forces. In this study, we demonstrate that DNA can also buckle in other bacteriophages including T7 and P22. Using a computational rod model for DNA, we demonstrate that a DNA buckle can initiate and grow within the small confines of a cavity under biologically-attainable force levels. The forces of DNA-cavity contact and DNA-DNA electrostatic repulsion ultimately limit cavity filling. Despite conforming to very different cavity geometries, the buckled DNA within T7 and P22 exhibits near equal volumetric energy density (∼1kT/nm(3)) and energetic cost of packaging (∼22kT). We hypothesize that a DNA buckle creates large forces on the cavity interior to signal the conformational changes to end packaging. In addition, a DNA buckle may help retain the genome prior to tail assembly through significantly increased contact area with the portal.
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Affiliation(s)
- Andrew D Hirsh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
| | - N C Perkins
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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22
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Rasheed M, Bajaj C. Highly Symmetric and Congruently Tiled Meshes for Shells and Domes. PROCEDIA ENGINEERING 2015; 124:213-225. [PMID: 27563368 PMCID: PMC4994975 DOI: 10.1016/j.proeng.2015.10.134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We describe the generation of all possible shell and dome shapes that can be uniquely meshed (tiled) using a single type of mesh face (tile), and following a single meshing (tiling) rule that governs the mesh (tile) arrangement with maximal vertex, edge and face symmetries. Such tiling arrangements or congruently tiled meshed shapes, are frequently found in chemical forms (fullerenes or Bucky balls, crystals, quasi-crystals, virus nano shells or capsids), and synthetic shapes (cages, sports domes, modern architectural facades). Congruently tiled meshes are both aesthetic and complete, as they support maximal mesh symmetries with minimal complexity and possess simple generation rules. Here, we generate congruent tilings and meshed shape layouts that satisfy these optimality conditions. Further, the congruent meshes are uniquely mappable to an almost regular 3D polyhedron (or its dual polyhedron) and which exhibits face-transitive (and edge-transitive) congruency with at most two types of vertices (each type transitive to the other). The family of all such congruently meshed polyhedra create a new class of meshed shapes, beyond the well-studied regular, semi-regular and quasi-regular classes, and their duals (platonic, Catalan and Johnson). While our new mesh class is infinite, we prove that there exists a unique mesh parametrization, where each member of the class can be represented by two integer lattice variables, and moreover efficiently constructable.
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Affiliation(s)
- Muhibur Rasheed
- Computational Visualization Center, Department of Computer Science and Institute of Computational Engineering and Sciences, University of Texas at Austin, Austin, TX 78731, USA
| | - Chandrajit Bajaj
- Computational Visualization Center, Department of Computer Science and Institute of Computational Engineering and Sciences, University of Texas at Austin, Austin, TX 78731, USA
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23
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May ER. Recent Developments in Molecular Simulation Approaches to Study Spherical Virus Capsids. MOLECULAR SIMULATION 2014; 40:878-888. [PMID: 25197162 DOI: 10.1080/08927022.2014.907899] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Viruses are a particularly challenging systems to study via molecular simulation methods. Virus capsids typically consist of over 100 subunit proteins and reach dimensions of over 100 nm; solvated viruses capsid systems can be over 1 million atoms in size. In this review, I will present recent developments which have attempted to overcome the significant computational expense to perform simulations which can inform experimental studies, make useful predictions about biological phenomena and calculate material properties relevant to nanotechnology design efforts.
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Affiliation(s)
- Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA 06269
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24
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Vashisth H, Skiniotis G, Brooks CL. Collective variable approaches for single molecule flexible fitting and enhanced sampling. Chem Rev 2014; 114:3353-65. [PMID: 24446720 PMCID: PMC3983124 DOI: 10.1021/cr4005988] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Harish Vashisth
- Department
of Chemical Engineering, University of New
Hampshire, Durham, New Hampshire 03824, United States
| | - Georgios Skiniotis
- Life Sciences Institute, Department
of Biological Chemistry, and
Biophysics Program, and Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles Lee Brooks
- Life Sciences Institute, Department
of Biological Chemistry, and
Biophysics Program, and Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
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May ER, Arora K, Brooks CL. pH-induced stability switching of the bacteriophage HK97 maturation pathway. J Am Chem Soc 2014; 136:3097-107. [PMID: 24495192 PMCID: PMC3985869 DOI: 10.1021/ja410860n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Many viruses undergo large-scale conformational changes during their life cycles. Blocking the transition from one stage of the life cycle to the next is an attractive strategy for the development of antiviral compounds. In this work, we have constructed an icosahedrally symmetric, low-energy pathway for the maturation transition of bacteriophage HK97. By conducting constant-pH molecular dynamics simulations on this pathway, we identify which residues are contributing most significantly to shifting the stability between the states along the pathway under differing pH conditions. We further analyze these data to establish the connection between critical residues and important structural motifs which undergo reorganization during maturation. We go on to show how DNA packaging can induce spontaneous reorganization of the capsid during maturation.
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Affiliation(s)
- Eric R May
- Department of Molecular and Cell Biology, University of Connecticut , Storrs, Connecticut 06269, United States
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26
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Zhou HX. Theoretical frameworks for multiscale modeling and simulation. Curr Opin Struct Biol 2014; 25:67-76. [PMID: 24492203 DOI: 10.1016/j.sbi.2014.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 12/25/2013] [Accepted: 01/10/2014] [Indexed: 02/08/2023]
Abstract
Biomolecular systems have been modeled at a variety of scales, ranging from explicit treatment of electrons and nuclei to continuum description of bulk deformation or velocity. Many challenges of interfacing between scales have been overcome. Multiple models at different scales have been used to study the same system or calculate the same property (e.g., channel conductance). Accurate modeling of biochemical processes under in vivo conditions and the bridging of molecular and subcellular scales will likely soon become reality.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
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27
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Cermelli P, Indelicato G, Twarock R. Nonicosahedral pathways for capsid expansion. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:032710. [PMID: 24125297 DOI: 10.1103/physreve.88.032710] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 06/26/2013] [Indexed: 06/02/2023]
Abstract
For a significant number of viruses a structural transition of the protein container that encapsulates the viral genome forms an important part of the life cycle and is a prerequisite for the particle becoming infectious. Despite many recent efforts the mechanism of this process is still not fully understood, and a complete characterization of the expansion pathways is still lacking. We present here a coarse-grained model that captures the essential features of the expansion process and allows us to investigate the conditions under which a viral capsid becomes unstable. Based on this model we demonstrate that the structural transitions in icosahedral viral capsids are likely to occur through a low-symmetry cascade of local expansion events spreading in a wavelike manner over the capsid surface.
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Affiliation(s)
- Paolo Cermelli
- Dipartimento di Matematica, Università di Torino, Torino, Italy
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28
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Lošdorfer Božič A, Šiber A, Podgornik R. Statistical analysis of sizes and shapes of virus capsids and their resulting elastic properties. J Biol Phys 2013; 39:215-28. [PMID: 23860870 DOI: 10.1007/s10867-013-9302-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 01/20/2013] [Indexed: 01/04/2023] Open
Abstract
From the analysis of sizes of approximately 130 small icosahedral viruses we find that there is a typical structural capsid protein, having a mean diameter of 5 nm and a mean thickness of 3 nm, with more than two thirds of the analyzed capsid proteins having thicknesses between 2 nm and 4 nm. To investigate whether, in addition to the fairly conserved geometry, capsid proteins show similarities in the way they interact with one another, we examined the shapes of the capsids in detail. We classified them numerically according to their similarity to sphere and icosahedron and an interpolating set of shapes in between, all of them obtained from the theory of elasticity of shells. In order to make a unique and straightforward connection between an idealized, numerically calculated shape of an elastic shell and a capsid, we devised a special shape fitting procedure, the outcome of which is the idealized elastic shape fitting the capsid best. Using such a procedure we performed statistical analysis of a series of virus shapes and we found similarities between the capsid elastic properties of even very different viruses. As we explain in the paper, there are both structural and functional reasons for the convergence of protein sizes and capsid elastic properties. Our work presents a specific quantitative scheme to estimate relatedness between different proteins based on the details of the (quaternary) shape they form (capsid). As such, it may provide an information complementary to the one obtained from the studies of other types of protein similarity, such as the overall composition of structural elements, topology of the folded protein backbone, and sequence similarity.
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Affiliation(s)
- Anže Lošdorfer Božič
- Department of Theoretical Physics, Jožef Stefan Institute, 1000, Ljubljana, Slovenia.
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Snijder J, Ivanovska I, Baclayon M, Roos W, Wuite G. Probing the impact of loading rate on the mechanical properties of viral nanoparticles. Micron 2012; 43:1343-50. [DOI: 10.1016/j.micron.2012.04.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 04/19/2012] [Accepted: 04/20/2012] [Indexed: 01/06/2023]
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30
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Abstract
Complex biological systems are intimately linked to their environment, a very crowded and equally complex solution compartmentalized by fluid membranes. Modeling such systems remains challenging and requires a suitable representation of these solutions and their interfaces. Here, we focus on particle-based modeling at an atomistic level using molecular dynamics (MD) simulations. As an example, we discuss important steps in modeling the solution chemistry of an ion channel of the ligand-gated ion channel receptor family, a major target of many drugs including anesthetics and addiction treatments. The bacterial pentameric ligand-gated ion channel (pLGIC) called GLIC provides clues about the functional importance of solvation, in particular for mechanisms such as permeation and gating. We present some current challenges along with promising novel modeling approaches.
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