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      Self-assembly of model proteins into virus capsids

      research-article
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      Journal of Physics
      IOP Publishing
      virus capsids, aggregation, structure-based models, proteins

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          Abstract

          We consider self-assembly of proteins into a virus capsid by the methods of molecular dynamics. The capsid corresponds either to SPMV or CCMV and is studied with and without the RNA molecule inside. The proteins are flexible and described by the structure-based coarse-grained model augmented by electrostatic interactions. Previous studies of the capsid self-assembly involved solid objects of a supramolecular scale, e.g. corresponding to capsomeres, with engineered couplings and stochastic movements. In our approach, a single capsid is dissociated by an application of a high temperature for a variable period and then the system is cooled down to allow for self-assembly. The restoration of the capsid proceeds to various extent, depending on the nature of the dissociated state, but is rarely complete because some proteins depart too far unless the process takes place in a confined space.

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          Most cited references49

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          Protein folding in the cell.

          In the cell, as in vitro, the final conformation of a protein is determined by its amino-acid sequence. But whereas some isolated proteins can be denatured and refolded in vitro in the absence of other macromolecular cellular components, folding and assembly of polypeptides in vivo involves other proteins, many of which belong to families that have been highly conserved during evolution.
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            Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo-electron microscopy.

            RNA-protein interactions stabilize many viruses and also the nucleoprotein cores of enveloped animal viruses (e.g. retroviruses). The nucleoprotein particles are frequently pleomorphic and generally unstable due to the lack of strong protein-protein interactions in their capsids. Principles governing their structures are unknown because crystals of such nucleoprotein particles that diffract to high resolution have not previously been produced. Cowpea chlorotic mottle virions (CCMV) are typical of particles stabilized by RNA-protein interactions and it has been found that crystals that diffract beyond 4.5 A resolution are difficult to grow. However, we report here the purification of CCMV with an exceptionally mild procedure and the growth of crystals that diffract X-rays to 3.2 A resolution. The 3.2 A X-ray structure of native CCMV, an icosahedral (T = 3) RNA plant virus, shows novel quaternary structure interactions based on interwoven carboxyterminal polypeptides that extend from canonical capsid beta-barrel subunits. Additional particle stability is provided by intercapsomere contacts between metal ion mediated carboxyl cages and by protein interactions with regions of ordered RNA. The structure of a metal-free, swollen form of the virus was determined by cryo-electron microscopy and image reconstruction. Modeling of this structure with the X-ray coordinates of the native subunits shows that the 29 A radial expansion is due to electrostatic repulsion at the carboxyl cages and is stopped short of complete disassembly by preservation of interwoven carboxyl termini and protein-RNA contacts. The CCMV capsid displays quaternary structural interactions that are unique compared with previously determined RNA virus structures. The loosely coupled hexamer and pentamer morphological units readily explain their versatile reassembly properties and the pH and metal ion dependent polymorphism observed in the virions. Association of capsomeres through inter-penetrating carboxy-terminal portions of the subunit polypeptides has been previously described only for the DNA tumor viruses, SV40 and polyoma.
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              Is Open Access

              VIPERdb2: an enhanced and web API enabled relational database for structural virology

              VIPERdb (http://viperdb.scripps.edu) is a relational database and a web portal for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the virology community, with an emphasis on the description and comparison of derived data from structural and computational analyses of the virus capsids. In the current release, VIPERdb2, we implemented a useful and novel method to represent capsid protein residues in the icosahedral asymmetric unit (IAU) using azimuthal polar orthographic projections, otherwise known as Φ–Ψ (Phi–Psi) diagrams. In conjunction with a new Application Programming Interface (API), these diagrams can be used as a dynamic interface to the database to map residues (categorized as surface, interface and core residues) and identify family wide conserved residues including hotspots at the interfaces. Additionally, we enhanced the interactivity with the database by interfacing with web-based tools. In particular, the applications Jmol and STRAP were implemented to visualize and interact with the virus molecular structures and provide sequence–structure alignment capabilities. Together with extended curation practices that maintain data uniformity, a relational database implementation based on a schema for macromolecular structures and the APIs provided will greatly enhance the ability to do structural bioinformatics analysis of virus capsids.
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                Author and article information

                Journal
                J Phys Condens Matter
                J Phys Condens Matter
                cm
                JCOMEL
                Journal of Physics
                IOP Publishing
                0953-8984
                1361-648X
                29 November 2017
                7 November 2017
                : 29
                : 47
                : 474003
                Affiliations
                Institute of Physics, Polish Academy of Sciences , Al. Lotników 32/46, 02-668 Warsaw, Poland mc@ 123456ifpan.edu.pl
                Author information
                https://orcid.org/0000-0002-9439-7277
                Article
                cmaa9351 aa9351 JPCM-109749.R2
                10.1088/1361-648X/aa9351
                7104874
                29027904
                52c547e9-eaf0-4f60-ae60-28e6611d77d5
                © 2017 IOP Publishing Ltd

                This article is made available via the PMC Open Access Subset for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.

                History
                : 10 July 2017
                : 29 September 2017
                : 13 October 2017
                Page count
                Pages: 14
                Funding
                Funded by: European Framework Programme VII NMP
                Award ID: 604530-2 (CellulosomePlus)
                Funded by: Narodowe Centrum Nauki https://doi.org/10.13039/501100004281
                Award ID: 2014/15/B/ST3/01905
                Award ID: 2015/19/P/ST3/03541
                Funded by: European Union’s Horion 2020
                Award ID: 665778
                Categories
                Paper
                Special Issue on Viral Capsids
                Custom metadata
                1361-648X/17/474003+14$33.00
                Printed in the UK
                yes

                virus capsids,aggregation,structure-based models,proteins

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