Structural Symmetry and Protein Function

A special issue of Symmetry (ISSN 2073-8994).

Deadline for manuscript submissions: closed (28 February 2018) | Viewed by 4176

Special Issue Editor


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Guest Editor
Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Roma, Italy
Interests: structural bioinformatics; structural biology; protein evolution; protein variants; protein structure and function; protein structure prediction; protein–protein interaction; protein–ligand interaction; genome biology and evolution
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Special Issue Information

Dear Colleagues,

Symmetry is a pervasive organizing principle of living systems, from the molecular level up to the anatomy level. In fact, symmetry at macroscopic levels is often the effect and the consequence of symmetry at molecular level. This Special Issue would like to collect studies aimed at clarifying the relevance and the influence of protein structural symmetry on biological functions and structures in all organisms. A possible, non-exhaustive list of pertinent arguments includes protein symmetry and function; protein symmetry and molecular evolution; protein symmetry and folding and stability; protein symmetry in molecular diseases; symmetry in protein–protein and protein–DNA interaction; protein symmetry and biological structures (for example virus capsids). Experimental, methodological studies or sound theoretical analyses will be welcome for consideration.

Prof. Dr. Stefano Pascarella
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Symmetry is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Protein symmetry

  • Protein quaternary structure

  • Protein function

  • Protein evolution

  • Protein stability

  • Protein folding

  • Molecular diseases

  • Protein–DNA recognition

  • Protein–Protein interaction

  • Protein engineering

  • Macromolecular assemblies

  • Virus capsid structure

  • Bioinformatics

  • Structural bioinformatics

  • Computational biology

  • Molecular dynamics

  • Structural bioinformatics

  • X-ray protein crystallography

  • NMR protein spectroscopy

  • Electron Microscopy

Published Papers (1 paper)

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Research

13 pages, 1609 KiB  
Article
A Critical Note on Symmetry Contact Artifacts and the Evaluation of the Quality of Homology Models
by Dipali Singh, Karen R. M. Berntsen, Coos Baakman, Gert Vriend and Tapobrata Lahiri
Symmetry 2018, 10(1), 25; https://doi.org/10.3390/sym10010025 - 11 Jan 2018
Cited by 1 | Viewed by 3782
Abstract
It is much easier to determine a protein’s sequence than to determine its three dimensional structure and consequently homology modeling will be an essential aspect of most studies that require 3D protein structure data. Homology modeling templates tend to be PDB files. About [...] Read more.
It is much easier to determine a protein’s sequence than to determine its three dimensional structure and consequently homology modeling will be an essential aspect of most studies that require 3D protein structure data. Homology modeling templates tend to be PDB files. About 88% of all protein structures in the PDB have been determined with X-ray crystallography, and thus are based on crystals that by necessity hold non-natural packing contacts in accordance with the crystal symmetry. Active site residues, residues involved in intermolecular interactions, residues that get post-translationally modified, or other sites of interest, normally are located at the protein surface so that it is particularly important to correctly model surface-located residues. Unfortunately, surface residues are just those that suffer most from crystal packing artifacts. Our study of the influence of crystal packing artifacts on the quality of homology models reveals that this influence is much larger than generally assumed, and that the evaluation of the quality of homology models should properly account for these artifacts. Full article
(This article belongs to the Special Issue Structural Symmetry and Protein Function)
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