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      Protein flexibility in the light of structural alphabets

      review-article
      1 , 2 , 3 , 4 , 5 , 6 , 1 , 2 , 3 , 4 , 1 , 2 , 3 , 4 , 1 , 2 , 3 , 4 , 1 , 2 , 3 , 4 , 1 , 2 , 3 , 4 , 1 , 2 , 3 , 4 , 7 , 1 , 3 , 4 , 8 , 9 , 10 , 11 , 12 , 11 , 13 , 1 , 2 , 3 , 4 , 14 , 1 , 2 , 3 , 4 , 15 , 16 , 17 , 17 , 1 , 2 , 3 , 4 , 11 , 1 , 2 , 3 , 4 , 1 , 2 , 3 , 4
      Frontiers in Molecular Biosciences
      Frontiers Media S.A.
      protein structures, disorder, secondary structure, structural alphabet, protein folding, allostery, protein complexes, protein—DNA interactions

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          Abstract

          Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases.

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          Why are ?natively unfolded? proteins unstructured under physiologic conditions?

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            PrDOS: prediction of disordered protein regions from amino acid sequence

            PrDOS is a server that predicts the disordered regions of a protein from its amino acid sequence (http://prdos.hgc.jp). The server accepts a single protein amino acid sequence, in either plain text or FASTA format. The prediction system is composed of two predictors: a predictor based on local amino acid sequence information and one based on template proteins. The server combines the results of the two predictors and returns a two-state prediction (order/disorder) and a disorder probability for each residue. The prediction results are sent by e-mail, and the server also provides a web-interface to check the results.
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              Protein disorder prediction: implications for structural proteomics.

              A great challenge in the proteomics and structural genomics era is to predict protein structure and function, including identification of those proteins that are partially or wholly unstructured. Disordered regions in proteins often contain short linear peptide motifs (e.g., SH3 ligands and targeting signals) that are important for protein function. We present here DisEMBL, a computational tool for prediction of disordered/unstructured regions within a protein sequence. As no clear definition of disorder exists, we have developed parameters based on several alternative definitions and introduced a new one based on the concept of "hot loops," i.e., coils with high temperature factors. Avoiding potentially disordered segments in protein expression constructs can increase expression, foldability, and stability of the expressed protein. DisEMBL is thus useful for target selection and the design of constructs as needed for many biochemical studies, particularly structural biology and structural genomics projects. The tool is freely available via a web interface (http://dis.embl.de) and can be downloaded for use in large-scale studies.
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                Author and article information

                Contributors
                URI : http://community.frontiersin.org/people/u/215318
                URI : http://community.frontiersin.org/people/u/238914
                URI : http://community.frontiersin.org/people/u/224201
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                URI : http://community.frontiersin.org/people/u/231390
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                Journal
                Front Mol Biosci
                Front Mol Biosci
                Front. Mol. Biosci.
                Frontiers in Molecular Biosciences
                Frontiers Media S.A.
                2296-889X
                27 May 2015
                2015
                : 2
                : 20
                Affiliations
                [1] 1Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France
                [2] 2UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France
                [3] 3Institut National de la Transfusion Sanguine, DSIMB Paris, France
                [4] 4UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
                [5] 5Rutherford Appleton Laboratory, Science and Technology Facilities Council Didcot, UK
                [6] 6Institut National de la Santé et de la Recherche Médicale U964,7 UMR Centre National de la Recherche Scientifique 7104, IGBMC, Université de Strasbourg Illkirch, France
                [7] 7Ets Poulain Pointe-Noire, Congo
                [8] 8National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health Bethesda, MD, USA
                [9] 9Centre National de la Recherche Scientifique UMR7590, Sorbonne Universités, Université Pierre et Marie Curie – MNHN – IRD – IUC Paris, France
                [10] 10Metagenopolis, INRA Jouy-en-Josas, France
                [11] 11Molecular Biophysics Unit, Indian Institute of Science, Bangalore Bangalore, India
                [12] 12Hospital for Sick Children, and Departments of Biochemistry and Molecular Genetics, University of Toronto Toronto, ON, Canada
                [13] 13Department of Theoretical Biophysics, Max Planck Institute of Biophysics Frankfurt, Germany
                [14] 14Laboratoire de Physique, École Normale Supérieure de Lyon, Université de Lyon, Centre National de la Recherche Scientifique UMR 5672 Lyon, France
                [15] 15Faculté des Sciences et Techniques, Université de Nantes, Unité Fonctionnalité et Ingénierie des Protéines, Centre National de la Recherche Scientifique UMR 6286, Université Nantes Nantes, France
                [16] 16Platelet Unit, Institut National de la Transfusion Sanguine Paris, France
                [17] 17Institute of Biotechnology, The Czech Academy of Sciences Prague, Czech Republic
                Author notes

                Edited by: Kris Pauwels, Vrije Universiteit Brussel, Belgium

                Reviewed by: Mark Pfuhl, King's College London, UK; Elena Papaleo, University of Copenhagen, Denmark

                *Correspondence: Alexandre G. de Brevern, Institut National de la Santé et de la Recherche Médicale U 1134, 6 Rue Alexandre Cabanel, 75015 Paris, France alexandre.debrevern@ 123456univ-paris-diderot.fr

                This article was submitted to Structural Biology, a section of the journal Frontiers in Molecular Biosciences

                Article
                10.3389/fmolb.2015.00020
                4445325
                26075209
                410a93cd-d3ad-475c-b6e3-2561c629c756
                Copyright © 2015 Craveur, Joseph, Esque, Narwani, Noël, Shinada, Goguet, Leonard, Poulain, Bertrand, Faure, Rebehmed, Ghozlane, Swapna, Bhaskara, Barnoud, Téletchéa, Jallu, Cerny, Schneider, Etchebest, Srinivasan, Gelly and de Brevern.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 28 February 2015
                : 30 April 2015
                Page count
                Figures: 11, Tables: 1, Equations: 2, References: 148, Pages: 20, Words: 14788
                Categories
                Molecular Biosciences
                Review

                protein structures,disorder,secondary structure,structural alphabet,protein folding,allostery,protein complexes,protein—dna interactions

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