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Protein flexibility in the light of structural alphabets
P. Craveur, AP. Joseph, J. Esque, TJ. Narwani, F. Noël, N. Shinada, M. Goguet, S. Leonard, P. Poulain, O. Bertrand, G. Faure, J. Rebehmed, A. Ghozlane, LS. Swapna, RM. Bhaskara, J. Barnoud, S. Téletchéa, V. Jallu, J. Cerny, B. Schneider, C....
Language English Country Switzerland
Document type Journal Article, Review
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- Publication type
- Journal Article MeSH
- Review MeSH
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.
Department of Theoretical Biophysics Max Planck Institute of Biophysics Frankfurt Germany
Ets Poulain Pointe Noire Congo
Institut National de la Santé et de la Recherche Médicale U 1134 Paris France
Institut National de la Transfusion Sanguine DSIMB Paris France
Institute of Biotechnology The Czech Academy of Sciences Prague Czech Republic
Metagenopolis INRA Jouy en Josas France
Molecular Biophysics Unit Indian Institute of Science Bangalore Bangalore India
Platelet Unit Institut National de la Transfusion Sanguine Paris France
Rutherford Appleton Laboratory Science and Technology Facilities Council Didcot UK
UMR_S 1134 DSIMB Laboratory of Excellence GR Ex Paris France
UMR_S 1134 DSIMB Université Paris Diderot Sorbonne Paris Cite Paris France
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