Review

Biophysical Reviews

, Volume 2, Issue 3, pp 137-145

First online:

A short survey on protein blocks

  • Agnel Praveen JosephAffiliated withDynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Université Paris Diderot Paris 7Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), INSERM, UMR-S 665Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Institut National de la Transfusion Sanguine (INTS)
  • , Garima AgarwalAffiliated withMolecular Biophysics Unit, Indian Institute of Science
  • , Swapnil MahajanAffiliated withMolecular Biophysics Unit, Indian Institute of ScienceNational Centre for Biological Sciences, Tata Institute of Fundamental Research
  • , Jean-Christophe GellyAffiliated withDynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Université Paris Diderot Paris 7Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), INSERM, UMR-S 665Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Institut National de la Transfusion Sanguine (INTS)
  • , Lakshmipuram S. SwapnaAffiliated withMolecular Biophysics Unit, Indian Institute of Science
  • , Bernard OffmannAffiliated withINSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)Faculté des Sciences et Technologies, Université de La Réunion
  • , Frédéric CadetAffiliated withINSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)Faculté des Sciences et Technologies, Université de La Réunion
  • , Aurélie BornotAffiliated withDynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Université Paris Diderot Paris 7Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), INSERM, UMR-S 665Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Institut National de la Transfusion Sanguine (INTS)
  • , Manoj TyagiAffiliated withComputational Biology Branch, National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM)
    • , Hélène ValadiéAffiliated withUMR 5168 CNRS–CEA–INRA–Université Joseph Fourier, Institut de Recherches en Technologies et Sciences pour le Vivant
    • , Bohdan SchneiderAffiliated withInstitute of Biotechnology AS CR
    • , Catherine EtchebestAffiliated withDynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Université Paris Diderot Paris 7Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), INSERM, UMR-S 665Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Institut National de la Transfusion Sanguine (INTS)
    • , Narayanaswamy SrinivasanAffiliated withMolecular Biophysics Unit, Indian Institute of Science
    • , Alexandre G. de BrevernAffiliated withDynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Université Paris Diderot Paris 7Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), INSERM, UMR-S 665Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Institut National de la Transfusion Sanguine (INTS) Email author 

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Abstract

Protein structures are classically described in terms of secondary structures. However, even if the regular secondary structures have relevant physical meaning, their recognition based on atomic coordinates has a number of important limitations, such as uncertainties in the assignment of the boundaries of the helical and β-strand regions. In addition, an average of about 50% of all residues are assigned to an irregular state, i.e., the coil. These limitations have led different research teams to focus on abstracting the conformation of the protein backbone in the localized short stretches. To this end, different geometric measures are being used to cluster local stretches in protein structures in a chosen number of states. A prototype representative of the local structures in each cluster is then generally defined. These libraries of local structure prototypes are named "structural alphabets". We have developed a structural alphabet, denoted protein blocks, not only to approximate the protein structure but also to predict them from the sequence. Since its development, we and others have explored numerous new research fields using this structural alphabet. Here, we review some of the most interesting applications of this structural alphabet.

Keywords

Protein structures Secondary structures Structural alphabet Structure prediction Structural superimposition Mutation Binding site