Biophysical Reviews

, Volume 2, Issue 3, pp 137–145

A short survey on protein blocks

Authors

  • Agnel Praveen Joseph
    • Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)Université Paris Diderot Paris 7
    • Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)INSERM, UMR-S 665
    • Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)Institut National de la Transfusion Sanguine (INTS)
  • Garima Agarwal
    • Molecular Biophysics UnitIndian Institute of Science
  • Swapnil Mahajan
    • Molecular Biophysics UnitIndian Institute of Science
    • National Centre for Biological SciencesTata Institute of Fundamental Research
  • Jean-Christophe Gelly
    • Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)Université Paris Diderot Paris 7
    • Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)INSERM, UMR-S 665
    • Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)Institut National de la Transfusion Sanguine (INTS)
  • Lakshmipuram S. Swapna
    • Molecular Biophysics UnitIndian Institute of Science
  • Bernard Offmann
    • INSERM, UMR-S 665Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)
    • Faculté des Sciences et TechnologiesUniversité de La Réunion
  • Frédéric Cadet
    • INSERM, UMR-S 665Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)
    • Faculté des Sciences et TechnologiesUniversité de La Réunion
  • Aurélie Bornot
    • Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)Université Paris Diderot Paris 7
    • Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)INSERM, UMR-S 665
    • Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)Institut National de la Transfusion Sanguine (INTS)
  • Manoj Tyagi
    • Computational Biology Branch, National Center for Biotechnology Information (NCBI)National Library of Medicine (NLM)
  • Hélène Valadié
    • UMR 5168 CNRS–CEA–INRA–Université Joseph FourierInstitut de Recherches en Technologies et Sciences pour le Vivant
  • Bohdan Schneider
    • Institute of Biotechnology AS CR
  • Catherine Etchebest
    • Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)Université Paris Diderot Paris 7
    • Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)INSERM, UMR-S 665
    • Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)Institut National de la Transfusion Sanguine (INTS)
  • Narayanaswamy Srinivasan
    • Molecular Biophysics UnitIndian Institute of Science
    • Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)Université Paris Diderot Paris 7
    • Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)INSERM, UMR-S 665
    • Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)Institut National de la Transfusion Sanguine (INTS)
Review

DOI: 10.1007/s12551-010-0036-1

Cite this article as:
Joseph, A.P., Agarwal, G., Mahajan, S. et al. Biophys Rev (2010) 2: 137. doi:10.1007/s12551-010-0036-1

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 structuresSecondary structuresStructural alphabetStructure predictionStructural superimpositionMutationBinding site

Copyright information

© International Union for Pure and Applied Biophysics (IUPAB) and Springer 2010