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Biophysical Reviews

, Volume 2, Issue 3, pp 137–145 | Cite as

A short survey on protein blocks

  • Agnel Praveen Joseph
  • Garima Agarwal
  • Swapnil Mahajan
  • Jean-Christophe Gelly
  • Lakshmipuram S. Swapna
  • Bernard Offmann
  • Frédéric Cadet
  • Aurélie Bornot
  • Manoj Tyagi
  • Hélène Valadié
  • Bohdan Schneider
  • Catherine Etchebest
  • Narayanaswamy Srinivasan
  • Alexandre G. de Brevern
Review

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 

Notes

Acknowledgments

The authors would like to thank the reviewers for their comments that help improve the manuscript. The research was supported by grants from the French Ministry of Research, University of Paris Diderot–Paris 7, University of Saint-Denis de la Réunion, French National Institute for Blood Transfusion (INTS), French Institute for Health and Medical Research (INSERM), and Indian Department of Biotechnology. APJ and GA are supported by CEFIPRA number 3903-E and Council of Scientific and Industrial Research, respectively. AB had a grant from the French Ministry of Research, MT has a post-doctoral fellowship from NIH, and HV had a post-doctoral fellowship from CEA. NS and AdB acknowledge CEFIPRA for collaborative grant (number 3903-E). BS and AdB acknowledge Partenariat Hubert Curien Barrande (2010–2011). BS is supported by grant AV0Z50520701.

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Copyright information

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

Authors and Affiliations

  • Agnel Praveen Joseph
    • 1
    • 2
    • 3
  • Garima Agarwal
    • 4
  • Swapnil Mahajan
    • 4
    • 5
  • Jean-Christophe Gelly
    • 1
    • 2
    • 3
  • Lakshmipuram S. Swapna
    • 4
  • Bernard Offmann
    • 6
    • 7
  • Frédéric Cadet
    • 6
    • 7
  • Aurélie Bornot
    • 1
    • 2
    • 3
  • Manoj Tyagi
    • 8
  • Hélène Valadié
    • 9
  • Bohdan Schneider
    • 10
  • Catherine Etchebest
    • 1
    • 2
    • 3
  • Narayanaswamy Srinivasan
    • 4
  • Alexandre G. de Brevern
    • 1
    • 2
    • 3
  1. 1.Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)Université Paris Diderot Paris 7Paris Cedex 15France
  2. 2.Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)INSERM, UMR-S 665Paris Cedex 15France
  3. 3.Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)Institut National de la Transfusion Sanguine (INTS)Paris Cedex 15France
  4. 4.Molecular Biophysics UnitIndian Institute of ScienceBangaloreIndia
  5. 5.National Centre for Biological SciencesTata Institute of Fundamental ResearchBangaloreIndia
  6. 6.INSERM, UMR-S 665Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB)Saint Denis Messag Cedex 09La RéunionFrance
  7. 7.Faculté des Sciences et TechnologiesUniversité de La RéunionSaint Denis Messag Cedex 09La RéunionFrance
  8. 8.Computational Biology Branch, National Center for Biotechnology Information (NCBI)National Library of Medicine (NLM)BethesdaUSA
  9. 9.UMR 5168 CNRS–CEA–INRA–Université Joseph FourierInstitut de Recherches en Technologies et Sciences pour le VivantGrenoble Cedex 9France
  10. 10.Institute of Biotechnology AS CRPragueCzech Republic

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