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Cis–trans isomerization of omega dihedrals in proteins

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Abstract

Peptide bonds in protein structures are mainly found in trans conformation with a torsion angle ω close to 180°. Only a very low proportion is observed in cis conformation with ω angle around 0°. Cis–trans isomerization leads to local conformation changes which play an important role in many biological processes. In this paper, we reviewed the recent discoveries and research achievements in this field. First, we presented some interesting cases of biological processes in which cis–trans isomerization is directly implicated. It is involved in protein folding and various aspect of protein function like dimerization interfaces, autoinhibition control, channel gating, membrane binding. Then we reviewed conservation studies of cis peptide bonds which emphasized evolution constraints in term of sequence and local conformation. Finally we made an overview of the numerous molecular dynamics studies and prediction methodologies already developed to take into account this structural feature in the research area of protein modeling. Many cis peptide bonds have not been recognized as such due to the limited resolution of the data and to the refinement protocol used. Cis–trans proline isomerization reactions represents a vast and promising research area that still needs to be further explored for a better understanding of isomerization mechanism and improvement of cis peptide bond predictions.

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Acknowledgments

This work was supported by grants from the Ministry of Research (France), University Paris Diderot, Sorbonne Paris Cité (France), National Institute for Blood Transfusion (INTS, France), National Institute for Health and Medical Research (INSERM, France) and “Investissements d’avenir”, Laboratories of Excellence GR-Exto APJ, PC, JR and AdB, (France);HFSP to APJ; and ANR NaturaDyRe (France, ANR-2010-CD2I-014-04) to JR.

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The authors declare that they have no conflict of interest.

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  1. Pierre Poulain

    Present address: , Ets Poulain, Pointe-Noire, Congo

Authors and Affiliations

  1. INSERM UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Université Denis Diderot–Paris 7, INTS, 6, rue Alexandre Cabanel, 75739, Paris cedex 15, France

    Pierrick Craveur, Pierre Poulain, Alexandre G. de Brevern & Joseph Rebehmed

  2. Univ. Paris Diderot, Sorbonne Paris Cité, UMR-S 665, 75739, Paris, France

    Pierrick Craveur, Pierre Poulain, Alexandre G. de Brevern & Joseph Rebehmed

  3. Institut National de la Transfusion Sanguine (INTS), 75739, Paris, France

    Pierrick Craveur, Pierre Poulain, Alexandre G. de Brevern & Joseph Rebehmed

  4. Laboratoire d’Excellence GR-Ex, 75739, Paris, France

    Pierrick Craveur, Pierre Poulain, Alexandre G. de Brevern & Joseph Rebehmed

  5. National Centre for Biological Sciences, UAS-GKVK Campus, Bellary Road, Bangalore, 560 065, Karnataka, India

    Agnel Praveen Joseph

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Correspondence to Alexandre G. de Brevern or Joseph Rebehmed.

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P. Craveur and A. Praveen Joseph contributed equally.

A. G. de Brevern and J. Rebehmed contributed equally.

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Craveur, P., Joseph, A.P., Poulain, P. et al. Cis–trans isomerization of omega dihedrals in proteins. Amino Acids 45, 279–289 (2013). https://doi.org/10.1007/s00726-013-1511-3

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