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Influence of assignment on the prediction of transmembrane helices in protein structures

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Abstract

α-Helical transmembrane proteins (TMPα) are composed of a series of helices embedded in the lipid bilayer. Due to technical difficulties, few 3D structures are available. Therefore, the design of structural models of TMPα is of major interest. We study the secondary structures of TMPα by analyzing the influence of secondary structures assignment methods (SSAMs). For this purpose, a published and updated benchmark databank of TMPα is used and several SSAMs (9) are evaluated. The analysis of the results points to significant differences in SSA depending on the methods used. Pairwise comparisons between SSAMs led to more than 10% of disagreement. Helical regions corresponding to transmembrane zones are often correctly characterized. The study of the sequence–structure relationship shows very limited differences with regard to the structural disagreement. Secondary structure prediction based on Bayes’ rule and using only a single sequence give correct prediction rates ranging from 78 to 81%. A structural alphabet approach gives a slightly better prediction, i.e., only 2% less than the best equivalent approach, whereas the prediction rate with a very different assignment bypasses 86%. This last result highlights the importance of the correct assignment choice to evaluate the prediction assessment.

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Abbreviations

PDB:

Protein DataBank

SSAM:

Secondary structure assignment method

DSSP:

Dictionary secondary structure protein

TMPα :

α-Helical transmembrane proteins

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Acknowledgments

The authors would like to thank the reviewers for their comments that helped improving the manuscript. They also thank Aurélie Urbain for her help in designing the new updated databank. This work was supported by grants from the Ministère de la Recherche, Université Paris Diderot-Paris 7, National Institute for Blood Transfusion (INTS) and National Institute for Health and Medical Research (INSERM). AB had a grant from the Ministère de la Recherche. AdB was also supported by an Indo-French collaborative grant (grant from CEFIPRA number 3903-E).

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  1. INSERM UMR-S 726, Equipe de Bioinformatique Génomique et Moléculaire (EBGM), DSIMB, Université Paris Diderot-Paris 7, case 7113, 2, place Jussieu, 75251, Paris, France

    Jean Pylouster, Aurélie Bornot, Catherine Etchebest & Alexandre G. de Brevern

  2. Régulation et dynamique des génomes, Laboratoire de Biophysique, MNHN, UMR CNRS INSERM 5153, 43 rue Cuvier, 75231, Paris Cedex 05, France

    Jean Pylouster

  3. INSERM UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Université Paris Diderot-Paris 7, Institut National de Transfusion Sanguine (INTS), 6, rue Alexandre Cabanel, 75739, Paris Cedex 15, France

    Aurélie Bornot, Catherine Etchebest & Alexandre G. de Brevern

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  1. Jean Pylouster
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  2. Aurélie Bornot
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  3. Catherine Etchebest
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  4. Alexandre G. de Brevern
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Corresponding author

Correspondence to Alexandre G. de Brevern.

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Pylouster, J., Bornot, A., Etchebest, C. et al. Influence of assignment on the prediction of transmembrane helices in protein structures. Amino Acids 39, 1241–1254 (2010). https://doi.org/10.1007/s00726-010-0559-6

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  • DOI: https://doi.org/10.1007/s00726-010-0559-6

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