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Protein Science (2004), 13:351-357. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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Analysis of forces that determine helix formation in {alpha}-proteins

Gelena T. Kilosanidze1,3,4, Alexey S. Kutsenko1,2,4, Natalia G. Esipova3 and Vladimir G. Tumanyan3

1 Microbiology and Tumor Biology Center and
2 Center for Genomics and Bioinformatics, Karolinska Institute, S-171 77 Stockholm, Sweden
3 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russian Federation

(RECEIVED September 15, 2003; FINAL REVISION October 15, 2003; ACCEPTED October 15, 2003)



Abstract

A model for prediction of {alpha}-helical regions in amino acid sequences has been tested on the mainly-{alpha} protein structure class. The modeling represents the construction of a continuous hypothetical {alpha}-helical conformation for the whole protein chain, and was performed using molecular mechanics tools. The positive prediction of {alpha}-helical and non-{alpha}-helical pentapeptide fragments of the proteins is 79%. The model considers only local interactions in the polypeptide chain without the influence of the tertiary structure. It was shown that the local interaction defines the {alpha}-helical conformation for 85% of the native {alpha}-helical regions. The relative energy contributions to the energy of the model were analyzed with the finding that the van der Waals component determines the formation of {alpha}-helices. Hydrogen bonds remain at constant energy independently whether {alpha}-helix or non-{alpha}-helix occurs in the native protein, and do not determine the location of helical regions. In contrast to existing methods, this approach additionally permits the prediction of conformations of side chains. The model suggests the correct values for ~60% of all {chi}-angles of {alpha}-helical residues.

Keywords: Protein secondary structure; structure prediction; {alpha}-helix; side-chain conformation; {chi}-angles; molecular mechanics

Reprint requests to: Alexey S. Kutsenko, Microbiology and Tumor Biology Center, Karolinska Institute, Box 280, S-171 77 Stockholm, Sweden; e-mail: alekut{at}ki.se; fax: 46 (8) 31-94-70; or Vladimir G. Tumanyan, Engelhardt Institute of Molecular Biology, Vavilova 32, Moscow 119991, Russian Federation; e-mail: tuman{at}imb.ac.ru; fax: 7 (095) 135-1405.

4 These two authors contributed equally to this work.

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.03429104.


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