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Advances in Bioinformatics
Volume 2011 (2011), Article ID 176813, 8 pages
http://dx.doi.org/10.1155/2011/176813
Research Article

Cotranslational Protein Folding and Terminus Hydrophobicity

Department of Statistics, Macquarie University, Sydney, NSW 2109, Australia

Received 27 December 2010; Revised 28 February 2011; Accepted 24 March 2011

Academic Editor: Huixiao Hong

Copyright © 2011 Sheenal Srivastava et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Peptides fold on a time scale that is much smaller than the time required for synthesis, whence all proteins potentially fold cotranslationally to some degree (followed by additional folding events after release from the ribosome). In this paper, in three different ways, we find that cotranslational folding success is associated with higher hydrophobicity at the N-terminus than at the C-terminus. First, we fold simple HP models on a square lattice and observe that HP sequences that fold better cotranslationally than from a fully extended state exhibit a positive difference (N−C) in terminus hydrophobicity. Second, we examine real proteins using a previously established measure of potential cotranslationality known as ALR (Average Logarithmic Ratio of the extent of previous contacts) and again find a correlation with the difference in terminus hydrophobicity. Finally, we use the cotranslational protein structure prediction program SAINT and again find that such an approach to folding is more successful for proteins with higher N-terminus than C-terminus hydrophobicity. All results indicate that cotranslational folding is promoted in part by a hydrophobic start and a less hydrophobic finish to the sequence.