Eur. Phys. J. E (2012) 35: 27
https://doi.org/10.1140/epje/i2012-12027-8

Regular Article

The mechanism of antiparallel β-sheet formation based on conditioned self-avoiding walk

¹ Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore, Singapore
² High Performance Computing Centre, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore, Singapore

^* e-mail: lockyue@ntu.edu.sg

Received: 20 December 2011
Revised: 10 February 2012
Accepted: 28 March 2012
Published online: 18 April 2012

Abstract

By introducing an additional hydrogen bond to hydrogen bond interaction in the force field of the CSAW (Conditioned Self-Avoiding Walk) model, we investigate into the mechanism of antiparallel β-sheet formation based on the folding of a short polyalanine in gas phase. Through our numerical simulation, we detect the possible presence of a transient helix during β-sheet formation, whose presence is shown to have slowed the formation of β-sheets by an order of magnitude. While we observe the mechanisms of nucleation, zipping and induction that drives the formation of a β-sheet, we uncover a new mechanism that involves transient β-turns and short β-sheets during the formation of long β-sheets. Our results have enabled us to provide an overview on the mechanisms of β-sheet formation via two main folding pathways: slow folding through the intermediate state of transient helix, and fast folding from the nucleation of β-turn.