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
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.
Key words: Living systems: Structure and Function
© EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg, 2012