The European Physical Journal E

, 35:27

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

  • Boon Chong Goh
  • Hon Wai Leong
  • Xiaohui Qu
  • Lock Yue Chew
Regular Article

DOI: 10.1140/epje/i2012-12027-8

Cite this article as:
Goh, B.C., Leong, H.W., Qu, X. et al. Eur. Phys. J. E (2012) 35: 27. doi:10.1140/epje/i2012-12027-8

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.

Keywords

Living systems: Structure and Function

Copyright information

© EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Boon Chong Goh
    • 1
  • Hon Wai Leong
    • 1
    • 2
  • Xiaohui Qu
    • 1
  • Lock Yue Chew
    • 1
  1. 1.Division of Physics and Applied Physics, School of Physical and Mathematical SciencesNanyang Technological UniversitySingaporeSingapore
  2. 2.High Performance Computing CentreNanyang Technological UniversitySingaporeSingapore
  3. 3.Department of PhysicsUniversity of Illinois at Urbana-ChampaignUrbanaUSA