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

• Main Authors: Goh, Boon Chong, Leong, Hon Wai, Qu, Xiaohui, Chew, Lock Yue
• Other Authors: School of Physical and Mathematical Sciences
• Format: Article
• Language: English
• Published: 2013
• Subjects: DRNTU::Science
• Online Access: https://hdl.handle.net/10356/99307; http://hdl.handle.net/10220/16223
• Institution: Nanyang Technological University

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.