title: The mechanism of antiparallel β-sheet formation based on conditioned self-avoiding walk.
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.
authors.affiliation: Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.
authors.forename: Boon Chong
authors.initials: BC
authors.lastname: Goh
authors.forename: Hon Wai
authors.initials: HW
authors.lastname: Leong
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Qu
authors.forename: Lock Yue
authors.initials: LY
authors.lastname: Chew
mesh_terms: D003198:Computer Simulation; D004735:Energy Transfer; D005740:Gases / Q000737:chemistry; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary
chemical_list: D005740:Gases; D010455:Peptides; C019529:polyalanine