The mechanism of antiparallel β-sheet formation based on conditioned self-avoiding walk
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 simulatio...
Saved in:
| Main Authors: | , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
2013
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/99307 http://hdl.handle.net/10220/16223 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Institution: | Nanyang Technological University |
| Language: | English |
| Summary: | 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. |
|---|