Enhanced molecular dynamics simulation of the transformation between α-helix and β-hairpin structures for peptide

ABSTRACT

Here, we investigated the secondary structure transformation for a design peptide, which has both the α-helix (PDB ID code 2DX3) and β-hairpin (PDB ID code 2DX4) structures in aqueous solution. We show that the transformation between α-helix and β-hairpin structures can be sampled efficiently using the enhanced sampling method based on integrated tempering without the definition of reaction coordinates. The reliable and smooth two-dimensional potential of mean force surfaces of the conformation space can be obtained efficiently, which has been used to propose the probable pathways for the transformation of the α-helix and β-hairpin structures. Our simulation results revealed the efficiency, and further suggested the general applicability of integrated tempering sampling method into complex biomolecule processes without prior structure knowledge.

KEYWORDS:

• Secondary structure transformation
• α-helix
• β-hairpin
• MD simulation
• ITS

Acknowledgments

We would like to thank Dr Hao Hu for providing significant comments to the paper. We are also grateful for insightful discussions with Dr Mingjun Yang.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This research was sponsored by the HKU strategy research themes on the topics of ‘Clean Energy’ and the HKU Small Project Funding [grant number 201309176150] to Zhe-Ning Chen.