Direct folding simulation of a long helix in explicit water
Zhang, John Z. H.
Date of Issue2013
School of Physical and Mathematical Sciences
A recently proposed Polarizable Hydrogen Bond (PHB) method has been employed to simulate the folding of a 53 amino acid helix (PDB ID 2KHK) in explicit water. Under PHB simulation, starting from a fully extended structure, the peptide folds into the native state as confirmed by measured time evolutions of radius of gyration, root mean square deviation (RMSD), and native hydrogen bond. Free energy and cluster analysis show that the folded helix is thermally stable under the PHB model. Comparison of simulation results under, respectively, PHB and standard nonpolarizable force field demonstrates that polarization is critical for stable folding of this long α-helix.
Applied physics letters
© 2013 AIP Publishing LLC. This paper was published in Applied Physics Letters and is made available as an electronic reprint (preprint) with permission of AIP Publishing LLC. The paper can be found at the following official DOI: [http://dx.doi.org/10.1063/1.4807145]. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law.