Journal article
Helix unfolding and intramolecular hydrogen bond dynamics in small α-helices in explicit solvent
Journal of Physical Chemistry B, Vol.106(41), pp.10748-10752
2002
DOI: 10.1021/jp0205158
Abstract
The dynamics of folding and unfolding of secondary structural motifs found in proteins is crucial to understanding the protein folding problem. In this paper we study the short-time dynamics of loop unfolding and hydrogen bond formation and breaking in the alanine pentapeptide at room temperature, using several constant-energy molecular dynamics simulations of about 4 ns of duration. We analyze the results in terms of time histories of “core” α-carbon dihedral angles. We also perform a principal component analysis of the data. We find that the time scale for a considerable deformation of the dihedral angles formed by the α-carbons is on the order of 1 ns whereas hydrogen bonds seem to break and form on a shorter time scale.
Details
- Title: Subtitle
- Helix unfolding and intramolecular hydrogen bond dynamics in small α-helices in explicit solvent
- Creators
- C. J MargulisH. A SternB. J Berne
- Resource Type
- Journal article
- Publication Details
- Journal of Physical Chemistry B, Vol.106(41), pp.10748-10752
- DOI
- 10.1021/jp0205158
- ISSN
- 1089-5647
- eISSN
- 1520-5207
- Language
- English
- Date published
- 2002
- Academic Unit
- Chemistry
- Record Identifier
- 9983985819702771
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