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Proteins. 2014 Jan;82(1):90-102. doi: 10.1002/prot.24373. Epub 2013 Sep 10.

Right- and left-handed three-helix proteins. II. Similarity and differences in mechanical unfolding of proteins.

Author information

1
Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.

Abstract

Here, we study mechanical properties of eight 3-helix proteins (four right-handed and four left-handed ones), which are similar in size under stretching at a constant speed and at a constant force on the atomic level using molecular dynamics simulations. The analysis of 256 trajectories from molecular dynamics simulations with explicit water showed that the right-handed three-helix domains are more mechanically resistant than the left-handed domains. Such results are observed at different extension velocities studied (192 trajectories obtained at the following conditions: v = 0.1, 0.05, and 0.01 Å ps(-1) , T = 300 K) and under constant stretching force (64 trajectories, F = 800 pN, T = 300 K). We can explain this by the fact, at least in part, that the right-handed domains have a larger number of contacts per residue and the radius of cross section than the left-handed domains.

KEYWORDS:

explicit model of water; handedness; intermediate state; mechanical unfolding pathway; molecular dynamics; number of contacts

PMID:
23873665
DOI:
10.1002/prot.24373
[Indexed for MEDLINE]

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