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Int J Mol Sci. 2012;13(2):1720-32. doi: 10.3390/ijms13021720. Epub 2012 Feb 7.

The effect of C-terminal helix on the stability of FF domain studied by molecular dynamics simulation.

Author information

  • 1Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Dezhou University, 566 University Rd. West, Dezhou 253023, China; E-Mails: zhaoll@dzu.edu.cn (L.Z.); qiayilai@mail.ustc.edu.cn (Z.C.).

Abstract

To investigate the effect of C-terminal helix on the stability of the FF domain, we studied the native domain FF3-71 from human HYPA/FBP11 and the truncated version FF3-60 with C-terminal helix being deleted by molecular dynamics simulations with GROMACS package and GROMOS 43A1 force field. The results indicated that the structures of truncated version FF3-60 were evident different from those of native partner FF3-71. Compared with FF3-71, the FF3-60 lost some native contacts and exhibited some similar structural characters to those of intermediate state. The C-terminal helix played a major role in stabilizing the FF3-71 domain. To a certain degree, the FF domain had a tendency to form an intermediate state without the C-terminal helix. In our knowledge, this was the first study to examine the role of C-terminal helix of FF domain in detail by molecular dynamics simulations, which was useful to understand the three-state folding mechanism of the small FF domain.

KEYWORDS:

C-terminal helix; FF domain; intermediate state; molecular dynamics simulation; structural stability

PMID:
22408419
[PubMed - in process]
PMCID:
PMC3291988
Free PMC Article
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