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Int. J. Mol. Sci. 2012, 13(2), 1720-1732; doi:10.3390/ijms13021720
Article

The Effect of C-Terminal Helix on the Stability of FF Domain Studied by Molecular Dynamics Simulation

1,2
,
1,2
 and
1,2,*
Received: 16 December 2011 / Revised: 20 January 2012 / Accepted: 29 January 2012 / Published: 7 February 2012
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
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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: FF domain; molecular dynamics simulation; C-terminal helix; structural stability; intermediate state FF domain; molecular dynamics simulation; C-terminal helix; structural stability; intermediate state
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Zhao, L.; Cao, Z.; Wang, J. The Effect of C-Terminal Helix on the Stability of FF Domain Studied by Molecular Dynamics Simulation. Int. J. Mol. Sci. 2012, 13, 1720-1732.

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