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

• Main Authors: Jihua Wang, Zanxia Cao, Liling Zhao
• Format: Article
• Language: English
• Published: MDPI AG 2012-02-01
• Series: International Journal of Molecular Sciences
• Subjects: FF domain; molecular dynamics simulation; C-terminal helix; structural stability; intermediate state
• Online Access: http://www.mdpi.com/1422-0067/13/2/1720/

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.