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Molecular Dynamics Simulations of a β ‐Hairpin Fragment of Protein G by Means of Atom‐Bond Electronegativity Equalization Method Fused into Molecular Mechanics (ABEEMδπ/MM)
Author(s) -
Chen Shuling,
Yang Zhongzhi
Publication year - 2010
Publication title -
chinese journal of chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.28
H-Index - 41
eISSN - 1614-7065
pISSN - 1001-604X
DOI - 10.1002/cjoc.201090350
Subject(s) - chemistry , molecular dynamics , hydrogen bond , force field (fiction) , chemical physics , folding (dsp implementation) , protein folding , computational chemistry , implicit solvation , hydrophobic effect , solvation , thermodynamics , molecule , organic chemistry , biochemistry , artificial intelligence , computer science , electrical engineering , engineering , physics
There are some controversial opinions about the origin of folding β ‐hairpin stability in aqueous solution. In this study, the structural and dynamic behavior of a 16‐residue β ‐hairpin from B1 domain of protein G has been investigated at 280, 300, 350 and 450 K using molecular dynamics (MD) simulations by means of Atom‐Bond Electronegativity Equalization Method Fused into Molecular Mechanics i.e ., ABEEMδπ/MM and the explicit ABEEM‐7P water solvent model. In addition, a 300 K simulation of one mutant having the aromatic residues substituted with alanines has been performed. The hydrophobic surface area, hydrophilic surface area and some structural properties have been used to measure the role of the hydrophobic interactions. It is found that the aromatic residues substituted with alanines have shown an evident destabilization of the structure and unfolding started after 1.5 ns. It is also found that the number of the main chain hydrogen bonds have different distributions through three different simulations. All above demonstrate that the hydrophobic interactions and the main chain hydrogen bonds play an important role in the stability of the folding structure of β ‐hairpin in solution. Furthermore, through the structural analyses of the β ‐hairpin structures from four temperature simulations and the comparison with other MD simulations of β ‐hairpin peptides, the new ABEEMδπ force field can reproduce the structural data in good agreement with the experimental data.