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)

2010 ◽  
Vol 28 (11) ◽  
pp. 2109-2118 ◽  
Author(s):  
Shuling Chen ◽  
Zhongzhi Yang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Mechanics ◽  
Protein G ◽  
Electronegativity Equalization ◽  
Electronegativity Equalization Method ◽  
Dynamics Simulations ◽  
Atom Bond ◽  
Equalization Method

STUDY ON COMPLEXES OF TRYPSIN AND ITS INHIBITORS BY MEANS OF ATOM-BOND ELECTRONEGATIVITY EQUALIZATION METHOD FUSED INTO MOLECULAR MECHANICS (ABEEM/MM)

2007 ◽  
Vol 06 (04) ◽  
pp. 731-746 ◽  
Author(s):  
QING-MEI GUAN ◽  
ZHONG-ZHI YANG
Keyword(s):  
Hydrogen Bond ◽  
Bond Length ◽  
Molecular Mechanics ◽  
Trypsin Inhibitor ◽  
Electrostatic Interactions ◽  
Hydrogen Atoms ◽  
Electronegativity Equalization ◽  
Electronegativity Equalization Method ◽  
Atom Bond ◽  
Equalization Method

Trypsin is one of the most important enzymes and plays important roles in the regulation of biological processes. The newly developed trypsin–inhibitor interaction potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) was employed to study complexes of trypsin and its inhibitors. Some structural properties, including root-mean-square deviations (RMSD) of bond length, bond angle and key dihedral, and coordinated RMS Shifts of atoms and hydrogen bond, were studied using ABEEM/MM method and compared with OPLS-AA force-field. At the same time, comparative study on the charges of the hydrogen atoms at the tail of the ligand was also discussed in order to investigate the effect of hydrogen bond between trypsin and its ligand. This work demonstrates that ABEEM/MM model can well reproduce good structures for these trypsin–inhibitor complexes with rather small RMSD of bond length, bond angles, key dihedrals, and RMS Shifts of atomic coordinates with respect to the experimental crystal structures, compared with the results from the OPLS-AA method. The charges obtained by ABEEM/MM model are in good accordance with those from an ab initio calculation. Moreover, both the polarization and the salt-bridge effects have been taken into account. It is shown that ABEEM charges can properly describe the electrostatic interactions between the protein trypsin and its inhibitors.

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