Acta Phys. -Chim. Sin. ›› 2006, Vol. 22 ›› Issue (10): 1243-1247.doi: 10.3866/PKU.WHXB20061014

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Modeling of Cyclic Peptides by the ABEEM/MM Fluctuating Charge Force Field

ZHANG Qiang;ZHANG Xia;YANG Zhong-Zhi   

  1. Bohai University, Jinzhou 121000, P. R. China; Liaoning Normal University, Dalian 116029, P. R. China
  • Received:2006-03-09 Revised:2006-05-29 Published:2006-10-11
  • Contact: YANG Zhong-Zhi

Abstract: The ABEEM/MM (atom-bond electronegativity equalization fused into molecular mechanic) fluctuating charge model was applied to simulate five realistic cyclic peptides. In the ABEEM/MM model, comparing to the classical force field with fixed charge electrostatic potential, the partial charges were allowed to fluctuate in the same molecule in response to the environment. The important non-atomic-center charge sites (chemical bond and lone pair) were added into this model to describe the charge population reasonably. The CPU time was not longer than that in other polarized force fields. The relevant structural information was analyzed, such as the root-mean-square deviation of the atomic coordinate shift, the deviation of hydrogen bond lengths and the deviation of dihedral angle of five cyclic peptides from the corresponding experimental data, whose values are 0.009 nm, 0.013 nm, and 5.16° respectively. The ABEEM/MM model could well reproduce the experimental structures of realistic peptides. All in all, the results from the ABEEM/MM model present higher accuracy than those from other force fields. It is proved to be suitable to explore and simulate the realistic protein systems.

Key words: Atom-bond electronegativity equalization fused into molecular mechanic(ABEEM/MM), Cyclic peptides, Polarized force field, Fluctuating charge model, Hydrogen bond