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Int. J. Mol. Sci. 2008, 9(9), 1652-1664; doi:10.3390/ijms9091652

Exact and Effective Pair-Wise Potential for Protein-Ligand Interactions Obtained from a Semiempirical Energy Partition

1
REQUIMTE/Department of Chemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
2
DEMEGI, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal
*
Author to whom correspondence should be addressed.
Received: 14 February 2008 / Revised: 28 July 2008 / Accepted: 28 August 2008 / Published: 2 September 2008
(This article belongs to the Special Issue The Chemical Bond and Bonding)
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Abstract

In this work, the partition method introduced by Carvalho and Melo was used to study the complex between Cucurbita maxima trypsin inhibitor (CMTI-I) and glycerol at the AM1 level. An effective potential, combining non-bonding and polarization plus charge transfer (PLCT) terms, was introduced to evaluate the magnitude of the interaction between each amino acid and the ligand. In this case study, the nonbonding–PLCT noncompensation characterizes the stabilization energy of the association process in study. The main residues (Gly29, Cys3 and Arg5) with net attractive effects and Arg1 (with a net repulsive effect), responsible by the stability of protein-ligand complex, are associated with large nonbonding energies non-compensated by PLCT effects. The results obtained enable us to conclude that the present decomposition scheme can be used for understanding the cohesive phenomena in proteins.
Keywords: Protein-ligand interactions; energy partition scheme; association processes; stabilization energy; quantum partition of molecules; semiempirical methods Protein-ligand interactions; energy partition scheme; association processes; stabilization energy; quantum partition of molecules; semiempirical methods
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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MDPI and ACS Style

Carvalho, A.R.F.; Puga, A.T.; Melo, A. Exact and Effective Pair-Wise Potential for Protein-Ligand Interactions Obtained from a Semiempirical Energy Partition. Int. J. Mol. Sci. 2008, 9, 1652-1664.

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