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Exact and Effective Pair-Wise Potential for Protein-Ligand Interactions Obtained from a Semiempirical Energy Partition
REQUIMTE/Department of Chemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
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; in revised form: 28 July 2008 / Accepted: 28 August 2008 / Published: 2 September 2008
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
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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.
Carvalho ARF, Puga AT, Melo A. Exact and Effective Pair-Wise Potential for Protein-Ligand Interactions Obtained from a Semiempirical Energy Partition. International Journal of Molecular Sciences. 2008; 9(9):1652-1664.
Carvalho, Alexandre R.F.; Puga, André T.; Melo, André. 2008. "Exact and Effective Pair-Wise Potential for Protein-Ligand Interactions Obtained from a Semiempirical Energy Partition." Int. J. Mol. Sci. 9, no. 9: 1652-1664.