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

International Journal of Molecular Sciences

Alexandre R. F. Carvalho²  André T. Puga¹ 

[1] DEMEGI, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal. E-Mail:;REQUIMTE/Department of Chemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal. E-Mail:

关键词: Protein-ligand interactions;    energy partition scheme;    association processes;    stabilization energy;    quantum partition of molecules;    semiempirical methods;   

DOI  :  10.3390/ijms9091652

来源: mdpi

【 摘 要 】

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 non-compensation 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.

【 授权许可】

CC BY   
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