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Exact and effective pair-wise potential for protein-ligand interactions obtained from a semiempirical energy partition.


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 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.

SUBMITTER: Carvalho AR 

PROVIDER: S-EPMC2635750 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature

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Exact and effective pair-wise potential for protein-ligand interactions obtained from a semiempirical energy partition.

Carvalho Alexandre R F ARF   Puga André T AT   Melo André A  

International journal of molecular sciences 20080902 9


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  ...[more]

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