Molecular insight into the interaction between IFABP and PA by using MM-PBSA and alanine scanning methods.
The molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method combined with alanine-scanning mutagenesis is a very important tool for rational drug design. In this study, molecular dynamics (MD) and MM-PBSA were applied to calculate the binding free energy between the rat intestinal fatty acid binding protein (IFABP) and palmitic acid (PA) to gain insight to the interaction details. Equally spaced snapshots along the trajectory were chosen to perform the binding free energy calculation, which yields a result highly consistent with experimental value with a deviation of 0.4 kcal/mol. Computational alanine scanning was performed on the same set of snapshots by mutating the residues in IFABP to alanine and recomputing the DeltaDeltaG(binding). By postprocessing a single trajectory of the wild-type complex, the average unsigned error of our calculated DeltaDeltaG(binding) is below 1.5 kcal/mol for most of the alanine mutations of the noncharged residues (67% in total). To further investigate some particular mutants, three additional dynamical simulations of IFABP Arg126Ala, Arg106Ala, and Arg106Gln mutants were conducted. Recalculated binding free energies are well consistent with the experimental data. Moreover, the ambiguous role of Arg106 caused by the free energy change of the opposite sign when it is mutated to alanine and glutamine respectively is clarified both structurally and energetically. Typically, this can be attributed to the partial electrostatic compensation mainly from Arg56 and the obvious entropy gain in Arg106Ala mutant while not in Arg106Gln mutant. The presented structural model of IFABP-PA complex could be used to guide future studies.
Zou
Hanjun
H
Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China.
Luo
Cheng
C
Zheng
Suxin
S
Luo
Xiaomin
X
Zhu
Weiliang
W
Chen
Kaixian
K
Shen
Jianhua
J
Jiang
Hualiang
H
D000409:Alanine / Q000737:chemistry* / Q000235:genetics; D000818:Animals; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D050556:Fatty Acid-Binding Proteins / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D009154:Mutation; D019308:Palmitic Acid / Q000737:chemistry*; D011485:Protein Binding; D051381:Rats; D013816:Thermodynamics
D050556:Fatty Acid-Binding Proteins; D019308:Palmitic Acid; D000409:Alanine