Molecular Dynamics Simulation Study on the Effect of Mutant(Met108→Leu108) on Interactions Between Arabinose-binding Protein and Ligand†

doi:10.7503/cjcu20130889

Abstract

Abstract:

In order to understand the effect of the mutant(Met108→Leu108) of the arabinose-binding protein(ABP) on the interactions between the protein and ligand, a series of 60 ns molecular dynamics simulations for the ABP, ABP bound ARA, ABP bound GAL and their mutants was performed, respectively. The results show that the mutation(Met108→Leu108) in ABP leads to the significant change of the van der Waals interaction between residue 108 and ligand, which further causes the changes of the protein’s internal motion and interactions between the protein and ligand. The varieties in interaction between the protein and ligand make the two globular domains of wild-type and mutation-type of ABP gradually open and the ligand binding can control the open movement of the protein.

Key words: Arabinose-binding protein, Molecular dynamics simulation, Non-polar interaction

CLC Number:

O641.12⁺1

TrendMD:

FENG Xianli, LI Zhuo, ZHAO Xi, YU Hui, LIU Huiling, HUANG Xuri. Molecular Dynamics Simulation Study on the Effect of Mutant(Met108→Leu108) on Interactions Between Arabinose-binding Protein and Ligand^†[J]. Chem. J. Chinese Universities, 2014, 35(2): 338.

Figures/Tables 9

Fig.1 Overview of protein ABP and ligand ARA(ball-and-stick) ABP color is marked by secondary structure.

Fig.2 Time evolution of backbone RMSD of the ABP bound ARA(a), ABP(b), ABP bound GAL(c)(A) and their corresponding mutants(a, b and c, B)

Fig.3 Radius of gyration of the ABP bound ARA(a), ABP(b), ABP bound GAL(c)(A) and their corresponding mutants(a, b and c, B)

Fig.4 Overlapping of the ABP molecular dynamics simulation structures at 0.2(green) and 50 ns(red)

Fig.5 Root mean square fluctuation(RMSF) of the Cα atoms around the average MD structures (A) a. ABP bound ARA; b. ABP bound GAL; (B) a. mutant ABP bound ARA; b. mutant ABP bound GAL.

Fig.6 Hydrogen bonding interaction between protein and ligand(A) ABP bound GAL; (B) ABP bound ARA; (C) mutant ABP bound GAL; (D) mutant ABP bound ARA.

Table 1 Binding free energy components of ABP bound GAL, ABP bound ARA, mutant ABP bound GAL and mutant ABP bound ARA complexes

System	E_coul/(kJ·mol^-1)	E_vdw/(kJ·mol^-1)	E_Total/(kJ·mol^-1)
ABP bound GAL	-122.813	-5.11859	-127.93
ABP bound ARA	-164.561	-62.7825	-227.34
Mutant ABP bound GAL	-173.963	-78.6312	-252.59
Mutant ABP bound ARA	-106.336	-4.034	-110.37

Fig.7 Distance of the pairs of atoms which are specified(A) a. ABP bound ARA, Met108 CE—(GAL C5); b. ABP bound ARA, Met108 CE—(GAL C5); (B) a. mutant ABP bound GAL, Leu108 CD1—(Pro254 CB); b. mutant ABP bOUND ARA, Leu108 CD1—(Pro254 CB).

Fig.8 Principal collective motions of the systems of ABP bound ARA(A), ABP bound GAL(B), mutant ABP bound ARA(C) and mutant ABP bound GAL(D) described by the first eigenvector represented as the red structure transforms into the blue structures as it moving in the direction

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