A Self-Adaptive Steered Molecular Dynamics Method Based on Minimization of Stretching Force Reveals the Binding Affinity of Protein-Ligand Complexes.
Binding affinity prediction of protein-ligand complexes has attracted widespread interest. In this study, a self-adaptive steered molecular dynamics (SMD) method is proposed to reveal the binding affinity of protein-ligand complexes. The SMD method is executed through adjusting pulling direction to find an optimum trajectory of ligand dissociation, which is realized by minimizing the stretching force automatically. The SMD method is then used to simulate the dissociations of 19 common protein-ligand complexes which are derived from two homology families, and the binding free energy values are gained through experimental techniques. Results show that the proposed SMD method follows a different dissociation pathway with lower a rupture force and energy barrier when compared with the conventional SMD method, and further analysis indicates the rupture forces of the complexes in the same protein family correlate well with their binding free energy, which reveals the possibility of using the proposed SMD method to identify the active ligand.
State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian 116023, China. jfgu@dlut.edu.cn.
Junfeng
J
Gu
School of Mechanical Engineering, Dalian University of Technology, Dalian 116023, China. hxli@dlut.edu.cn.
Hongxia
H
Li
State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian 116023, China. guixum@dlut.edu.cn.
Xicheng
X
Wang
D020134:Catalytic Domain; D016333:HIV Protease / Q000737:chemistry; D008024:Ligands; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017027:Protein Tyrosine Phosphatases / Q000737:chemistry; D013816:Thermodynamics
D008024:Ligands; D017027:Protein Tyrosine Phosphatases; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1
binding affinity; optimization; protein–ligand unbinding; rupture force; steered molecular dynamics