title: Binding free-energy calculation of an ion-peptide complex by constrained dynamics.
abstract: Binding free energy is the most important physical parameter that describes the binding affinity of a receptor-ligand complex. Conventionally, it was obtained based on the thermodynamic cycle or alchemical reaction. These strategies have been widely used, but they would be problematic if the receptors and/or ligands have large conformational changes during the binding processes. In this paper, we present a way to calculate the binding free energy: constrained dynamics along a fragmental and high-dimensional transition path. This method directly considers unbound states in the simulation. The application to the calmodulin loop-calcium complexes shows that it is practical and the calculated relative binding affinities are in good agreement with experimental results.
authors.affiliation: Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
authors.forename: Changjun
authors.initials: C
authors.lastname: Chen
authors.forename: Yanzhao
authors.initials: Y
authors.lastname: Huang
authors.forename: Xuewei
authors.initials: X
authors.lastname: Jiang
authors.forename: Yi
authors.initials: Y
authors.lastname: Xiao
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D004735:Energy Transfer; D007477:Ions / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011485:Protein Binding; D013816:Thermodynamics
chemical_list: D007477:Ions; D010455:Peptides