title: Interaction entropy for protein-protein binding.
abstract: Protein-protein interactions are at the heart of signal transduction and are central to the function of protein machine in biology. The highly specific protein-protein binding is quantitatively characterized by the binding free energy whose accurate calculation from the first principle is a grand challenge in computational biology. In this paper, we show how the interactionentropy approach, which was recently proposed for protein-ligand binding free energy calculation, can be applied to computing the entropic contribution to the protein-protein binding free energy. Explicit theoretical derivation of the interactionentropy approach for protein-protein interaction system is given in detail from the basic definition. Extensive computational studies for a dozen realistic protein-protein interaction systems are carried out using the present approach and comparisons of the results for these protein-protein systems with those from the standard normal mode method are presented. Analysis of the present method for application in protein-protein binding as well as the limitation of the method in numerical computation is discussed. Our study and analysis of the results provided useful information for extracting correct entropic contribution in protein-protein binding from molecular dynamics simulations.
authors.affiliation: School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
authors.forename: Zhaoxi
authors.initials: Z
authors.lastname: Sun
authors.affiliation: School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
authors.forename: Yu N
authors.initials: YN
authors.lastname: Yan
authors.affiliation: School of Science, Qilu University of Technology, Jinan, Shandong 250353, China.
authors.forename: Maoyou
authors.initials: M
authors.lastname: Yang
authors.affiliation: School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
authors.forename: John Z H
authors.initials: JZ
authors.lastname: Zhang
mesh_terms: D019277:Entropy; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins