title: Interfacial water effect on cooperativity and signal communication in Scapharca dimeric hemoglobin.
abstract: Cooperativity is important in controlling the biological functions of allosteric proteins. Understanding the detailed mechanisms of cooperativity and allosteric regulation in such proteins is essential to understanding their function; however, the mechanism by which allosteric proteins undergo conformational transitions to aid the ligand escape process and its relevance to interfacial water molecules is not well understood. Here, we perform molecular dynamics simulations to examine these issues in Scapharca dimeric hemoglobin. The effects of interfacial water on dimeric motion, ligand escape probability, gate function, and cross-correlation are considered. The results reveal that interfacial water exhibits an unbalanced stress distribution in the interface region, leading to a bias helix bundle motion that not only can expedite the escape of the first ligand but also can increase the interval between the escape of both ligands. Correspondingly, the gate function follows the same time scale as the F-helix movement, and the gate opening is non-stochastic; moreover, the inconsistent motion between the gate parts resembles cooperative behavior. An explicit analysis of the intersubunit communication map provides at least 14 signal transduction pathways. Our results significantly aid in understanding the role of interfacial water in manipulating cooperativity and will lead to further applications involving molecular machines.
authors.affiliation: Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan. sysheu@ym.edu.tw and Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan.
authors.forename: Sheh-Yi
authors.identifier: http://orcid.org/0000-0002-4416-4336
authors.initials: SY
authors.lastname: Sheu
authors.affiliation: Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan.
authors.forename: Yu-Cheng
authors.initials: YC
authors.lastname: Liu
authors.affiliation: Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan. dyyang@po.iams.sinica.edu.tw.
authors.forename: Dah-Yen
authors.initials: DY
authors.lastname: Yang
mesh_terms: D000494:Allosteric Regulation; D000818:Animals; D019281:Dimerization; D006454:Hemoglobins / Q000737:chemistry*; D008024:Ligands; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D049894:Scapharca / Q000378:metabolism*; D015398:Signal Transduction; D014867:Water / Q000737:chemistry*
chemical_list: D006454:Hemoglobins; D008024:Ligands; D014867:Water