title: Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains.
abstract: Ligand binding modulates the energy landscape of proteins, thus altering their folding and allosteric conformational dynamics. To investigate such interplay, calmodulin has been a model protein. Despite much attention, fully resolved mechanisms of calmodulin folding/binding have not been elucidated. Here, by constructing a computational model that can integrate folding, binding, and allosteric motions, we studied in-depth folding of isolated calmodulin domains coupled with binding of two calcium ions and associated allosteric conformational changes. First, mechanically pulled simulations revealed coexistence of three distinct conformational states: the unfolded, the closed, and the open states, which is in accord with and augments structural understanding of recent single-molecule experiments. Second, near the denaturation temperature, we found the same three conformational states as well as three distinct binding states: zero, one, and two calcium ion bound states, leading to as many as nine states. Third, in terms of the nine-state representation, we found multiroute folding/binding pathways and shifts in their probabilities with the calcium concentration. At a lower calcium concentration, "combined spontaneous folding and induced fit" occurs, whereas at a higher concentration, "binding-induced folding" dominates. Even without calcium binding, we observed that the folding pathway of calmodulin domains can be modulated by the presence of metastable states. Finally, full-length calmodulin also exhibited an intriguing coupling between two domains when applying tension.
authors.affiliation: National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China; and.
authors.forename: Wenfei
authors.initials: W
authors.lastname: Li
authors.affiliation: National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China; and takada@biophys.kyoto-u.ac.jp wangwei@nju.edu.cn.
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan takada@biophys.kyoto-u.ac.jp wangwei@nju.edu.cn.
authors.forename: Shoji
authors.initials: S
authors.lastname: Takada
mesh_terms: D000494:Allosteric Regulation / Q000187:drug effects; D001665:Binding Sites; D002118:Calcium / Q000494:pharmacology; D002147:Calmodulin / Q000737:chemistry* / Q000378:metabolism*; D003198:Computer Simulation; D008958:Models, Molecular; D011485:Protein Binding / Q000187:drug effects; D011489:Protein Denaturation; D017510:Protein Folding / Q000187:drug effects; D017434:Protein Structure, Tertiary; D013314:Stress, Mechanical; D013696:Temperature; D013816:Thermodynamics
chemical_list: D002147:Calmodulin; D002118:Calcium
keywords: coarse grained; force; metal; molecular dynamics; multiscale simulations