title: Synergy of molecular dynamics and isothermal titration calorimetry in studies of allostery.
abstract: Despite decades of intensive study, allosteric effects have eluded an intellectually satisfying integrated understanding that includes a description of the reaction coordinate in terms of species distributions of structures and free energy levels in the conformational ensemble. This chapter illustrates a way to fill this gap by interpreting thermodynamic and structural results through the lens of molecular dynamics simulation analysis to link atomic-level detail with global response. In this synergistic approach molecular dynamics forms an integral part of a feedback loop of hypothesis, experimental design, and interpretation that conforms to the scientific method.
authors.affiliation: Chemistry Department, Princeton University, Princeton, New Jersey, USA.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Strawn
authors.forename: Thomas
authors.initials: T
authors.lastname: Stockner
authors.forename: Milan
authors.initials: M
authors.lastname: Melichercik
authors.forename: Lihua
authors.initials: L
authors.lastname: Jin
authors.forename: Wei-Feng
authors.initials: WF
authors.lastname: Xue
authors.forename: Jannette
authors.initials: J
authors.lastname: Carey
authors.forename: Rüdiger
authors.initials: R
authors.lastname: Ettrich
mesh_terms: D000494:Allosteric Regulation; D000495:Allosteric Site; D001419:Bacteria / Q000737:chemistry / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry; D002151:Calorimetry / Q000379:methods*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D012097:Repressor Proteins / Q000737:chemistry; D013816:Thermodynamics
chemical_list: C087018:ArgR protein, Bacteria; D001426:Bacterial Proteins; D012097:Repressor Proteins