title: Coarse-Grained Langevin Equation for Protein Dynamics: Global Anisotropy and a Mode Approach to Local Complexity.
abstract: We utilize a multiscale approach where molecular dynamic simulations are performed to obtain quantitative structural averages used as input to a coarse-grained Langevin equation for protein dynamics, which can be solved analytically. The approach describes proteins as fundamentally semiflexible objects collapsed into the free energy well representing the folded state. The normal-mode analytical solution to this Langevin equation naturally separates into global modes describing the fully anisotropic tumbling of the macromolecule as a whole and internal modes which describe local fluctuations about the folded structure. Complexity in the configurational free-energy landscape of the macromolecule leads to a renormalization of the internal modes, while the global modes provide a basis set in which the dipolar orientation and global anisotropy can be accounted for when comparing to experiments. This simple approach predicts the dynamics of both global rotational diffusion and internal motion from the picosecond to the nanosecond regime and is quantitative when compared to time correlation functions calculated from molecular dynamic simulations and in good agreement with nuclear magnetic resonance relaxation experiments. Fundamental to this approach is the inclusion of internal dissipation, which is absent in any rigid-body hydrodynamical modeling scheme.
authors.affiliation: Department of Chemistry and Biochemistry and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, United States.
authors.forename: J
authors.initials: J
authors.lastname: Copperman
authors.affiliation: Department of Chemistry and Biochemistry and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, United States.
authors.forename: M G
authors.initials: MG
authors.lastname: Guenza
mesh_terms: D016880:Anisotropy; D002244:Carbon / Q000737:chemistry; D057446:Hydrodynamics; D006859:Hydrogen / Q000737:chemistry; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D009038:Motion; D009584:Nitrogen / Q000737:chemistry; D019906:Nuclear Magnetic Resonance, Biomolecular; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D025801:Ubiquitin / Q000737:chemistry; D014783:Viscosity; D014867:Water / Q000737:chemistry
chemical_list: D011506:Proteins; D012997:Solvents; D025801:Ubiquitin; D014867:Water; D002244:Carbon; D006859:Hydrogen; D009584:Nitrogen