Coarse-grained simulations of conformational dynamics of proteins: application to apomyoglobin.
A coarse-grained dynamic Monte Carlo method is proposed for investigating the conformational dynamics of proteins. Each residue is represented by two interaction sites, one at the alpha-carbon, and the other on the amino acid sidechain. Geometry and energy parameters extracted from databank structures are used. The method is applied to the crystal structure of apomyoglobin (apo-Mb). Equilibrium and dynamic properties of apo-Mb are characterized within computation times one order of magnitude shorter than conventional molecular dynamics (MD) simulations. The calculated rms fluctuations in alpha-carbons are in good agreement with crystallographic temperature factors. Regions exhibiting enhanced conformational mobilities are identified. Among the loops connecting the eight helices A to H, the loop CD undergoes the fastest motions, leading to partial unwinding of helix D. Helix G is the most stable helix on the basis of the kinetic stability of dihedral angles, followed by the respective helices A, E, H, and B. These results, in agreement with H/D exchange and two-dimensional NMR experiments, as well as with MD simulations, lend support to the use of the proposed approach as an efficient, yet physically plausible, means of characterizing protein conformational dynamics.
Haliloglu
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Polymer Research Center and Chemical Engineering Department, Bogazici University, Istanbul, Turkey.
Bahar
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D000818:Animals; D001059:Apoproteins / Q000737:chemistry*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D016208:Databases, Factual; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009010:Monte Carlo Method; D009038:Motion; D009211:Myoglobin / Q000737:chemistry*; D011487:Protein Conformation; D012399:Rotation; D013997:Time Factors
D001059:Apoproteins; D009211:Myoglobin; C010857:apomyoglobin