Molecular dynamics simulation of horse-heart cytochrome c in water-methanol solvent systems
Gautam, Devaki Nandan
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Molecular Dynamics simulations have been carried out to investigate the dynamics of horse heart Cytochrome C and associated crystallographic water molecules in different water-methanol systems. The 100 ns simulation predicts that hh-CytC undergoes different dynamical transitions with some common conformations in different solvents. With increase of methanol concentration in solvents, hh-CytC has increased flexibility, fluctuating its hydrophobic solvent accessible surface area (SASA), and number of persistent internal hydrogen bonds with long hydrogen-bond-lifetime. The protein became more liquid-like in mixed solvents compared to pure solvents; flexibility increases in the absence of the crystallographic water. Similarly, the number of hydrogen bonds between solvent molecules and hh-CytC decreased with increasing of methanol concentration. Water-protein and methanol-protein hydrogen bond lifetimes were computed 11.5 and 16.6 picoseconds, respectively, in pure solvents. However, in mixtures, solvent-protein hydrogen bond lifetime was higher in twenty percent methanol than in fourty percent in water. The surface crystallographic water molecules diffused easily in bulk solvents within 1 nanosecond and protein surface is stabilized by hydrogen bonds with a solvation layer. The two crystallographic water molecules which are buried internally in hh-CytC have 5 to more than 100 nanoseconds residence time in the conserved sites with 100's of picoseconds of hydrogen bond lifetime depending on the solvent compositions. The residence time might depend on the mechanism of conformational transition of protein in simulation. Solvent water molecules exchange these buried water molecules but exchange is less frequent than that in hydration layer. Even though methanol has succeeded to reside into these conserved sites in pure methanol solvent but its distance with hydrogen bonding partners more than 5 A with labile hydrogen bonding state.
Thesis (M.S.)--Wichita State University, Fairmount College of Liberal Arts, Dept. of Chemistry