title: Terahertz spectral domain computational analysis of hydration shell of proteins with increasingly complex tertiary structure.
abstract: Solvation dynamics of biomolecules and water in a hydration shell have been studied by different methods; however, a clear picture of this process is not yet established. Terahertz (THz) studies of molecular behavior in binary solutions present unique information on the picosecond motions of molecules. A complete mechanical interpretation of THz absorption spectra associated with solvated biomolecules remains a challenging task. The Gromacs molecular dynamics (MD) simulation package is used here to examine the spectral characteristics of water molecules in close proximity to biomolecules using vibrational density of states (VDOS). Systematic simulation of solvation dynamics of proteins of different size and tertiary structure are presented. The following have been selected for analysis. They range from less to more complex tertiary structure (corresponding to an increased number of secondary structure elements): TRP-cage13-20 peptide, TRP-cage, BPTI, and lysozyme. The initial study predicts that the depth of the hydration shell, determined by VDOS of water, extends to approximately 10 Å and does not depend on protein size. Furthermore the integral perturbation coefficient of the whole solvation layer is found to be increased for larger proteins due to a higher retardation rate of water molecules in their shells. Differences in solvation dynamics among the proteins considered originate primarily from the water molecules buried in the interior of the protein and not from the on-surface molecules.
authors: School of Electronic Engineering and Computer Science, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom.
authors: Oleksandr
authors: O
authors: Sushko
authors: Rostyslav
authors: R
authors: Dubrovka
authors: Robert S
authors: RS
authors: Donnan
mesh_terms: D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D055068:Terahertz Spectroscopy
chemical_list: D011506:Proteins; D012997:Solvents