%0 Journal Article
%T Analysis of Water and Hydrogen Bond Dynamics at the Surface of an Antifreeze Protein
%A Yao Xu
%A Ramachandran Gnanasekaran
%A David M. Leitner
%J Journal of Atomic and Molecular Physics
%D 2012
%R 10.1155/2012/125071
%X We examine dynamics of water molecules and hydrogen bonds at the water-protein interface of the wild-type antifreeze protein from spruce budworm Choristoneura fumiferana and a mutant that is not antifreeze active by all-atom molecular dynamics simulations. Water dynamics in the hydration layer around the protein is analyzed by calculation of velocity autocorrelation functions and their power spectra, and hydrogen bond time correlation functions are calculated for hydrogen bonds between water molecules and the protein. Both water and hydrogen bond dynamics from subpicosecond to hundred picosecond time scales are sensitive to location on the protein surface and appear correlated with protein function. In particular, hydrogen bond lifetimes are longest for water molecules hydrogen bonded to the ice-binding plane of the wild type, whereas hydrogen bond lifetimes between water and protein atoms on all three planes are similar for the mutant. 1. Introduction While the complex dynamics of large biological molecules and the connection to function have fascinated physical scientists for some time, in more recent years researchers have turned their attention to the interface of biomolecules with water. Coupling of protein and water dynamics, for example, has been examined by molecular simulations [1¨C10] and a growing number of experimental probes [11¨C14], and a wide variety of dynamical time scales have been found [15, 16] due to the heterogeneity of protein-water interactions. One class of proteins for which protein-water interactions are critical to function is antifreeze proteins (AFPs). AFPs are widely distributed in certain plants, vertebrates, fungi, and bacteria to provide cells protection in cold environments [17¨C20] but the mechanism for antifreeze activity is still not well understood. In this paper we analyze by all-atom molecular dynamics (MD) simulations the dynamics of water molecules and hydrogen bonds at the protein-water interface of the AFP from the spruce budworm Choristoneura fumiferana and a mutant that has little antifreeze activity. We calculate velocity autocorrelation functions and their power spectra for water molecules around the protein and we compute hydrogen bond time correlation functions for bonds between the protein and water. We obtain distinct spectra for the water around different regions of the protein, which are affected by mutation. Moreover, we observe longer hydrogen bonding between water molecules and the ice-binding plane of this AFP compared to other parts of the protein, a difference that nearly disappears with
%U http://www.hindawi.com/journals/jamp/2012/125071/