Analysis of Water and Hydrogen Bond Dynamics at the Surface of an Antifreeze Protein

Yao Xu,David M. Leitner,Ramachandran Gnanasekaran

doi:10.1155/2012/125071

Yao Xu, David M. Leitner + Show 1 more

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https://doi.org/10.1155/2012/125071

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Abstract

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.

Highlights

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
We have calculated at 300 K the velocity autocorrelation function and its power spectra for the water molecules in the hydration layer around the protein, which can provide insights into THz spectra of solvated proteins [40]
We examined the power spectrum of the velocity autocorrelation function for water molecules near the surface of the antifreeze protein (AFP) from the spruce budworm Choristoneura fumiferana and analyzed the hydrogen bond lifetimes for bonds between water molecules and the protein

Summary

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. 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.

Results

Conclusion