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Diffusion of Water, Ions and Amino Acids in Protein Crystals: A Molecular Simulation Study

Zhongqiao Hu and Jianwen Jiang. Chemical and Biological Engineering, National University of Singapore, Singapore, Singapore

Protein crystals have recently emerged as a class of novel bio- and nano-materials with a wide variety of applications in pharmaceutically important bioseparation and biocatalysis. We present a molecular simulation study for the spatial and temporal behaviors of water and ions in three protein crystals with different morphologies and topologies: tetragonal lysozyme, orthorhombic lysozyme and tetragonal thermolysin. The solvent-accessible-surface area per residue is nearly identical in the three protein crystals, the hydrophobic and hydrophilic residues in each crystal possess approximately the same solvent-accessible-surface area. Water distributes heterogeneously and has different local structures within the biological nanopores of the three protein crystals. The mobility of water and ions in the crystals is enhanced as the porosity increases and also by the fluctuations of protein atoms. Anisotropic diffusion is found preferentially in the pore axis, as experimentally observed. The anisotropy of the three crystals increases in the order of tetragonal thermolysin < tetragonal lysozyme < orthorhombic lysozyme. We further investigate the transport of amino acids through protein crystals. Fairly good separation is achieved and the separation mechanism is explored at the molecular scale.