Glycine Amino Acid Transport inside the Nanopores of Lysozyme Protein Crystal
Transport of glycine amino acid molecules inside the fully hydrated nanopores of a lysozyme protein crystal was investigated using molecular dynamics (MD) simulations. Mean square displacement (MSD) analysis of glycine molecules suggested that there are different regimes during glycine transport inside the lysozyme nanopores. Glycine molecules undergo a diffusive behavior along the main pore of the protein crystal with the self-diffusion coefficient of about 1.98 × 10<sup>−13</sup> m<sup>2</sup> s<sup>−1</sup>, four orders of magnitude less than that in pure water. This observation is in good agreement with available experimental data. Moreover, analyses based on density and radial distribution functions (RDFs) showed that most interactions of glycine molecules with lysozyme take place on LYS96, ARG14, and ASP87 residues. These interactions are the result of hydrogen-bonding interactions between both amino and carboxylic groups of glycine molecules and active sites of protein residues. These interactions change the effective pore size of the lysozyme crystal.
- Chemistry letters
Chemistry letters 40(12), 1420-1422, 2011-12-05
The Chemical Society of Japan