Dynamics Simulation Of The Interaction Between Water And Biomolecules

Neutron scattering spectra of anhydrous and monohydrated amino acids were simulated using density functional theory (DFT). The interaction between human aquaporin-1(hAQPl) and one of its blockers was also simulated with the molecular dynamics (MD) method.Proteins play important roles in the organisms, such as to construct cells, catalyze chemical reactions and so on. It is believed that the proteins functional performing depend heavily on their structures, which are closely associated with water. It is difficult to investigate the interaction between protein and water directly due to the complexity of the macromolecule structure. As the basic building blocks of the protein, amino acids are useful models to mimic the thermodynamic behavior of proteins in solution. In this report, neutron scattering spectra of some amino acids, serine, proline, glycine and alanine were simulated. The hydrophobic rule between water and amino acids are discussed by analyzing the vibration modes and the formation of the hydrogen-bond (H-bond).Different side chain leads to a different hydrophobicity of the amino acids. For example, alanine, which has a-CH3side chain, shows hydrophobic property, on the other hand, serine, which has a-CH2OH side chain, is hydrophilic. While water molecules penetrate into the anhydrous serine or proline crystal, H-bonds between the amino acid molecules tend to be released and form new structures with water, which makes the system more stable; however, when it comes to the glycine and alanine crystal, amino acid molecules would rather keep closer to themselves. Our simulations show that there exist two conformations for water molecule in monohydrated serine:one, the O atom of H2O forms a hydrogen bond with the H of the amino group; two, the O of H2O forms a hydrogen bond with the H of the hydroxyl group. The latter is a metastable state than the former structure. At a higher hydration level, the structure deformation may decrease the energy barrier, and more H2O will shift to the amino group side for lower potential. hAQPl is one kind of membrane protein that facilitates the permeation of water and other small uncharged solutes across biological membrane. Research shows the pharmacological modulation of hAQP1activity may provide novel opportunities for the treatment of some diseases, such as glaucoma, brain edema, and tumor growth. The hAQPl blockers can inhibit the water flux across the cell membrane by combining with the hAQP1and may work as drug for the human disorders. In our model, the blocker combined with a monomer of the hAQP1tetramer. The result of a10ns MD simulation show that there are15full-permeation events across through the other three monomers during the process, and no permeation happened to the monomer with blockers. The result indicates that the blocker model we used in the simulation takes good effect in inhibiting water flux.