A precise 100-ns molecular dynamics simulation in aquo was performed for the heterotetrameric sarcosine oxidase bound with a substrate analogue, dimethylglycine. The spatial region including the protein was divided into small rectangular cells. The average number of the water molecules locating within each cell was calculated based on the simulation trajectory. The clusters of the cells filled with water molecules were used to determine the water channels. The narrowness of the channels, the average hydropathy indices of the residues of the channels, and the number of migration events of water molecules through the channels were consistent with the selective transport hypothesis whereby tunnel T3 is the pathway for the exit of the iminium intermediate of the enzyme reaction.

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We analyzed residue pairing patterns in β-sheets to understand the mechanism of β-sheet formation which is one of the key steps for forming the tertiary structure of proteins. Only 12 pairs showed different pairing propensity between hydrogen-bonding (HB) and non-bonding (nHB) pairs in anti-parallel sheets when pairs including Pro were neglected. When edge and central strand pairs were distinguished, however, 37 and 39 pairs showed different pairing propensity for edge and central strand pairs, respectively, and only 7 of these pairs showed similar propensity between edge and central strand pairs. These results indicated that edge and central pairs possessed quite different propensity each other and this difference might be one of criteria to select edge strand pairs. A force field is widely used in the field of molecular simulations for biomolecular systems. Recently, we proposed a new method for refining force-filed parameters, which modifies the force-field parameters for each amino acid to minimize the root-mean-square deviation of backbone dihedral angles in various protein structures. Here, we compared the experimental data obtained from NMR with the trajectory data obtained from molecular dynamics simulations. In addition, we also applied an energy-based reweighting approach to a molecular dynamics trajectory to efficiently screen a large number of trial force fields in order to decrease the simulation cost. In this study, we examined the parameter dependency of optimized force filed for each amino acid. Heterotetrameric sarcosine oxidase (SO) containing FAD and FMN catalyzes the oxidative demethylation of sarcosine. The structural and biochemical analyses have shown that the SO-dimethylglycine (DMG) complex contains a large cavity near the catalytic site and have suggested channeling of reactants and products through several tunnels. Toward realistic simulations of channeling, we have carried out molecular dynamics simulations for the SO-DMG complex using the GROMACS program with the Amber force field. As a result, the structure simulated was in good agreement with the X-ray data. In our present study, the trajectories of water molecules were analyzed accurately to understand their pathways and obtain new insights into the channeling related to the catalysis of SO. Neutron scattering length (b [cm]) is independent of sinθ/λ unlike X-ray atomic form factor (f [cm]). However, the resolution or a set of reflections of NPC has been determined as observed minimum d-spacing by considering R-merge etc, like in case of X-ray's. In order to find new criteria in NPC, we drew several Fourier maps by including a set of calculated Fc(hkl) from neutron PDB data, which consists of only larger |Fc|s than the mean value at the higher resolution range, and found that the quality of the map became better than one at the conventional resolution. This suggests that the practical improvement on the map will be possible if we use reflections ignored by the conventional method. We analyzed the structure of glucagon-like peptide...