A crystal mounting device made from a capillary tube for cryogenic macromolecular crystallography

Solvent density and long-range dipole field around a DNA-binding protein studied by molecular dynamics

The distribution and orientation of solvent around a DNA-binding protein, 434 Cro, were investigated by molecular dynamics simulations with a periodic-boundary condition. The protein was treated in two states: charged and neutral. The computed high-density sites of the solvent around the protein correlated well with the experimentally determined crystal-water sites, in both the charged and neutral states. A local density map, introduced to investigate the solvent density around the highly mobile regions of the protein, showed a hydration shell around hydrophobic sidechains and hydrogen-bondable sites around hydrophilic sidechains, and also showed that the solvent density is sensitive to the slight concaves of the sidechain surface. The long-range solvent-dipole field was observed around the protein, where the pattern of the dipole ordering was considerably different between the charged and neutral states. A local solvent-dipole field was introduced, and the pattern of the dipole ordering was different between the hydrophobic and hydrophilic sidechains. The dipole field from the charged state provided a higher correlation to the electrostatic field obtained from the Poisson-Boltzmann's equation than that from the neutral state, although the correlation become weak quickly for the both states with increasing the protein-solvent distance.

Cryogenic X-ray crystal structure analysis for the complex of scytalone dehydratase of a rice blast fungus and its tight-binding inhibitor, carpropamid: the structural basis of tight-binding inhibition

Scytalone dehydratase is a member of the group of enzymes involved in fungal melanin biosynthesis in a phytopathogenic fungus, Pyricularia oryzae, which causes rice blast disease. Carpropamid [(1RS,3SR)-2, 2-dichloro-N-[(R)-1-(4-chlorophenyl)ethyl]-1-ethyl-3-methylcyclopropa necarboxamide] is a tight-binding inhibitor of the enzyme. To clarify the structural basis for tight-binding inhibition, the crystal structure of the enzyme complexed with carpropamid was analyzed using diffraction data collected at 100 K. The structural model was refined to a crystallographic R-factor of 0.180 against reflections up to a resolution of 2.1 A. Carpropamid was bound in a hydrophobic cavity of the enzyme. Three types of interactions appeared to contribute to the binding. (i) A hydrogen bond was formed between a chloride atom in the dichloromethylethylcyclopropane ring of carpropamid and Asn-131 of the enzyme. (ii) The (chlorophenyl)ethyl group of carpropamid built strong contacts with Val-75, and this group further formed a cluster of aromatic rings together with four aromatic residues in the enzyme (Tyr-50, Phe-53, Phe-158, and Phe-162). (iii) Two hydration water molecules bound to the carboxamide group of carpropamid, and they were further hydrogen-bonded to Tyr-30, Tyr-50, His-85, and His-110. As a result of interactions between carpropamid and the phenylalanine residues (Phe-158 and Phe-162) in the C-terminal region of the enzyme, the C-terminal region completely covered the inhibitor, ensuring its localization in the cavity.