Large-scale networks of hydration water molecules around bovine beta-trypsin revealed by cryogenic X-ray crystal structure analysis.
The hydration structure of bovine beta-trypsin was investigated in cryogenic X-ray diffraction experiments. Three crystal forms of the enzyme inhibited by benzamidine with different molecular packing were selected to deduce the hydration structure for the entire surface of the enzyme. The crystal structures in all three of the crystal forms were refined at the resolution of 1.8 A at 100 K and 293 K. The number of hydration water molecules around the enzyme at 100 K was 1.5 to two times larger than that at 293 K, indicating that the motion of hydration water was quenched by cooling. In particular, the increase in the number of hydration water molecules was prominent on flat and electrostatically neutral surface areas. The water-to-protein mass ratio and the radius of gyration of a structural model of hydrated trypsin at 100 K was consistent with the results obtained by other experimental techniques for proteins in solution. Hydration water molecules formed aggregates of various shapes and dimensions, and some of the aggregates even covered hydrophobic residues by forming oligomeric arrangements. In addition, the aggregates brought about large-scale networks of hydrogen bonds. The networks covered a large proportion of the surface of trypsin like a patchwork, and mechanically linked several secondary structures of the enzyme. By merging the hydration structures of the three crystal forms at 100 K, a distribution function of hydration water molecules was introduced to approximate the static hydration structure of trypsin in solution. The function showed that the negatively charged active site of trypsin tended to be easily exposed to bulk solvent. This result is of interest with respect to the solvent shielding effect and the recognition of a positively charged substrate by trypsin.
Nakasako
M
M
Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Corporation (JST), Institute of Molecular and Cellular Biosciences, University of Tokyo, Yayoi 1-1-1, Bunkyoku, Tokyo, Japan. nakasako@iam.u-tokyo.ac.jp
D000818:Animals; D002417:Cattle; D003460:Crystallization; D018360:Crystallography, X-Ray / Q000379:methods*; D005615:Freezing; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011487:Protein Conformation; D014357:Trypsin / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
D014867:Water; D014357:Trypsin