Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations.
A 1 ns trajectory from a molecular dynamics study of 1.4 ns total length was used for a detailed analysis of the residence times of water molecules located near 227 selected bovine pancreatic trypsin inhibitor (BPTI) atoms. The simulation was performed using the GROMOS force field, with apolar hydrogen atoms treated as united atoms, and the SPC/E water model. The system consisted of 568 BPTI atoms and 2371 water molecules. The theoretical results are in good agreement with experimental data available from nuclear magnetic resonance spectroscopy. The residence times of individual water molecules coming near a given BPTI atom, as obtained from the simulation, vary greatly and range between 10 and 500 ps. The effective residence time, calculated using a correlation function technique from the presence of all individual water molecules visiting the hydration shell of a given BPTI atom, never exceeds 200 ps. The average residence time near backbone and side-chain atoms is approximately 39 ps and 24 ps, respectively. The shortest residence times, on average, are found near charged atoms (19 ps), whereas near non-polar and polar side-chain atoms the residence times are 25 ps and 36 ps, respectively. There is no apparent correlation between the residence times of the hydration water molecules of solvent-accessible residues and their location in different regular or non-regular secondary structures.
Brunne
R M
RM
Laboratorium für Physikalische Chemie, ETH-Zentrum, Zürich, Switzerland.
Liepinsh
E
E
Otting
G
G
Wüthrich
K
K
van Gunsteren
W F
WF
D000595:Amino Acid Sequence; D007611:Aprotinin / Q000737:chemistry*; D003198:Computer Simulation; D008956:Models, Chemical; D008969:Molecular Sequence Data; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D014867:Water; D007611:Aprotinin