Water penetration and escape in proteins

The kinetics of water penetration and escape in cytochrome c (cyt c) is stu died by molecular dynamics (MD) simulations at various temperatures. Water molecules that penetrate the protein interior during the course of an MD si mulation are identified by monitoring the number of water molecules in the first coordination shell (within 3.5 Angstrom) of each water molecule in th e system. Water molecules in the interior of cyt c have 0-3 water molecules in their first hydration shell and this coordination number persists for e xtended periods of time. At T = 300 K we identify over 200 events in which water molecules penetrate the protein and reside inside for at least 5 pico seconds (ps) within a 1.5 nanoseconds (ns) time period. Twenty-seven (27) w ater molecules reside for at least 300 ps, 17 water molecules reside in the protein interior for times longer than 500 ps, and two interior water mole cules do not escape; at T = 360 K one water molecule does not escape; at 43 0 K all water molecules exchange, Some of the internal water molecules show mean square displacements (MSD) of 1 Angstrom(2) characteristic of structu ral waters. Others show MSD as large as 12 Angstrom(2), suggesting that som e of these water molecules occupy transient cavities and diffuse extensivel y within the protein. Motions of protein-bound water molecules are rotation ally hindered, but show large librations. Analysis of the kinetics of water escape in terms of a survival time correlation function shows a power law behavior in time that can be interpreted in terms of a broad distribution o f energy barriers, relative to kappa(B)T, for water exchange. At T = 300 K estimates of the roughness of the activation energy distribution is 4-10 kJ /mol (2-4 kappa(B)T) Activation enthalpies for water escape are 6-23 kJ/mol , The difference in activation entropies between fast exchanging (0.01 ns) and slow exchanging (0.1-1 ns) water molecules is -27 J/K/mol. Dunitz (Scie nce 1997;264:670.) has estimated the maximum entropy loss of a water molecu le due to binding to be 28 J/K/mol. Therefore, our results suggest that the entropy of interior water molecules is similar to entropy of bulk water. P ublished 2000 Wiley-Liss, Inc.(dagger)