Water penetration and escape in proteins

Abstract

The kinetics of water penetration and escape in cytochrome c (cyt c) is studied by molecular dynamics (MD) simulations at various temperatures. Water molecules that penetrate the protein interior during the course of an MD simulation are identified by monitoring the number of water molecules in the first coordination shell (within 3.5 A) of each water molecule in the 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 extended 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 picoseconds (ps) within a 1.5 nanoseconds (ns) time period. Twenty-seven (27) water 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 molecules do not escape; at T = 360 K one water molecule does not escape; at 430 K all water molecules exchange. Some of the internal water molecules show mean square displacements (MSD) of 1 A2 characteristic of structural waters. Others show MSD as large as 12 A2, suggesting that some of these water molecules occupy transient cavities and diffuse extensively within the protein. Motions of protein-bound water molecules are rotationally hindred, 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 of energy barriers, relative to kappa BT, for water exchange. At T = 300 K estimates of the roughness of the activation energy distribution is 4-10 kJ/mol (2-4 kappa BT). 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 (Science 1997;264:670.) has estimated the maximum entropy loss of a water molecule 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.

MHC–Peptide Binding is Assisted by Bound Water Molecules

“…Nevertheless, this description bears some limitations, and has to be reformulated for large cavities that accommodate major solvent clusters. 48,49 In this work, we trace solvent molecules involved in the interface between MHC and bound peptide by following the time-history of their coordination number. In this way, we can identify water penetration and escape events.…”

“…This number is obtained for every saved configuration by counting all water molecules within a range of 3.5 Å from the water oxygen atom, which defines the first hydration shell of water. 48 Water molecules in bulk have four to six water molecules in their first hydration shell. However, the instantaneous coordination number covers a range of 0 -12 coordinated neighbors per water molecule, having its peak in N c ¼ 5 for bulk water.…”

X-ray and Thermodynamic Studies of Staphylococcal Nuclease Variants I92E and I92K: Insights into Polarity of the Protein Interior

“…Twenty-seven molecules stayed for at least 300 ps. 18,19 They have obtained similar, unpublished results for nuclease. (2) Our X-ray studies of nuclease show that welllocalized water molecules are often seen in the hydrophobic core in association with polar residues placed there by site-directed mutagenesis.…”

Water as a Conformational Editor in Protein Folding

“…Firstly, the use of an implicit-solvent PMF ignores the time-dependent response of the solute surroundings, and we are assuming the reconfiguration of the solvent is fast relative to contact formation. 37 Secondly, we are assuming pairwise additivity in our potentials. Simulations of the association of three methane molecules in water have shown that the three-body PMF is not additive and requires an additional cooperative term.…”