The high frequency dielectric constant of poly-adenine (poly-A) was measured between 1 MHz and 1 GHz. The purpose of these experiments was to investigate the state of water molecules that are bound to the charged groups of the poly-A molecule. Analysis of the data using the Maxwell's mixture equation revealed the dielectric constant of bound water higher than we expected. Using Onsager's intern...

This paper reports computational studies of substrate water binding to the oxygen-evolving centre (OEC) of photosystem II (PSII), completely ligated by amino acid residues, water, hydroxide and chloride. The calculations are based on quantum mechanics/molecular mechanics hybrid models of the OEC of PSII, recently developed in conjunction with the X-ray crystal structure of PSII from the cyanoba...

High-resolution protein ground-state structures of proton pumps and channels have revealed internal protein-bound water molecules. Their possible active involvement in protein function has recently come into focus. An illustration of the formation of a protonated protein-bound water cluster that is actively involved in proton transfer was described for the membrane protein bacteriorhodopsin (bR...

The crystal structure of human carbonic anhydrase II (HCA II) obtained at 0.9 A resolution reveals that a water molecule, termed deep water, Dw, and bound in a hydrophobic pocket of the active site forms a short, strong hydrogen bond with the zinc-bound solvent molecule, a conclusion based on the observed oxygen-oxygen distance of 2.45 A. This water structure has similarities with hydrated hydr...

Different strategies for the in silico generation of ligand molecules in the binding site of poly(ADP-ribose)polymerase (PARP) were studied in order to observe the effect of the targeting and displacement of tightly bound water molecules. Several molecular scaffolds were identified as having better interactions in the binding site when targeting one or two tightly bound water molecules in the N...

The importance of the consideration of water molecules in the structural interpretation of ligand-derived pharmacophore models is explored. We compare and combine results from recently introduced methods for bound-water molecule identification in protein binding sites and ligand-superposition-based pharmacophore derivation, for the interpretation of ligand-derived pharmacophore models. In the a...

The dynamics following charge transfer to solvent from iodide to a water cluster are studied using time-resolved photoelectron imaging of I-(H2O)n and I-(D2O)n clusters with n< or =28. The results show spontaneous conversion, on a time scale of approximately 1 ps, from water cluster anions with surface-bound electrons to structures in which the excess electron is more strongly bound and possibl...

Matchedeld methods are known to have a severe ambiguity problem. In low signal-to-noise-ratios (SNR's), where the estimator cannot distinguish between the ambiguity function peak near the true source location and ambiguous ones, its mean square error deviates radically from the Cramer-Rao lower bound (CRLB). In this paper, the Barankin bound for the source localization problem in an uncertain s...