Internal water molecules and H‐bonding in biological macromolecules: A review of structural features with functional implications

Abstract

Conserved structural patterns of internal water molecules and/or H-bond chains were observed and are here correlated in this review, which then describes two functional properties: equilibration of hydrostatic pressure and proton transport. Available evidence in support of these hypotheses is presented, together with suggested experiments to test them. High-resolution crystal structures of a variety of proteins were studied with interactive computer graphics. Conserved H-bonding linkages may be used as a paradigm for a rationalization of proton transport in membranes. The concept of the "proton wire," which links buried active-site amino acids with the surface of the protein raises the more general question of the functional role of the various molecular components

Protein Hydration Dynamics in Aqueous Solution: A Comparison of Bovine Pancreatic Trypsin Inhibitor and Ubiquitin by Oxygen-17 Spin Relaxation Dispersion

“…Since the number (N I ) of internal water molecules shows large (relative) variations (not directly correlated with N S or surface area) among different proteins (Finney, 1979;Edsall & McKenzie, 1983;Baker & Hubbard, 1984;Rashin et al, 1986;Meyer, 1992), we expect a correspondingly large variation of the ratio b/a. In particular, b/a should be much larger for BPTI, which contains four buried water molecules in all three investigated crystal forms (Deisenhofer & Steigemann, 1975;Wlodawer et al, 1984Wlodawer et al, , 1987a as well as in solution (Otting & Wü thrich, 1989;Otting et al, 1991a), than for ubiquitin, the crystal structure of which does not reveal any internal water molecules (Vijay-Kumar et al, 1987).…”

Thermal stability determinants of chicken egg‐white lysozyme core mutants: Hydrophobicity, packing volume, and conserved buried water molecules

“…The roles of conserved water molecules in a number of different proteins have been discussed (e.g., Wlodawer et al, 1987;Meyer, 1992;Berghuis et al, 1994). Zhang and Matthews (1994) observed that those most conserved are frequently internal and are characterized by low crystallographic thermal factors.…”

“…Zhang and Matthews (1994) observed that those most conserved are frequently internal and are characterized by low crystallographic thermal factors. It has been suggested that well-ordered, internal water molecules are significant factors in determining structural stability (Alber et al, 1987;Williams et al, 1994) or function (Alexander et al, 1991;Meyer, 1992). The subject has been reviewed by Westhof (1993) and by Teeter (1991).…”

Protein hydration dynamics in solution: a critical survey

“…Protein-water interactions thus shape the free energy landscape that governs the folding, structure and stability of proteins (Kauzmann 1959;Dill 1990). Moreover, the functional processes mediated by proteins, such as binding, recognition and catalysis, often involve specific interactions with individual water molecules (Meyer 1992;Williams et al 1994;Baker 1995).…”