Conservation of solvent‐binding sites in 10 crystal forms of T4 lysozyme

Abstract

Solvent-binding sites were compared in 10 different crystal forms of phage T4 lysozyme that were refined using data from 2.6 A to 1.7 A resolution. The sample included 18 crystallographically independent lysozyme molecules.Despite different crystallization conditions, variable crystal contacts, changes due to mutation, and varying attention to solvent during crystallographic refinement, 62% of the 20 most frequently occupied sites were conserved. Allowing for potential steric interference from neighboring molecules in the crystal lattice, this fraction increased to 79% of the sites. There was, however, no solvent-binding site that was occupied in all 18 lysozyme molecules. A buried double site was occupied in 17 instances and 2 other internal sites were occupied 15 times. Apart from these buried sites, the most frequently occupied sites were often at the amino-termini of a-helices. Solvent molecules at the most conserved sites tended to have crystallographic thermal factors lower than average, but atoms with low E-factors were not restricted to these sites.Although superficial inspection may suggest that only 50-60'70 (or less) of solvent-binding sites are conserved in different crystal forms of a protein, it appears that many sites appear to be empty either because of steric interference or because the apparent occupancy of a given site can vary from crystal to crystal. The X-ray method of identifying sites is somewhat subjective and tends to result in specification only of those solvent molecules that are well ordered and bound with high occupancy, even though there is clear evidence for solvent bound at many additional sites. Because similar sites are occupied under a variety of crystallization conditions, it seems likely that binding of solvent to such sites will be maintained in solution under physiological conditions.

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

“…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).…”

Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway

“…28,29 In this application, we focused on the wildtype T4L and investigated conformational transition pathway between open and close structures using PaCS-MD. As the reactant and product, the wild-type close (PDB entry 2LZM 30 ) and M6I-mutant open structure (PDB entry 150L 31 ) mutated back to the wild type were employed, respectively. AMBER ff99SB force field 32 was employed for chignolin and T4L.…”

A “structural” water molecule in the family of fatty acid binding proteins

“…This idea is based on the assumption that buried main-chain ϾCO and ϾNH groups without hydrogen bonding partners provided by internal water molecules would be structurally destabilizing~Baker & Hubbard, 1984!. Further support for this thesis is provided by the fact that certain internal water molecules are well ordered and highly conserved in homologous proteins, as well as in various crystal forms of the same protein~Sreenivasan & Axelsen, 1992;Zhang & Matthews, 1994!. Buried water molecules, especially those considered to be of structural importance, have been extensively investigated in recent years. In the landmark study of internal water in bovine pancreatic trypsin inhibitor~BPTI!, a displacement of a single water molecule resulted in protein destabilization of 0.7 kcal0mol~Berndt et al, 1993!…”