Biomedical subjects

G W Harris

Publications and source records attributed to G W Harris.

At least 19 recordsLinked to original sources

PubMed1992

The segmented anisotropic refinement of monoclinic papain by the application of the rigid-body TLS model and comparison to bovine ribonuclease A.

The anisotropic displacements of selected rigid groups in monoclinic papain have been refined from X-ray diffraction data by application of the rigid-body TLS model. The rigid groups chosen were the aromatic side chains of tryptophan, tyrosine, histidine and phenylalanine, and the planar carboxylic and guanidinium side chains of aspartic acid, glutamic acid, glutamine, asparagine and arginine. The derived translation and libration tensors have been compared with those previously derived for bovine ribonuclease A and provide evidence for different modes and anisotropies of displacement over the two proteins.

Amino Acids↗

PubMed1992

Some different strategies of least-squares refinement of a molecule.

Refinements of a macromolecule (ribonuclease-A) based on structure amplitudes, magnitude of F, and structure amplitude squares, magnitude of F2, were carried out and the results compared. Although the conventional R values are higher for the magnitude of F2 refinement, positional parameters from both types of refinement were not significantly different. However, the mean-square displacements from magnitude of F2 refinements were systematically higher than for those using magnitude F. Various resolution windows and weighting schemes were employed during the work. Electron density maps were examined for magnitude of F2 refinements and were very similar to those using magnitude of F in spite of a conventional R factor of 0.29 using all 1.4 A data. While magnitude of F2 refinements may be formally more correct than magnitude of F refinements, there is little evidence that magnitude of F2 refinement is superior provided that a reasonable weighting strategy is adopted.

Least-Squares Analysis↗

PubMed1989

Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body TLS model.

The anisotropic displacements of selected rigid groups in bovine ribonuclease A have been refined from X-ray diffraction data by the application of the rigid-body TLS model. The rigid groups chosen were the side chains of tyrosine, histidine and phenylalanine and the planar side chains of aspartic acid, glutamic acid, glutamine, asparagine and arginine. The method has also been applied to the co-crystallizing active-site sulfate anion. This has enabled the description of the motion of the above-mentioned side-chain atoms by anisotropic displacement ellipsoids from a 1.45 A refinement. The hydrophobic side groups in the protein core show mainly translational motion, with mean-square librations of 20 deg2 which are similar to those found in some close-packed crystals of small organic molecules. Librational displacements are much more significant in the hydrophilic side groups where their magnitudes can be correlated with solvent accessibility. Large librations of some solvent exposed side chains correspond with the breakdown of a simple TLS model and the existence of multiple orientations of the side groups. The TLS model has also been applied to the whole protein molecule and shows that the average motion is approximately isotropic with little librational character.

Animals↗

PubMed1987

X-ray refinement study on the binding of cytidylic acid (2'-CMP) to ribonuclease A.

The X-ray structure of the inhibitor complex of bovine ribonuclease A with cytidylic acid (2'-CMP) has been determined at 2.3 A (1 A = 0.1 nm) resolution and refined by restrained least-squares refinement to R = 0.132 for 5650 reflections. Incorporation of the inhibitor molecule has occurred with little disturbance of the protein main-chain atoms, although significant displacement of some side-chain atoms has occurred, particularly in the region of the active site. The binding of 2'-CMP to ribonuclease A is different from that of the related cytidine-N(3)-oxide 2'-phosphate, which has an extra oxygen on N(3) of the cytidine base. The PO4(2-) group is held by hydrogen bond interactions to the side-groups of His 12, Glu 11 and His119. Thr45 is involved in stabilizing the enzyme-ligand complex by forming hydrogen bond interactions between O(gamma) and the pyrimidine base N(3) atom and between the main-chain N(45) and O(2) of the base. Phe120 is much closer to the inhibitor than in the cytidine N(3)-oxide 2'-phosphate structure.

Amino Acid Sequence↗

PubMed1987

Ribonuclease A. Analysis of the hydrogen bond geometry, and spatial accessibility at the active site.

The hydrogen bonding of bovine ribonuclease A derived from the high resolution X-ray structure has been studied in detail. Correlations have been examined for main-chain-main-chain hydrogen bond angles, torsion angles and distances, respectively. Differences are found consistently for correlations associated with alpha-helix and beta-sheet, respectively. Ten of the 124 side-chains have four or more hydrogen bond contacts; two, including Glu-101, have five or more. Three potential C = O---H, three N---X and three potential side-chain H-bonds fail to form. A search for highly inaccessible buried residues resulted in nine outstanding examples, all of which are conserved across 38 known mammalian ribonuclease A sequences, indicating the importance of these residues for structural stability. Of the two histidines in the active site, His-12 has five hydrogen bonds and His-119 three. The conformational space accessible to these two catalytically important residues studied by means of simple non-bonded contact energy calculations confirms the existence of two alternative, interchangeable locations for His-119, while His-12 is locked in a local energy minimum.

Binding Sites↗

PubMed1983

Trace nitrogenous species in urban atmospheres.

Recent results concerning the identification and measurement of nitrogenous air pollutants in the California South Coast Air Basin (CSCAB) are presented. In planning or evaluating studies of the human health effects of these pollutants, it is important to consider the entire range of species which may be present. We provide estimates of typical exposures to nitrogenous air pollutants during a single day oxidant event in the CSCAB.

Air Pollutants↗

PubMed1978