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D W Rice

Publications and source records attributed to D W Rice.

At least 109 records · Page 6Linked to original sources
PubMed1994

A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures.

This paper discusses the use of graph-theoretic methods for the representation and searching of three-dimensional patterns of side-chains in protein structures. The position of a side-chain is represented by pseudo-atoms, and the relative positions of pairs of side-chains by the distances between them. This description of the geometry can be represented by a labelled graph in which the nodes and the edges of the graph represent the pseudo-atoms and the sets of inter-pseudo-atomic distances, respectively. Given such a representation, a protein can be searched for the presence of a user-defined query pattern of side-chains by means of a subgraph-isomorphism algorithm which is implemented in the program ASSAM. Experiments with one such algorithm, that due to Ullmann, show that it provides both an effective and a highly efficient way of searching for patterns of side-chains. The method is illustrated by searches for the serine protease catalytic triad, for residues involved in the catalytic activity of staphyloccocal nuclease, and for the zinc-binding side-chains of thermolysin. The catalytic triad pattern search revealed the existence of a second Asp-His-Ser triad-like arrangement of residues in trypsinogen and chymotrypsinogen, in addition to the catalytic residues. In addition the program can be used to search for hypothetical patterns, as is shown for a pattern of three tryptophan side-chains. These searches demonstrate that the search algorithm can successfully retrieve the great majority of the expected proteins, as well as other, previously unreported proteins that contain the pattern of interest.

Algorithms↗
PubMed1994

The catalytic role of aspartate in the active site of glutamate dehydrogenase.

A putative catalytic aspartyl residue, Asp-165, in the active site of clostridial glutamate dehydrogenase has been replaced with serine by site-directed mutagenesis. The mutant enzyme is efficiently overexpressed in Escherichia coli as a soluble protein and can be successfully purified by the dye-ligand chromatographic procedure normally employed for the wild-type enzyme. By several criteria, including circular dichroism spectrum, sulphydryl reactivity with Ellman's reagent, crystallization and mobility in non-denaturing electrophoresis, the enzyme appears to be correctly folded. NAD+ protects the D165S mutant against modification by Ellman's reagent, suggesting unimpaired binding of coenzyme. In standard assays the specific activity is decreased 10(3)-fold in the reductive amination reaction and 10(5)-fold for oxidative deamination. Kinetic studies show that apparent Km values for NADH and 2-oxoglutarate are almost unchanged. The large reduction in the reaction rate coincides with a weakening of the affinity for ammonium ion (Km > 300 mM, compared with 60 mM for the wild-type). The data are entirely consistent with the direct involvement of D165 in catalysis rather than in the binding of coenzyme or 2-oxoglutarate.

Amino Acid Sequence↗
PubMed1994

Crystallization of the NADH-specific enoyl acyl carrier protein reductase from Brassica napus.

The tetrameric, NADH-dependent enoyl acyl carrier protein reductase from developing seeds of Brassica napus (oil seed rape) has been crystallized from solutions containing ammonium sulphate as the precipitant in the presence of NAD+ or NADH using the hanging drop method of vapour diffusion. The crystals belong to the tetragonal system and are in space group P4(2)2(1)2 with cell dimensions a = b = 70.5 A, c = 117.8 A. Considerations of the possible values of Vm indicate that the asymmetric unit contains a single subunit. The crystals are resistant to radiation damage and X-ray diffraction photographs taken with synchrotron radiation show measurable reflections to beyond 1.9 A resolution. Determination of the structure of this enzyme will advance the understanding of the mechanisms of lipid biosynthesis in plants and provide an opportunity to study the interactions between this enzyme and its acyl carrier protein substrate.

Brassica↗
PubMed1994

Crystallization and quaternary structure analysis of the NAD(+)-dependent leucine dehydrogenase from Bacillus sphaericus.

The NAD(+)-dependent leucine dehydrogenase from Bacillus sphaericus has been crystallized by the hanging drop method of vapour diffusion, using ammonium sulphate as the precipitant. The crystals belong to the tetragonal system and are in space group I4, with unit cell dimensions of a = b = 138.4 A and c = 121.8 A. Considerations of the values of Vm, the space group symmetry and an analysis of a self-rotation function calculated on a preliminary data set collected to 3 A resolution show that the asymmetric unit contains a dimer with the twofold axis perpendicular to the crystallographic four fold, indicating that the quaternary structure of this enzyme is octameric. Leucine dehydrogenase belongs to a superfamily of amino acid dehydrogenases which display considerable differences in amino acid specificity and elucidation of its three-dimensional structure should enable the molecular basis of this differential specificity to be examined in detail.

Amino Acid Oxidoreductases↗
PubMed1994

Structural similarity between binding sites in influenza sialidase and isocitrate dehydrogenase: implications for an alternative approach to rational drug design.

Using searching techniques based on algorithms derived from graph theory, we have established a similarity between a 3-dimensional cluster of side chains implicated in drug binding in influenza sialidase and side chains involved in isocitrate binding in Escherichia coli isocitrate dehydrogenase. The possible implications of the use of such comparative methods in drug design are discussed.

Algorithms↗
PubMed1994

Mixed-function oxidase-specific activity in wild and caged speckled sanddabs Citharichthys stigmaeus in Elkhorn Slough, Moss Landing Harbor and nearshore Monterey Bay, California.

The goal of this study was to characterize the spatial, seasonal and annual hepatic activities of mixed-function oxidase (MFO) in the speckled sanddab Citharichthys stigmaeus, the most common fish in the Moss Landing area. In addition, techniques to monitor MFO activities in caged speckled sanddabs were developed and tested. Once the relationship between MFO activities in caged and wild fish populations is determined, caged fish could be used to monitor potential hydrocarbon impacts at Moss Landing, or other marine sites. During each of the spatial, seasonal and annual sediment samplings conducted in 1985-1987 as part of a separate hydrocarbon variability study at Moss Landing, 12 wild speckled sanddabs were collected from Moss Landing Harbor, Elkhorn Slough and nearshore Monterey Bay sites. In addition, four locations were chosen for a 14-day field caged fish experiment. The caged fish experiments successfully demonstrated the feasibility of using caged sanddabs as indicators of hydrocarbon exposure. The major source of variability in hepatic aryl hydrocarbon hydroxylase activity in wild speckled sanddabs from the Moss Landing area is due to seasonal rather than site differences. Significant relationships between caged fish MFO response and sediment hydrocarbon concentrations were found. It is possible that caged fish could be used in place of costly sediment sampling and analysis, and provide a more direct method to assess biological impacts. Many of the caging techniques demonstrated in this study can easily be transferred to other benthic flatfish, and other marine and freshwater environments.

Journal Article↗
PubMed1993

Evolution of substrate diversity in the superfamily of amino acid dehydrogenases. Prospects for rational chiral synthesis.

We have analysed the sequence homology between glutamate, leucine and phenylalanine dehydrogenases in the light of the solution of the structure of the glutamate dehydrogenase from Clostridium symbiosum. This analysis indicates that the elements of secondary structure comprising the core of the two domains in glutamate dehydrogenase are conserved in the other two enzymes. There is a striking conservation of the residues responsible for the recognition of the nicotinamide ring of the nucleotide cofactor and the backbone of the amino acid substrates. Furthermore, residues involved in a major conformational rearrangement on amino acid binding are preserved, as are those implicated in the catalytic chemistry. In contrast, the pattern of insertions/deletions between these enzymes is consistent with possible differences in quaternary structure. Differential substrate specificity between these enzymes is achieved by critical substitutions at the base of the binding pocket, which accommodates the side-chain of the amino acid substrate. This provides insights into the mutations necessary to produce new catalysts for the chiral synthesis of novel amino acids.

Amino Acid Oxidoreductases↗
PubMed1993

Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis.

We have solved the structure of the binary complex of the glutamate dehydrogenase from Clostridium symbiosum with glutamate to 1.9 A resolution. In this complex, the glutamate side-chain lies in a pocket on the enzyme surface and a key determinant of the enzymic specificity is an interaction of the substrate gamma-carboxyl group with the amino group of Lys89. In the apo-enzyme, Lys113 from the catalytic domain forms an important hydrogen bond to Asn373, in the NAD(+)-binding domain. On glutamate binding, the side-chain of this lysine undergoes a significant movement in order to optimize its hydrogen bonding to the alpha-carboxyl group of the substrate. Despite this shift, the interaction between Lys113 and Asn373 is maintained by a large-scale conformational change that closes the cleft between the two domains. Modelling studies indicate that in this "closed" conformation the C-4 of the nicotinamide ring and the alpha-carbon atom of the amino acid substrate are poised for efficient hydride transfer. Examination of the structure has led to a proposal for the catalytic activity of the enzyme, which involves Asp165 as a general base, and an enzyme-bound water molecule, hydrogen-bonded to an uncharged lysine residue, Lys125, as an attacking nucleophile in the reaction.

Bacterial Proteins↗
PubMed1993

Three-dimensional structural resemblance between the ribonuclease H and connection domains of HIV reverse transcriptase and the ATPase fold revealed using graph theoretical techniques.

Using 3D searching techniques based on algorithms derived from graph theory, we have established two previously unreported structural similarities involving the ribonuclease H (RNase H) domain of HIV-1 reverse transcriptase (RT). First, we report that there is a strong similarity between the 3D folds of the RNase H domain of RT and the 'ATPase folds' of hexokinase, the 70 kDa heat-shock cognate protein and actin. Like RNase H, these enzymes are involved in nucleotide binding and metal ion-catalysed cleavage of a phosphodiester bond. Similarities of the folding motif and the position of the metal-binding site in these enzymes suggest possible functional analogies and evolutionary relationships with RNase H. Second, we find there is a strong resemblance between the folds of the RNase H domain and of the p66 and p51 'connection' domains of RT. It is possible that this striking similarity within the RT structure indicates a possible ancestral gene doubling event. The similarity may also indicate that the connection domains possess functional roles in addition to those previously suggested, and they may therefore represent a further target for the design of therapeutic agents.

Adenosine Triphosphatases↗
PubMed1993

Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm.

A program called PROTEP is described that permits the rapid comparison of pairs of three-dimensional protein structures to identify the patterns of secondary structure elements that they have in common. The representation of the protein structures as labelled graphs, where the secondary structure elements in a protein and the spatial and angular relationships between them correspond to the nodes and edges of a graph, was developed for use with an earlier program, called POSSUM, which identified subgraph isomorphisms in protein structures. PROTEP takes this representation and uses a different and more flexible approach to locating structural patterns in pairs of proteins, using a maximal common subgraph isomorphism algorithm that is based on a clique detection procedure. A range of searches is described to demonstrate that areas of common structural overlap between protein structures taken from the Protein Data Bank can be identified both effectively and efficiently.

Algorithms↗
PubMed1993

Seasonal and annual distribution of organic contaminants in marine sediments from Elkhorn slough, moss landing harbor and nearshore Monterey Bay, California.

This 3-year study provides data on the spatial, seasonal and annual variability of hydrocarbons and total organic carbon present in marine sediments at three sites: Elkhorn Slough, Moss Landing Harbor and nearshore Monterey Bay in the vicinity of Moss Landing, California. The study provides baseline information that could be used to evaluate the potential impacts of future fuel oil releases occuring in the Moss Landing area. Groups of hydrocarbons were chosen to represent the hydrocarbon inputs into the Moss Landing area. These included the pesticide dichlorodiphenyltrichloroethane (DDT), polychlorinated biphenyl (PCB), phthalic acid ester (PAE), polycyclic aromatic hydrocarbon (PAH) and combustion PAHs (SigmaCOMBs). For SigmaDDTs, SigmaPCBs, SigmaPAEs, SigmaPAHs and SigmaCOMBs, the major sources of variability were between sites and random effects. Subsites within each site contributed little variability. No significant seasonal differences in any chemical contaminant group were found at any site. Significant seasonal differences in total organic carbon (TOC) and significant annual differences in SigmaPCBs, SigmaPAHs, SigmaCOMBs and SigmaPAEs were found at the nearshore Monterey Bay site. Significant annual differences in SigmaPAEs and TOC were found within Moss Landing Harbor, and significant annual differences in SigmaPAEs were found within the Elkhorn Slough site. Implications for future sampling designs in the Moss Landing area are that given the current baseline conditions (a stable, low rate of hydrocarbon input), a variability of 75-150 m(2) may not need to be heavily sampled. Spatial variability, not seasonal or annual variability, is the major source of hydrocarbon variability in Moss Landing sediments, although 3 years may not be long enough to establish long-term annual trends. Further research to determine the SigmaPAH spatial sampling scale for oil spills is needed.

Journal Article↗
PubMed1992

Purification and crystallization of the light harvesting LH1 complex from Rhodobacter sphaeroides.

The LH1 light harvesting complex has been purified from a mutant of the photosynthetic bacterium Rhodobacter sphaeroides which synthesizes LH1 as the sole pigment protein. Crystallization trials using polyethylene glycol as the precipitant in the presence of the detergent n-octyl glucoside have resulted in the formation of needle like crystals which diffract beyond 3.5 A and which are relatively resistant to radiation damage. X-ray photographs have established that the crystals belong to the tetragonal system and are probably in space group P4(2)2(1)2. Estimates of the crystal density indicate that the asymmetric unit of the crystals contains two oligomers each with an alpha 6 beta 6 stoichiometry.

Bacterial Proteins↗
PubMed1992

Structural consequences of sequence patterns in the fingerprint region of the nucleotide binding fold. Implications for nucleotide specificity.

The dinucleotide binding beta alpha beta motif in the crystal structures of seven different enzymes has been analysed in terms of their three-dimensional structures and primary sequences. We have identified that the hydrogen bonding of the adenine ribose to the glycine-rich turn containing the fingerprint sequence GXGXXG/A occurs via a direct or indirect mechanism, depending on the nature of the fingerprint sequence but independent of coenzyme specificity. The major determinant of the type of interaction is the nature of the residue occupying the last position of the above fingerprint. In the NAD(+)-linked dehydrogenases, an acidic residue is commonly used to form important hydrogen bonds to the adenine ribose hydroxyls and, hitherto, this residue has been thought to be an indicator of NAD+ specificity. However, on the basis of the three-dimensional structure of the NAD(+)-linked glutamate dehydrogenase (GDH) from Clostridium symbiosum we have demonstrated that this residue is not a universal requirement for the construction of an NAD+ binding site. Furthermore, considerations of sequence homology unambiguously identify an equivalent acidic residue in both NADP+ and dual specificity glutamate dehydrogenases. The conservation of this residue in these enzymes, coupled to its close proximity to the 2' phosphate implied by the necessary similarity in three-dimensional structure to C. symbiosum GDH, implicates this residue in the recognition of the 2' phosphate either via water-mediated or direct hydrogen-bonding schemes. Analysis of the latter has led us to suggest that two patterns of recognition for the 2' phosphate group of NADP(+)-binding enzymes may exist, which are distinguished by the ionization state of the 2' phosphate.

Adenosine Diphosphate Ribose↗
PubMed1992

Structural relationship between the hexameric and tetrameric family of glutamate dehydrogenases.

The family of glutamate dehydrogenases include a group of hexameric oligomers with a subunit M(r) of around 50,000, which are closely related in amino acid sequence and a smaller group of tetrameric oligomers based on a much larger subunit with M(r) 115,000. Sequence comparisons have indicated a low level of similarity between the C-terminal portion of the tetrameric enzymes and a substantial region of the polypeptide chain for the more widespread hexameric glutamate dehydrogenases. In the light of the solution of the three-dimensional structure of the hexameric NAD(+)-linked glutamate dehydrogenase from Clostridium symbiosum, we have undertaken a detailed examination of the alignment of the sequence for the C-terminal domain of the tetrameric Neurospora crassa glutamate dehydrogenase against the sequence and the molecular structure of that from C. symbiosum. This analysis reveals that the residues conserved between these two families are clustered in the three-dimensional structure and points to a remarkably similar layout of the glutamate-binding site and the active-site pocket, though with some differences in the mode of recognition of the nucleotide cofactor.

Amino Acid Sequence↗
PubMed1992

Three-dimensional structural resemblance between leucine aminopeptidase and carboxypeptidase A revealed by graph-theoretical techniques.

Using 3-D searching techniques based on algorithms derived from graph theory we have established a striking structural similarity between the structure of bovine carboxypeptidase A and that of the C-terminal domain of bovine leucine aminopeptidase. There is no significant sequence homology between the aminopeptidases and the carboxypeptidases but the strong structural relationship detected in this complex fold suggests that there may be a very remote divergent evolutionary relationship between these two enzyme classes.

Animals↗
PubMed1992

Effect of additives on the crystallization of glutamate dehydrogenase from Clostridium symbiosum. Evidence for a ligand-induced conformational change.

A new crystal form of the hexameric NAD(+)-linked glutamate dehydrogenase (GDH) from Clostridium symbiosum has been grown using the hanging drop method of vapour diffusion. The crystals are obtained either by using high concentrations of the amino acid substrate of the enzyme, glutamate, as the precipitant or by co-crystallization from ammonium sulphate in the presence of either p-chloromercuribenzene sulphonate or potassium tetracyanoplatinate. The crystals diffract well and X-ray photographs have established that they are in the space group R32. Considerations of the values of Vm indicate that the asymmetric unit of the R32 crystals contains a single subunit. Packing considerations based on the structure of the native enzyme determined from a different crystal form suggest that the molecule must undergo a significant conformational change in order to be accommodated in the new cell. Such a conformational rearrangement may represent an important step in the catalytic cycle.

Clostridium↗