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G J Barton

Publications and source records attributed to G J Barton.

At least 37 records · Page 2Linked to original sources
PubMed1994

Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility.

Side-chain to side-chain contacts, accessibility, secondary structure and RMS deviation were compared within 607 pairs of proteins having similar three-dimensional (3D) structures. Three types of protein 3D structural similarities were defined: type A having sequence and usually functional similarity; type B having functional, but no sequence similarity; and type C having only 3D structural similarity. Within proteins having little or no sequence similarity (types B and C), structural features frequently had a degree of conservation comparable to dissimilar 3D structures. Despite similar protein folds, as few as 30% of residues within similar protein 3D structures can form a common core. RMS deviations on core C alpha atoms can be as high as 3.2 A. Similar protein structures can have secondary structure identities as low as 41%, which is equivalent to that expected by chance. By defining three categories of amino acid accessibility (buried, half buried and exposed), some similar protein 3D structures have as few as 30% of positions in the same category, making them indistinguishable from pairs of dissimilar protein structures. Similar structures can also have as few as 12% of common side-chain to side-chain contacts, and virtually no similar energetically favourable side-chain to side-chain interactions. Complementary changes are defined as structurally equivalent pairs of interacting residues in two structures with energetically favourable but different side-chain interactions. For many proteins with similar three-dimensional structures, the proportion of complementary changes is near to that expected by chance, suggesting that many similar structures have fundamentally different stabilising interactions. All of the results suggest that proteins having similar 3D structures can have little in common apart from a scaffold of core secondary structures. This has profound implications for methods of protein fold detection, since many of the properties assumed to be conserved across similar protein 3D structures (e.g. accessibility, side-chain to side-chain contacts, etc.) are often unconserved within weakly similar (i.e. type B and C) protein 3D structures. Little difference was found between type B and C similarities suggesting that the structure of similar proteins can evolve beyond recognition even when function is conserved. Our findings suggest that it is more general features of protein structure, such as the requirements for burial of hydrophobic residues and exposure of polar residues, rather than specific residue-residue interactions that determine how well a particular sequence adopts a particular fold.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1994

A structural analysis of phosphate and sulphate binding sites in proteins. Estimation of propensities for binding and conservation of phosphate binding sites.

The high resolution X-ray structures of 38 proteins that bind phosphate containing groups and 36 proteins binding sulphate ions were analysed to characterise the structural features of anion binding sites in proteins. 34 of the 66 phosphates found were in close proximity to the amino terminus of an alpha-helix. 27% of phosphate groups bind to only one amino acid, but there is a wide distribution, with 3% of phosphates binding to seven residues. Similarly, there is a large variability in the number of contacts each phosphate group makes to the protein. This ranges from none (3% of phosphates) to nine (3% of phosphates). The most common number of contacts is two (23% of phosphates). The most commonly found residue at helix-type binding sites is glycine, followed by Arg, Thr, Ser and Lys. At non-helix binding sites, the most commonly found residue is Arg followed by Tyr, His, Lys and Ser. There is no typical phosphate binding site. There are marked differences between propensities for phosphate binding at helix and non-helix type binding sites. Non-helix binding sites show more discrimination between the types of residues involved in binding when compared to the helix set. The propensities for binding of the amino acids reveal the expected trend of positively charged and polar residues being good at binding (although that for lysine is unexpectedly low) with the bulky non-polar residues being poor at binding. Bulky residues are less likely to bind with the amide nitrogen. Sulphate binding sites show similar trends. Analysis of multiple sequence alignments that include phosphate and sulphate binding proteins reveals the degree of conservation at the binding site residues compared to the average conservation of residues in the protein. Phosphate binding site residues are more conserved than sulphate binding sites.

Crystallography, X-Ray↗
PubMed1994

Conservation analysis and structure prediction of the protein serine/threonine phosphatases. Sequence similarity with diadenosine tetraphosphatase from Escherichia coli suggests homology to the protein phosphatases.

A multiple sequence alignment of 44 serine/threonine-specific protein phosphatases has been performed. This reveals the position of a common conserved catalytic core, the location of invariant residues, insertions and deletions. The multiple alignment has been used to guide and improve a consensus secondary-structure prediction for the common catalytic core. The location of insertions and deletions has aided in defining the positions of surface loops and turns. The prediction suggests that the core protein phosphatase structure comprises two domains: the first has a single, beta sheet flanked by alpha helices, while the second is predominantly alpha helical. Knowledge of the core secondary structures provides a guide for the design of site-directed-mutagenesis experiments that will not disrupt the native phosphatase fold. A sequence similarity between eukaryotic serine/threonine protein phosphatases and the Escherichia coli diadenosine tetraphosphatase has been identified. This extends over the N-terminal 100 residues of bacteriophage phosphatases and E. coli diadenosine tetraphosphatase. Residues which are invariant amongst these classes are likely to be important in catalysis and protein folding. These include Arg92, Asn138, Asp59, Asp88, Gly58, Gly62, Gly87, Gly93, Gly137, His61, His139 and Val90 and fall into three clusters with the consensus sequences GD(IVTL)HG, GD(LYF)V(DA)RG and GNH, where brackets surround alternative amino acids. The first two consensus sequences are predicted to fall in the beta-alpha and beta-beta loops of a beta-alpha-beta-beta secondary-structure motif. This places the predicted phosphate-binding site at the N-terminus of the alpha helix, where phosphate binding may be stabilised by the alpha-helix dipole.

Acid Anhydride Hydrolases↗
PubMed1994

Secondary structure prediction from multiple sequence data: blood clotting factor XIII and Yersinia protein-tyrosine phosphatase.

Predictions of protein structure are best tested without prior knowledge of the protein three-dimensional structure. Three-dimensional atomic models will soon be determined by X-ray crystallography for the alpha-subunit of human blood clotting factor XIII and members of the family of protein tyrosine specific phosphatases. Accordingly, we here present secondary structure predictions for each of these proteins. The secondary structure predictions were generated from aligned sets of protein sequences. This technique has previously provided reliable predictions for the Annexins and the SH2 domains. The factor XIII alpha prediction contains 39 regions predicted in strand conformation (34% of the protein) with only 3 helices (4%). The protein tyrosine phosphatases have 12 predicted strands and 5 helices (30 and 17%, respectively). We expect greater reliability from regions of alignments that show clear patterns of residue conservation (61% of factor XIII alpha and 57% of the protein tyrosine phosphatases). The aligned protein tyrosine phosphatases show two regions (L39-L80 and I138-E253) with clear patterns of residue conservation separated by a region of variable amino acid composition. We suggest this indicates that the tyrosine phosphatase fold comprises two domains separated by an exposed linker. Potential phosphate binding sites are identified in the protein tyrosine phosphatases.

Amino Acid Sequence↗
PubMed1994

Mutational analysis of human papillomavirus E4 proteins: identification of structural features important in the formation of cytoplasmic E4/cytokeratin networks in epithelial cells.

We have previously demonstrated that human papillomavirus type 1 (HPV 1) and 16 (HPV 16) E4 proteins form cytoplasmic filamentous networks which specifically colocalize with cytokeratin intermediate-filament (IF) networks when expressed in simian virus 40-transformed keratinocytes. The HPV 16 (but not the HPV 1) E4 protein induced the collapse of the cytokeratin networks. (S. Roberts, I. Ashmole, G. D. Johnson, J. W. Kreider, and P. H. Gallimore, Virology 197:176-187, 1993). The mode of interaction of E4 with the cytokeratin IFs is unknown. To identify E4 sequences important in mediating this interaction, we have constructed a large panel of mutant HPV (primarily HPV 1) E4 proteins and expressed them by using the same simian virus 40-epithelial expression system. Mutation of HPV 1 E4 residues 10 to 14 (LLGLL) abrogated the formation of cytoplasmic filamentous networks. This sequence corresponds to a conserved motif, LLXLL, found at the N terminus of other E4 proteins, and similar results were obtained on deletion of the HPV 16 motif, LLKLL (residues 12 to 16). Our findings indicate that this conserved motif is likely to play a central role in the association between E4 and the cytokeratins. An HPV 1 E4 mutant protein containing a deletion of residues 110 to 115 induced the collapse of the cytokeratin IFs in a manner analogous to the HPV 16 E4 protein. The sequence deleted, DLDDFC, is highly conserved between cutaneous E4 proteins. HPV 1 E4 residues 42 to 80, which are rich in charged amino acids, appeared to be important in the cytoplasmic localization of E4. In addition, we have mapped the N-terminal residues of HPV 1 E4 16-kDa and 10/11-kDa polypeptides expressed by using the baculovirus system and shown that they begin at tyrosine 16 and alanine 59, respectively. Similar-sized E4 proteins are also found in vivo. N-terminal deletion proteins, which closely resemble the 16-kDa and 10/11-kDa species, expressed in keratinocytes were both cytoplasmic and nuclear but did not form cytoplasmic filamentous networks. These findings support the postulate that N-terminal proteolytic processing of the E1-- E4 protein may modulate its function in vivo.

Adult↗
PubMed1993

The limits of protein secondary structure prediction accuracy from multiple sequence alignment.

The expected best residue-by-residue accuracies for secondary structure prediction from multiple protein sequence alignment have been determined by an analysis of known protein structural families. The results show substantial variation is possible among homologous protein structures, and that 100% agreement is unlikely between a consensus prediction and one member of a protein structural family. The study provides the range of agreement to be expected between a perfect secondary structure prediction from a multiple alignment and each protein within the alignment. The results of this study overcome the difficulties inherent in the use of residue-by-residue accuracy for assessing the quality of consensus secondary structure predictions. The accuracies of recent consensus predictions for the annexins, SH2 domains and SH3 domains fall within the expected range for a perfect prediction.

Amino Acid Sequence↗
PubMed1993

An efficient algorithm to locate all locally optimal alignments between two sequences allowing for gaps.

An efficient algorithm is described to locate locally optimal alignments between two sequences allowing for insertions and deletions. The algorithm is based on that of Smith and Waterman which returns the single best local alignment. However, the algorithm described here permits all non-intersecting locally optimal alignments to be determined in a single pass through the comparison matrix. The algorithm simplifies the location of repeats, multiple domains and shuffled motifs, and is fast enough to be used on a conventional workstation to scan large sequence databanks.

Algorithms↗
PubMed1993

Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation.

An algorithm is described for the systematic characterization of the physico-chemical properties seen at each position in a multiple protein sequence alignment. The new algorithm allows questions important in the design of mutagenesis experiments to be quickly answered since positions in the alignment that show unusual or interesting residue substitution patterns may be rapidly identified. The strategy is based on a flexible set-based description of amino acid properties, which is used to define the conservation between any group of amino acids. Sequences in the alignment are gathered into subgroups on the basis of sequence similarity, functional, evolutionary or other criteria. All pairs of subgroups are then compared to highlight positions that confer the unique features of each subgroup. The algorithm is encoded in the computer program AMAS (Analysis of Multiply Aligned Sequences) which provides a textual summary of the analysis and an annotated (boxed, shaded and/or coloured) multiple sequence alignment. The algorithm is illustrated by application to an alignment of 67 SH2 domains where patterns of conserved hydrophobic residues that constitute the protein core are highlighted. The analysis of charge conservation across annexin domains identifies the locations at which conserved charges change sign. The algorithm simplifies the analysis of multiple sequence data by condensing the mass of information present, and thus allows the rapid identification of substitutions of structural and functional importance.

Algorithms↗
PubMed1993

Secondary structure prediction for modelling by homology.

An improved method of secondary structure prediction has been developed to aid the modelling of proteins by homology. Selected data from four published algorithms are scaled and combined as a weighted mean to produce consensus algorithms. Each consensus algorithm is used to predict the secondary structure of a protein homologous to the target protein and of known structure. By comparison of the predictions to the known structure, accuracy values are calculated and a consensus algorithm chosen as the optimum combination of the composite data for prediction of the homologous protein. This customized algorithm is then used to predict the secondary structure of the unknown protein. In this manner the secondary structure prediction is initially tuned to the required protein family before prediction of the target protein. The method improves statistical secondary structure prediction and can be incorporated into more comprehensive systems such as those involving consensus prediction from multiple sequence alignments. Thirty one proteins from five families were used to compare the new method to that of Garnier, Osguthorpe and Robson (GOR) and sequence alignment. The improvement over GOR is naturally dependent on the similarity of the homologous protein, varying from a mean of 3% to 7% with increasing alignment significance score.

Algorithms↗
PubMed1992

Conservation analysis and structure prediction of the SH2 family of phosphotyrosine binding domains.

Src homology 2 (SH2) regions are short (approximately 100 amino acids), non-catalytic domains conserved among a wide variety of proteins involved in cytoplasmic signaling induced by growth factors. It is thought that SH2 domains play an important role in the intracellular response to growth factor stimulation by binding to phosphotyrosine containing proteins. In this paper we apply the techniques of multiple sequence alignment, secondary structure prediction and conservation analysis to 67 SH2 domain amino acid sequences. This combined approach predicts seven core secondary structure regions with the pattern beta-alpha-beta-beta-beta-beta-alpha, identifies those residues most likely to be buried in the hydrophobic core of the native SH2 domain, and highlights patterns of conservation indicative of secondary structural elements. Residues likely to be involved in phosphotyrosine binding are shown and orientations of the predicted secondary structures suggested which could enable such residues to cooperate in phosphate binding. We propose a consensus pattern that encapsulates the principal conserved features of the SH2 domains. Comparison of the proposed SH2 domain of akt to this pattern shows only 12/40 matches, suggesting that this domain may not exhibit SH2-like properties.

Amino Acid Sequence↗
PubMed1992

Mast cell tryptases: examination of unusual characteristics by multiple sequence alignment and molecular modeling.

Tryptases are trypsin-like serine proteinases found in the granules of mast cells. Although they show 40% sequence identity with trypsin and contain only 20 or 21 additional residues, tryptases display several unusual features. Unlike trypsin, the tryptases only make limited cleavages in a few proteins and are not inhibited by natural trypsin inhibitors, they form tetramers, bind heparin, and their activity on synthetic substrates is progressively inhibited as the concentration of salt increases above 0.2 M. Unique sequence features of seven tryptases were identified by comparison to other serine proteinases. The three-dimensional structures of the tryptases were then predicted by molecular modeling based on the crystal structure of bovine trypsin. The models show two large insertions to lie on either side of the active-site cleft, suggesting an explanation for the limited activity of tryptases on protein substrates and the lack of inhibition by natural inhibitors. A group of conserved Trp residues and a unique proline-rich region make two surface hydrophobic patches that may account for the formation of tetramers and/or inhibition with increasing salt. Although they contain no consensus heparin-binding sequence, the tryptases have 10-13 more His residues than trypsin, and these are positioned on the surface of the model. In addition, clustering of Arg and Lys residues may also contribute to heparin binding. Putative Asn-linked glycosylation sites are found on the opposite side of the model from the active site. The model provides structural explanations for some to the unusual characteristics of the tryptases and a rational basis for future experiments, such as site-directed mutagenesis.

Amino Acid Sequence↗