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J M Thornton

Publications and source records attributed to J M Thornton.

At least 127 records · Page 7Linked to original sources
PubMed1994

A mutation data matrix for transmembrane proteins.

The widely used Mutation Data Matrix (MDM), is an amino acid comparison matrix calculated from a study of the exchange probabilities (or odds) derived from an analysis of the evolutionary changes seen in groups of very similar proteins. In this work, a mutation data matrix is calculated for membrane spanning segments. This new mutation data matrix is found to be very different from matrices calculated from general sequence sets which are biased towards water-soluble globular proteins, and the differences are discussed in the context of specific structural requirements of membrane spanning segments. This new matrix will help improve the accuracy of integral membrane protein sequence alignments, and could also be of use in the rational design of site directed mutagenesis experiments for this class of proteins.

Amino Acid Sequence↗
PubMed1994

Modeling studies of the change in conformation required for cleavage of limited proteolytic sites.

Previous analyses of limited proteolytic sites within native, folded protein structures have shown that a significant conformational change is required in order to facilitate binding into the active site of the attacking proteinase. For the serine proteinases, the optimum conformation to match the proteinase binding-site geometry has been well characterized crystallographically by the conserved main-chain geometry of the reactive site loops of their protein inhibitors. A good substrate must adopt a conformation very similar to this "target" main-chain conformation prior to cleavage. Using a "loop-closure" modeling approach, we have tested the ability of a set of tryptic-limited proteolytic sites to achieve this target conformation and further tested their suitability for cleavage. The results show that in most cases, significant changes in the conformation of at least 12 residues are required. All the putative tryptic cleavage sites in 1 protein, elastase, were also modeled and tested to compare the results to the actual nicksite in that protein. These results strongly suggest that large local motions proximate to the scissile bond are required for proteolysis, and it is this ability to unfold locally without perturbing the overall protein conformation that is the prime determinant for limited proteolysis.

Algorithms↗
PubMed1994

Buried waters and internal cavities in monomeric proteins.

We have analyzed the buried water molecules and internal cavities in a set of 75 high-resolution, nonhomologous, monomeric protein structures. The number of hydrogen bonds formed between each water molecule and the protein varies from 0 to 4, with 3 being most common. Nearly half of the water molecules are found in pairs or larger clusters. Approximately 90% are shown to be associated with large cavities within the protein, as determined by a novel program, PRO_ACT. The total volume of a protein's large cavities is proportional to its molecular weight and is not dependent on structural class. The largest cavities in proteins are generally elongated rather than globular. There are many more empty cavities than hydrated cavities. The likelihood of a cavity being occupied by a water molecule increases with cavity size and the number of available hydrogen bond partners, with each additional partner typically stabilizing the occupied state by 0.6 kcal/mol.

Camphor 5-Monooxygenase↗
PubMed1994

A revised set of potentials for beta-turn formation in proteins.

Three thousand eight hundred ninety-nine beta-turns have been identified and classified using a nonhomologous data set of 205 protein chains. These were used to derive beta-turn positional potentials for turn types I' and II' for the first time and to provide updated potentials for formation of the more common types I, II, and VIII. Many of the sequence preferences for each of the 4 positions in turns can be rationalized in terms of the formation of stabilizing hydrogen bonds, preferences for amino acids to adopt a particular conformation in phi, psi space, and the involvement of turn types I' and II' in beta-hairpins. Only 1,632 (42%) of the turns occur in isolation; the remainder have at least 1 residue in common with another turn and have hence been classified as multiple turns. Several types of multiple turn have been identified and analyzed.

Amino Acids↗
PubMed1994

NMR and crystallography--complementary approaches to structure determination.

A knowledge of the three-dimensional structure of a protein is essential to understand how a protein performs its functions. It is also a prime requirement for the rational design of novel sequences with specific structural, chemical or catalytic properties. Until recently, such information could only be obtained from X-ray diffraction studies on protein crystals. In the past few years, however, nuclear magnetic resonance (NMR) spectroscopy in solution has rapidly become established as an effective alternative method. This review briefly examines the two techniques and their relevance to protein engineering and design.

Animals↗
PubMed1994

An algorithm for automatically generating protein topology cartoons.

An algorithm is described for automatically generating protein topology cartoons. This algorithm optimally places circles and triangles depicting alpha-helices and beta-strands respectively giving a pictorial topological summary of any protein structure. beta-Sheets, sandwiches and barrels are automatically identified and represented using special templates. The output from this algorithm may be controlled by adjustment of variable weights during the optimization step giving a preferred result. The rules for generating protein toplogy cartoons, including consideration of the handedness of local structure motifs, are discussed. The design of this algorithm is completely general and is easily adapted to include further rules that dictate the generation of the cartoons.

Algorithms↗
PubMed1994

The BC loop in poliovirus coat protein VP1: an ideal acceptor site for major insertions.

In poliovirus the BC loop of the VP1 coat protein is hypervariable and can accommodate numerous foreign sequences introduced by genetic engineering. This paper examines the characteristics of the VP1 BC loop of the picornaviruses to see why this loop is so variable and particularly favourable for the insertion of foreign sequences leading to the formation of chimeric particles. The characteristics which make this loop distinctive can be used to find equally permissive loops in other proteins.

Amino Acid Sequence↗
PubMed1993

Alpha plus beta folds revisited: some favoured motifs.

BACKGROUND: By performing extensive pairwise structural comparisons, we recently identified a set of unique folds from the Brookhaven protein structure data bank. This analysis revealed considerable similarities between a large subgroup of the alpha+beta folds, which led us to re-examine the types of folds occurring in this class and the nature of the relationships between them. RESULTS: Two major alpha+beta fold groups can be distinguished. In the first, described as alpha-beta sandwiches because alpha-helices and beta-strands occupy separate and distinct layers, a split beta alpha beta motif recurs frequently. The other group, alpha-beta rolls, contains fewer helices and is more diverse. In these, the beta-sheet has folded or rolled over, providing a cradle for the alpha-helix. A beta beta beta alpha-meander motif is found throughout the alpha+beta class. CONCLUSION: Although many alpha-beta sandwiches have very similar folds, few share common functions and the active sites are distributed over the whole surface of the fold. The ability of the alpha-beta sandwich to accommodate a range of functions suggests that it is a stable fold and one that is able to adapt a number of sites to satisfy different functional requirements. In contrast, amongst the alpha-beta rolls, folds having the same roll type often have common functions.

Animals↗
PubMed1993

Main-chain bond lengths and bond angles in protein structures.

The main-chain bond lengths and bond angles of protein structures are analysed as a function of resolution. Neither the means nor standard deviations of these parameters show any correlation with resolution over the resolution range investigated. This is as might be expected as bond lengths and bond angles are likely to be heavily influenced by the geometrical restraints applied during structure refinement. The size of this influence is then investigated by performing an analysis of variance on the mean values across the five most commonly used refinement methods. The differences in means are found to be highly statistically significant, suggesting that the different target values used by the different methods leave their imprint on the structures they refine. This has implications concerning the actual target values used during refinement and stresses the importance of the values being not only accurate but also consistent from one refinement method to another.

Analysis of Variance↗
PubMed1993

A study into the effects of protein binding on nucleotide conformation.

In this study, we examine the effects of binding to protein upon nucleotide conformation, by the comparison of X-ray crystal structures of free and protein-bound nucleotides. A dataset of structurally non-homologous protein-nucleotide complexes was derived from the Brookhaven Protein Data Bank by a novel protocol of dual sequential and structural alignments, and a dataset of native nucleotide structures was obtained from the Cambridge Structural Database. The nucleotide torsion angles and sugar puckers, which describe nucleotide conformation, were analysed in both datasets and compared. Differences between them are described and discussed. Overall, the nucleotides were found to bind in low energy conformations, not significantly different from their 'free' conformations except that they adopted an extended conformation in preference to the 'closed' structure predominantly observed by free nucleotide. The archetypal conformation of a protein-bound nucleotide is derived from these observations.

Crystallography↗
PubMed1993

Accommodating sequence changes in beta-hairpins in proteins.

A systematic study of homologous beta-hairpins in proteins of known structure reveals how insertions and deletions (herein known as indels) in the sequence are accommodated. The study was made for 12 protein families comprising 50 different structures, in which there were 49 independent hairpins. Each hairpin was classified according to its loop length and hydrogen bonding pattern. Most indels were found to occur in the loops and their frequency decreases rapidly with the size of the indel and approximately halves for each extra residue inserted. In very short loops, critical glycines are the primary determinants of loop structure and conversions between the two classic two-residue hairpin loops (with type I' and II' beta-turns) are quite common. Longer insertions are often accommodated by extending the beta-ladder and forming extra hydrogen bonds. There are also several indels that are not accommodated in the loop, but by forming a beta-bulge in one of the strands. This study should provide a useful aid to modelling hairpins in homologous structures.

Amino Acid Sequence↗
PubMed1993

Identification, classification, and analysis of beta-bulges in proteins.

A beta-bulge is a region of irregularity in a beta-sheet involving two beta-strands. It usually involves two or more residues in the bulged strand opposite to a single residue on the adjacent strand. These irregularities in beta-sheets were identified and classified automatically, extending the definition of beta-bulges given by Richardson et al. (Richardson, J.S., Getzoff, E.D., & Richardson, D.C., 1978, Proc. Natl. Acad. Sci. USA 75, 2574-2578). A set of 182 protein chains (170 proteins) was used, and a total of 362 bulges were extracted. Five types of beta-bulges were found: classic, G1, wide, bent, and special. Their characteristic amino acid preferences were found for most classes of bulges. Basically, bulges occur frequently in proteins; on average there are more than two bulges per protein. In general, beta-bulges produce two main changes in the structure of a beta-sheet: (1) disrupt the normal alternation of side-chain direction; (2) accentuate the twist of the sheet, altering the direction of the surrounding strands.

Amino Acid Sequence↗
PubMed1993

Comparison of conformational characteristics in structurally similar protein pairs.

Although it is known that three-dimensional structure is well conserved during the evolutionary development of proteins, there have been few studies that consider other parameters apart from divergence of the main-chain coordinates. In this study, we align the structures of 90 pairs of homologous proteins having sequence identities ranging from 5 to 100%. Their structures are compared as a function of sequence identity, including not only consideration of C alpha coordinates but also accessibility, Ooi numbers, secondary structure, and side-chain angles. We discuss how these properties change as the sequences become less similar. This will be of practical use in homology modeling, especially for modeling very distantly related or analogous proteins. We also consider how the average size and number of insertions and deletions vary as sequences diverge. This study presents further quantitative evidence that structure is remarkably well conserved in detail, as well as at the topological level, even when the sequences do not show similarity that is significant statistically.

Algorithms↗
PubMed1993

Conformational analysis of protein structures derived from NMR data.

A study is presented of the conformational characteristics of NMR-derived protein structures in the Protein Data Bank compared to X-ray structures. Both ensemble and energy-minimized average structures are analyzed. We have addressed the problem using the methods developed for crystal structures by examining the distribution of phi, psi, and chi angles as indicators of global conformational irregularity. All these features in NMR structures occur to varying degrees in multiple conformational states. Some measures of local geometry are very tightly constrained by the methods used to generate the structure, e.g., proline phi angles, alpha-helix phi,psi angles, omega angles, and C alpha chirality. The more lightly restrained torsion angles do show increased clustering as the number of overall experimental observations increases. phi, psi, and chi 1 angle conformational heterogeneity is strongly correlated with accessibility but shows additional differences which reflect the differing number of observations possible in NMR for the various side chains (e.g., many for Trp, few for Ser). In general, we find that the core is defined to a notional resolution of 2.0 to 2.3 A. Of real interest is the behavior of surface residues and in particular the side chains where multiple rotameric states in different structures can vary from 10% to 88%. Later generation structures show a much tighter definition which correlates with increasing use of J-coupling information, stereospecific assignments, and heteronuclear techniques. A suite of programs is being developed to address the special needs of NMR-derived structures which will take into account the existence of increased mobility in solution.

Analysis of Variance↗
PubMed1993

Molecular modelling and epitope prediction of gp29 from lymphatic filariae.

The sequence of the major soluble protein component of the cuticle of filarial nematodes is homologous to that of bovine glutathione peroxidase, for which an X-ray structure is available. Due to the high degree of sequence identity (42%), it has been possible to build an apparently reliable three-dimensional model of the gp29 cuticular protein from Brugia spp. that will aid studies of the molecule both as a target immunogen and secreted enzyme. The modelled core of the gp29 structure is conserved compared to the bovine enzyme, consisting of a beta-sheet surrounded by alpha-helices. Experimental data showed that Brugia spp. gp29 has four subunits, and a tetrameric form of gp29 has also been modelled. The two N-linked glycosylation sites per subunit were predicted to lie on the surface of the tetramer. Most of the variation in amino acid sequence compared to that of mammalian enzymes, occurs in the surface loops, several of which are larger and more exposed in gp29. Deglycosylated gp29 was demonstrated to be immunogenic in human infection, and six likely B-cell epitopes have been predicted on the basis of a high protrusion index and sequence variability.

Amino Acid Sequence↗
PubMed1993

Recurring structural motifs in proteins with different functions.

BACKGROUND: Structures that have diverged from a common ancestor often retain functional and sequence similarity, although the latter may be very reduced. Even so, the overall fold of the structure is generally highly conserved. Now however, several have been identified of proteins that have been identified that have different functions but which have converged to a similar fold. These proteins will also have low sequence identities. RESULTS: By comparing the complete structure databank against itself, using sequence and structure alignment techniques, we have been able to identify six new examples of structurally related folds that have no apparent sequence or functional similarity. These related proteins include a family of crambin-like folds and a family of ferredoxin II folds. We found that all the similarities between structures are present in small proteins and occur as motifs within the core of a larger protein. CONCLUSION: The low sequence similarity and the lack of any obvious functional relationship between proteins with similar structures suggest that the proteins have diverged from independent ancestors. The similarities may therefore be of interest for understanding the various stereochemical and physical criteria that operate to generate a favourable fold.

Journal Article↗