Multigenerational diabetes mellitus

Gestational diabetes (GDM) changes the maternal metabolic and uterine environment, thus increasing the risk of short- and long-term adverse outcomes for both mother and child. Children of mothers who have GDM during their pregnancy are more likely to develop Type 2 Diabetes (T2D), early-onset cardiovascular disease and GDM when they themselves become pregnant, perpetuating a multigenerational increased risk of metabolic disease. The negative effect of GDM is exacerbated by maternal obesity, which induces a greater derangement of fetal adipogenesis and growth. Multiple factors, including genetic, epigenetic and metabolic, which interact with lifestyle factors and the environment, are likely to contribute to the development of GDM. Genetic factors are particularly important, with 30% of women with GDM having at least one parent with T2D. Fetal epigenetic modifications occur in response to maternal GDM, and may mediate both multi- and transgenerational risk. Changes to the maternal metabolome in GDM are primarily related to fatty acid oxidation, inflammation and insulin resistance. These might be effective early biomarkers allowing the identification of women at risk of GDM prior to the development of hyperglycaemia. The impact of the intra-uterine environment on the developing fetus, "developmental programming", has a multisystem effect, but its influence on adipogenesis is particularly important as it will determine baseline insulin sensitivity, and the response to future metabolic challenges. Identifying the critical window of metabolic development and developing effective interventions are key to our ability to improve population metabolic health.

Resolvin D2 promotes host defense in a 2 - hit model of sepsis with secondary lung infection

In the development of sepsis, there is early, massive inflammation which can lead to multiple organ failure. Later there is an immunosuppressed phase where the host is susceptible to secondary infections or is unable to clear existing infection. Specialized Pro-resolving Mediators (SPMs) are endogenously produced lipids which resolve infection by decreasing bacteria load and reducing systemic inflammatory response. There has been little work studying if SPMs given late, can promote host defense. We examined if an SPM, Resolvin D2 (RvD2) could promote host defense in a 2-hit mouse model of cecal ligation and puncture (CLP) sepsis and secondary Pseudomonas aeruginosa lung infection. RvD2 given 48 h after mild CLP (1st hit), increased gene expression of Toll-like receptor-2 (TLR-2) and alveolar macrophage/monocyte phagocytic ability compared to CLP mice given saline vehicle. In this model, RvD2 did not affect plasma IL-6 or IL-10. These effects induced by RvD2, lowered lung bacterial load and decreased mortality after the secondary infection of Pseudomonas aeruginosa (2nd hit). Splenic T-cell numbers were also increased in RvD2 treated mice compared to saline vehicle treated animals. The results suggest that RvD2 promoted mechanisms of host defense in a 2-hit model sepsis and secondary lung infection.

Lipoxin A4 promotes reduction and antibiotic efficacy against Pseudomonas aeruginosa biofilm

Pseudomonas aeruginosa (P. aeruginosa) is an opportunistic bacterium commonly found in wound infections and airways of cystic fibrosis patients. P. aeruginosa readily forms biofilms which can reduce the efficacy of antibiotics used to eradicate the pathogen. We have previously shown that a Specialized Pro-resolving Mediator (SPM), Lipoxin A4 (LxA₄) is a quorum sensing inhibitor which can reduce P. aeruginosa virulence. In this study, we examined the direct actions of LxA₄ and RvD₂ on P. aeruginosa biofilm formation and virulence gene expression. The influence of LxA₄ on antibiotic efficacy and the combined effects on biofilm formation were also investigated. LxA₄ and RvD₂ reduced P. aeruginosa biofilm formation and virulence gene expression. LxA₄ increased ciprofloxacin inhibition on biofilm formation but did not affect ciprofloxacin's action on non-adherent bacteria. On the other hand, LxA₄ increased bacterial killing action of imipenem but did not affect imipenem's action on biofilm. We also found that LxA₄ can increase ciprofloxacin's bacterial killing ability in established biofilm. Together these results suggest that LxA₄ has direct effects on P. aeruginosa biofilm formation and can increase antibiotic efficacy directly.

Modeling birds on wires

In this paper we introduce a mathematical model to study the group dynamics of birds resting on wires. The model is agent-based and postulates attraction-repulsion forces between the interacting birds: the interactions are "topological", in the sense that they involve a given number of neighbors irrespective of their distance. The model is first mathematically analyzed and then simulated to study its main properties: we observe that the model predicts birds to be more widely spaced near the borders of each group. We compare the results from the model with experimental data, derived from the analysis of pictures of pigeons and starlings taken in New Jersey: two different image elaboration protocols allow us to establish a good agreement with the model and to quantify its main parameters. We also discuss the potential handedness of the birds, by analyzing the group organization features and the group dynamics at the arrival of new birds. Finally, we propose a more refined mathematical model that describes landing and departing birds by suitable stochastic processes.

HydroCoils, occlusion rates, and outcomes: a large single-center study

BACKGROUND AND PURPOSE

The HydroCoil is an expansile hydrogel coil designed to produce a greater degree of volumetric packing within cerebral aneurysms when compared with bare platinum coils. This increased packing is, in turn, believed to decrease the risk of recurrence within aneurysms and hence the risk of their rupture in the long term. The aim of this work was to assess whether the use of HydroCoils and the proportion of HydroCoil used have any influence on the subsequent occlusion and recurrence rates of treated aneurysms.

MATERIALS AND METHODS

A retrospective study was performed of 328 patients during 5 years at a single institution. The initial angiographic and follow-up angiographic occlusion rates were recorded as were any procedural complications. The proportion of HydroCoil used was described as the relative amount of HydroCoil length to the total coil length used during an aneurysm treatment, thus forming 4 groups: 0%-19%, 20%-49%, 50%-69%, 70%-100%, and the subgroups with 100%.

RESULTS

Two hundred seventy patients had angiographic follow-up during an average of 13 months. The overall risk of permanent neurologic deficit and death was 3%. The rate of complete occlusion was 31% immediately postcoiling and 64.8% on follow-up. At the latest follow-up, 25.6% had residual necks and 9.6% had residual aneurysms. There was a statistically significant trend for HydroCoils to produce greater occlusion rates on follow-up when >70% HydroCoil was used (P = .025). The overall rate of recurrence for all aneurysms as a group was 15.5%. The retreatment rate was 6.6%. There has been 1 rebleed in the 328 patients.

CONCLUSIONS

The overall results following the use of HydroCoils to occlude aneurysms compare well with those in other reported series. HydroCoils do produce a statistically significantly greater rate of occlusion when >70% of total aneurysm coil length is HydroCoil compared with coiling with <20% HydroCoil. There was no significant difference, however, in the recurrence or retreatment rate when comparing these groups.

Modelling antibody combining sites: a review

The combining site in an antibody is built up from six hypervariable loop regions, three from the light chain and three from the heavy chain. Three-dimensional structures have been elucidated by X-ray crystallographic studies for a variety of combining sites and for four protein-antibody complexes. Since sequence determination is relatively straightforward, whilst structure determination is often difficult and time consuming, it would be useful to be able to predict the structure of a combining site from its sequence. Knowledge of the structure would facilitate modifications of antibodies for specific aims. The structure of an antibody combining site for which only the sequence is known can be modelled on the basis of homology with a protein of known structure. The most demanding steps are modelling of the hypervariable loops and inclusion of the amino acid side chains. Final energy refinement of the model is achieved by conventional energy minimization techniques, but simulated annealing promises to be a powerful way of predicting side chain conformation. Four different groups have modelled antibody combining sites and compared their predictions with observed structures: for the main chain conformations resolutions of less than 1 A have been achieved. Future developments will increase the efficiency of the modelling procedures and permit accurate predictions of side chain conformations.

SPINE bioinformatics and data-management aspects of high-throughput structural biology

SPINE (Structural Proteomics In Europe) was established in 2002 as an integrated research project to develop new methods and technologies for high‐throughput structural biology. Development areas were broken down into workpackages and this article gives an overview of ongoing activity in the bioinformatics workpackage. Developments cover target selection, target registration, wet and dry laboratory data management and structure annotation as they pertain to high‐throughput studies. Some individual projects and developments are discussed in detail, while those that are covered elsewhere in this issue are treated more briefly. In particular, this overview focuses on the infrastructure of the software that allows the experimentalist to move projects through different areas that are crucial to high‐throughput studies, leading to the collation of large data sets which are managed and eventually archived and/or deposited.

Haplotypes in the CTLA4 region are associated with coeliac disease in the Irish population

Chromosomal region 2q33 encodes the immune regulatory genes, CTLA4, ICOS and CD28, which are involved in regulation of T-cell activity and has been studied as a candidate gene locus in autoimmune diseases, including coeliac disease (CD). We have investigated whether an association exists between this region and CD in the Irish population using a comprehensive analysis for genetic variation. Using a haplotype-tagging approach, this gene cluster was investigated for disease association in a case-control study comprising 394 CD patients and 421 ethnically matched healthy controls. Several SNPs, including CTLA4_CT60, showed association with disease; however, after correction for multiple-testing, CTLA4-658C/T was the only polymorphism found to show significant association with disease when allele, genotype, or carrier status frequency were analysed (carrier status (Allele C), P = 0.0016). Haplotype analysis revealed a haplotype incorporating the CD28/CTLA4 and two 5' ICOS polymorphisms to be significantly associated with disease (patients 24.1%; controls 31.5%; P = 0.035), as was a shorter haplotype composed of the CTLA4 markers only (30.9 vs 34.9%; P = 0.042). The extended haplotype incorporating CD28/CTLA4 and 5' ICOS is more strongly associated with disease than haplotypes of individual genes. This suggests a causal variant associated with this haplotype may be associated with disease in this population.

Amino acid architecture and the distribution of polar atoms on the surfaces of proteins

We propose that a necessary condition for a protein to be soluble is the absence of large hydrophobic patches on its solvent-accessible surface, which can cause aggregation to occur. We note that the polar nature of the backbone of all amino acids guarantees a minimum polar content and hence can interrupt such patches. As a result, a carefully conserved detailed atomic placement of residues on the protein surface is not necessary for solubility. In order to demonstrate this, we construct a measure based on the average hydrophobicity of a simply defined patch. We use this measurement to compare surfaces that exhibit a clear difference in their solubility properties, namely, a) the solvent accessible surfaces for a set of homo-dimers and the surfaces buried in their interfaces and b) for a set of monomers the surfaces of fragments of secondary structure which are solvent accessible/inaccessible. Having demonstrated a difference in the first set of distributions, we characterize the solvent accessible surfaces of monomeric proteins. To test if cooperative behavior occurs between the atoms for these surfaces, we construct a set of randomized surfaces, which obey a very simple stereochemical constraint. We find that the observed and randomized distributions are much more similar than the previous sets we examined. This implies that while surfaces of soluble proteins must have sufficient polar content, the relative placement of atoms of one amino acid with respect to the atoms of neighboring amino acid need not be finely tuned, which provides an innate robustness for protein design and folding.

HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif

SUMMARY

HTHquery is a web-based service to determine if a protein structure has a helix-turn-helix structural motif which could bind to DNA. It is based on a similarity with a set of structural templates, the accessibility of a putative structural motif and a positive electrostatic potential in the neighbourhood of the putative motif. A set of scores are computed, based on each template, using a linear predictor. From the training set used, the predictor has a true positive rate of 83.5% and a false positive rate of 0.8%. The emphasis for the website is on providing a straightforward interface which can be easily used by a bench-based scientist.

AVAILABILITY

HTHquery is implemented using a set of Perl scripts and C program and can be accessed freely on the website http://www.ebi.ac.uk/thornton-srv/databases/HTHquery.

Chromosome 5q candidate genes in coeliac disease: Genetic variation at IL4, IL5, IL9, IL13, IL17B and NR3C1

Genetic predisposition to coeliac disease (CD) is determined primarily by alleles at the HLA-DQB locus, and evidence exists implicating other major histocompatibility complex-linked genes (6p21) and the CTLA4 locus on chromosome 2q33. In addition, extensive family studies have provided strong, reproducible evidence for a susceptibility locus on chromosome 5q (CELIAC2). However, the gene responsible has not been identified. We have assayed genetic variation at the IL4, IL5, IL9, IL13, IL17B and NR3C1 (GR) loci, all of which are present on chromosome 5q and have potential or demonstrated involvement in autoimmune and/or inflammatory disease, in a sample of 409 CD cases and 355 controls. Thirteen single nucleotide polymorphisms were chosen on the basis of functional relevance, prior disease association and, where possible, prior knowledge of the haplotype variation present in European populations. There were no statistically significant allele or haplotype frequency differences between cases and controls. Therefore, these results provide no evidence that these loci are associated with CD in this sample population.

Haplotype variation at the IBD5/SLC22A4 locus (5q31) in coeliac disease in the Irish population

In addition to the well-established association of coeliac disease (CD) with HLA-DQ (6p21) and possibly CTLA4 (2q33), there is considerable evidence for a susceptibility locus on chromosome 5q, which contains many potential candidates for inflammatory disease, including a cluster of cytokine genes in 5q31. CD cases and controls were genotyped for four single-nucleotide polymorphism (SNP) markers that together characterize >90% of the haplotype variation at the IBD5 locus encoding, among others, the SLC22A4 gene. IBD5 and SLC22A4 map to 5q31 and have recently been associated with Crohn's disease and rheumatoid arthritis. Haplotype frequencies do not differ significantly between CD cases and controls in the Irish population, and therefore the chromosome 5 CD susceptibility locus most likely lies elsewhere on 5q.

An examination of the conservation of surface patch polarity for proteins

MOTIVATION

The solubility of a protein is crucial for its function and is therefore an evolutionary constraint. As the solubility of a protein is related to the distribution of polar and hydrophobic residues on its solvent accessible surface, such a constraint should provide a valuable insight into the evolution of protein surfaces. We examine how the surfaces of proteins have evolved by considering how the average hydrophobicities of patches of surface residues vary across homologous proteins. We derive distributions for the average hydrophobicity/philicity of surface patches at a residue-based level-which we refer to as the residue hydrophobic density. This is computed for a set of 28 monomeric proteins and their homologues. The resulting distributions are compared with a set of randomized sequences, with the same residue content.

RESULTS

We find that the patches, involving typically more than 10 residues, maintain a more hydrophilic surface than one would expect from a random substitution model, indicating a cooperative behaviour for these surfaces residues in terms of this single variable.

SUPPLEMENTARY INFORMATION

Additional plots for all of the proteins examined in this paper can be found at: http://www.ebi.ac.uk/~shanahan/PCon/index.html

Small-molecule metabolism: an enzyme mosaic

Escherichia coli has been a popular organism for studying metabolic pathways. In an attempt to find out more about how these pathways are constructed, the enzymes were analysed by defining their protein domains. Structural assignments and sequence comparisons were used to show that 213 domain families constitute approximately 90% of the enzymes in the small-molecule metabolic pathways. Catalytic or cofactor-binding properties between family members are often conserved, while recognition of the main substrate with change in catalytic mechanism is only observed in a few cases of consecutive enzymes in a pathway. Recruitment of domains across pathways is very common, but there is little regularity in the pattern of domains in metabolic pathways. This is analogous to a mosaic in which a stone of a certain colour is selected to fill a position in the picture.

On the molecular discrimination between adenine and guanine by proteins

The molecular recognition and discrimination of adenine and guanine ligand moieties in complexes with proteins have been studied using empirical observations on carefully selected crystal structures. The distribution of protein folds that bind these purines has been found to differ significantly from that across the whole PDB, but the most populated architectures and folds are also the most common in three genomes from the three different domains of life. The protein environments around the two nucleic acid bases were significantly different, in terms of the propensities of amino acid residues to be in the binding site, as well as their propensities to form hydrogen bonds to the bases. Plots of the distribution of protein atoms around the two purines clearly show different clustering of hydrogen bond donors and acceptors opposite complimentary acceptors and donors in the rings, with hydrophobic areas below and above the rings. However, the clustering pattern is fuzzy, reflecting the variety of ways that proteins have evolved to recognise the same molecular moiety. Furthermore, an analysis of the conservation of residues in the protein chains binding guanine shows that residues in contact with the base are in general better conserved than the rest of the chain.

The (betaalpha)(8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships

There are currently at least nine distinct glycosidase sequence families which are all known to adopt a TIM barrel fold [Henrissat,B. and Davies,G. (1997) CURR: Opin. Struct. Biol., 7, 637-644]. To explore the relationships between these enzymes and their evolution, comprehensive sequence and structure comparisons were performed, generating four distinct clusters. The first cluster, S1, comprises the alpha-amylase related enzymes, all with the retention mechanism (axial-->axial). The second cluster, S2, included two functional subgroups, one composed of various kinds of glucosidases all with the retention mechanism (equatorial-->equatorial) (the so-called 4/7 superfamily), and the other subgroup including the beta-amylases with the inversion mechanism (axial--> equatorial). The third cluster, S3, with the retention mechanism (equatorial-->equatorial), could be subdivided, based on the catalytic residues and mechanisms, into two functional subgroups: the chitinase group, catalysed by two acidic residues on the C-termini of beta-4 and beta-6, and the hevamine group, using two acidic residues on the C-termini of beta-4 for catalysis. The fourth cluster, S4, is composed of chitobiase with the retention mechanism (equatorial--> equatorial). These clusters are compared with the sequence families derived by Henrissat and coworkers. PSI-BLAST profiles and multiple-alignments of tertiary structures suggest that S1 and S2 are distantly related, as are S3 and S4, which have N-acetylated substrates. This work highlights the difficulties of untangling distant evolutionary relationships in ubiquitous folds such as the TIM barrel.

Conservation helps to identify biologically relevant crystal contacts

Some crystal contacts are biologically relevant, most are not. We assess the utility of combining measures of size and conservation to discriminate between biological and non-biological contacts. Conservation and size information is calculated for crystal contacts in 53 families of homodimers and 65 families of monomers. Biological contacts are shown to be usually conserved and typically the largest contact in the crystal. A range of neural networks accepting different combinations and encodings of this information is used to answer the following questions: (1) is a given crystal contact biological, and (2) given all crystal contacts in a homodimer, which is the biological one? Predictions for (1) are performed on both homodimer and monomer datasets. The best performing neural network combined size and conservation inputs. For the homodimers, it correctly classified 48 out of 53 biological contacts and 364 out of 366 non-biological contacts, giving a combined accuracy of 98.3 %. A more robust performance statistic, the phi-coefficient, which accounts for imbalances in the dataset, gave a value of 0.92. Taking all 535 non-biological contacts from the 65 monomers, this predictor made erroneous classifications only 4.3 % of the time. Predictions for (2) were performed on homodimers only. The best performing network achieved a prediction accuracy of 98.1 % using size information alone. We conclude that in answering question (1) size and conservation combined discriminate biological from non-biological contacts better than either measure alone. For answering question (2), we conclude that in our dataset size is so powerful a discriminant that conservation adds little predictive benefit.

The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli

The 106 small molecule metabolic (SMM) pathways in Escherichia coli are formed by the protein products of 581 genes. We can define 722 domains, nearly all of which are homologous to proteins of known structure, that form all or part of 510 of these proteins. This information allows us to answer general questions on the structural anatomy of the SMM pathway proteins and to trace family relationships and recruitment events within and across pathways. Half the gene products contain a single domain and half are formed by combinations of between two and six domains. The 722 domains belong to one of 213 families that have between one and 51 members. Family members usually conserve their catalytic or cofactor binding properties; substrate recognition is rarely conserved. Of the 213 families, members of only a quarter occur in isolation, i.e. they form single-domain proteins. Most members of the other families combine with domains from just one or two other families and a few more versatile families can combine with several different partners. Excluding isoenzymes, more than twice as many homologues are distributed across pathways as within pathways. However, serial recruitment, with two consecutive enzymes both being recruited to another pathway, is rare and recruitment of three consecutive enzymes is not observed. Only eight of the 106 pathways have a high number of homologues. Homology between consecutive pairs of enzymes with conservation of the main substrate-binding site but change in catalytic mechanism (which would support a simple model of retrograde pathway evolution) occurs only six times in the whole set of enzymes. Most of the domains that form SMM pathways have homologues in non-SMM pathways. Taken together, these results imply a pervasive "mosaic" model for the formation of protein repertoires and pathways.

Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level

To assess whether there are universal rules that govern amino acid-base recognition, we investigate hydrogen bonds, van der Waals contacts and water-mediated bonds in 129 protein-DNA complex structures. DNA-backbone interactions are the most numerous, providing stability rather than specificity. For base interactions, there are significant base-amino acid type correlations, which can be rationalised by considering the stereochemistry of protein side chains and the base edges exposed in the DNA structure. Nearly two-thirds of the direct read-out of DNA sequences involves complex networks of hydrogen bonds, which enhance specificity. Two-thirds of all protein-DNA interactions comprise van der Waals contacts, compared to about one-sixth each of hydrogen and water-mediated bonds. This highlights the central importance of these contacts for complex formation, which have previously been relegated to a secondary role. Although common, water-mediated bonds are usually non-specific, acting as space-fillers at the protein-DNA interface. In conclusion, the majority of amino acid-base interactions observed follow general principles that apply across all protein-DNA complexes, although there are individual exceptions. Therefore, we distinguish between interactions whose specificities are 'universal' and 'context-dependent'. An interactive Web-based atlas of side chain-base contacts provides access to the collected data, including analyses and visualisation of the three-dimensional geometry of the interactions.

Identification of higher brain centres that may encode the cardiorespiratory response to exercise in humans

1. Positron emission tomography (PET) was used to identify the neuroanatomical correlates underlying 'central command' during imagination of exercise under hypnosis, in order to uncouple central command from peripheral feedback. 2. Three cognitive conditions were used: condition I, imagination of freewheeling downhill on a bicycle (no change in heart rate, HR, or ventilation, V(I)): condition II, imagination of exercise, cycling uphill (increased HR by 12 % and V(I) by 30 % of the actual exercise response): condition III, volitionally driven hyperventilation to match that achieved in condition II (no change in HR). 3. Subtraction methodology created contrast A (II minus I) highlighting cerebral areas involved in the imagination of exercise and contrast B (III minus I) highlighting areas activated in the direct volitional control of breathing (n = 4 for both; 8 scans per subject). End-tidal P(CO(2)) (P(ET,CO(2))) was held constant throughout PET scanning. 4. In contrast A, significant activations were seen in the right dorso-lateral prefrontal cortex, supplementary motor areas (SMA), the right premotor area (PMA), superolateral sensorimotor areas, thalamus, and bilaterally in the cerebellum. In contrast B, significant activations were present in the SMA and in lateral sensorimotor cortical areas. The SMA/PMA, dorso-lateral prefrontal cortex and the cerebellum are concerned with volitional/motor control, including that of the respiratory muscles. 5. The neuroanatomical areas activated suggest that a significant component of the respiratory response to 'exercise', in the absence of both movement feedback and an increase in CO(2) production, can be generated by what appears to be a behavioural response.

Evolution of function in protein superfamilies, from a structural perspective

The recent growth in protein databases has revealed the functional diversity of many protein superfamilies. We have assessed the functional variation of homologous enzyme superfamilies containing two or more enzymes, as defined by the CATH protein structure classification, by way of the Enzyme Commission (EC) scheme. Combining sequence and structure information to identify relatives, the majority of superfamilies display variation in enzyme function, with 25 % of superfamilies in the PDB having members of different enzyme types. We determined the extent of functional similarity at different levels of sequence identity for 486,000 homologous pairs (enzyme/enzyme and enzyme/non-enzyme), with structural and sequence relatives included. For single and multi-domain proteins, variation in EC number is rare above 40 % sequence identity, and above 30 %, the first three digits may be predicted with an accuracy of at least 90 %. For more distantly related proteins sharing less than 30 % sequence identity, functional variation is significant, and below this threshold, structural data are essential for understanding the molecular basis of observed functional differences. To explore the mechanisms for generating functional diversity during evolution, we have studied in detail 31 diverse structural enzyme superfamilies for which structural data are available. A large number of variations and peculiarities are observed, at the atomic level through to gross structural rearrangements. Almost all superfamilies exhibit functional diversity generated by local sequence variation and domain shuffling. Commonly, substrate specificity is diverse across a superfamily, whilst the reaction chemistry is maintained. In many superfamilies, the position of catalytic residues may vary despite playing equivalent functional roles in related proteins. The implications of functional diversity within supefamilies for the structural genomics projects are discussed. More detailed information on these superfamilies is available at http://www.biochem.ucl.ac.uk/bsm/FAM-EC/.

Protein-RNA interactions: a structural analysis

A detailed computational analysis of 32 protein-RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein-double-stranded DNA and protein-single-stranded DNA complexes. The interface properties of the protein-RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein-RNA and protein-DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein-RNA complexes, backbone contacts were more dominant in the protein-DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level.

Protein-protein interfaces: analysis of amino acid conservation in homodimers

Evolutionary information derived from the large number of available protein sequences and structures could powerfully guide both analysis and prediction of protein-protein interfaces. To test the relevance of this information, we assess the conservation of residues at protein-protein interfaces compared with other residues on the protein surface. Six homodimer families are analyzed: alkaline phosphatase, enolase, glutathione S-transferase, copper-zinc superoxide dismutase, Streptomyces subtilisin inhibitor, and triose phosphate isomerase. For each family, random simulation is used to calculate the probability (P value) that the level of conservation observed at the interface occurred by chance. The results show that interface conservation is higher than expected by chance and usually statistically significant at the 5% level or better. The effect on the P values of using different definitions of the interface and of excluding active site residues is discussed.

Ventricular activation during sympathetic imbalance and its computational reconstruction

We characterized the epicardial activation sequence during a norepinephrine (NE)-induced ventricular arrhythmia in anesthetized pigs and studied factors that modulated it. Subepicardial NE infusion caused the QRS complex to invert within a single beat (n = 35 animals, 101 observations), and the earliest epicardial activation consistently shifted to the randomly located infusion site (n = 14). This preceded right atrial activation, whereas the total ventricular epicardial activation time increased from 20 +/- 4 to 50 +/- 9 ms (P < 0.01). These events were accompanied by a ventricular tachycardia and a drop in left ventricular pressure, which were fully reversed after the infusion was stopped. Epicardial pacing at the infusion site mimicked all electrical and hemodynamic changes induced by NE. The arrhythmia was prevented by propranolol and abolished by cardiac sympathetic or vagal nerve stimulation. Focal automaticity was computationally reconstructed using a two-dimensional sheet of 256 x 256 resistively coupled ventricular cells, where calcium handling was abnormally high in the central region. We conclude that adrenergic stimulation to a small region of the ventricle elicits triggered automaticity and that computational reconstruction implicates calcium overload. Interventions that reduce spatial inhomogeneities of intracellular calcium may prevent this type of arrhythmia.

A rapid classification protocol for the CATH Domain Database to support structural genomics

In order to support the structural genomic initiatives, both by rapidly classifying newly determined structures and by suggesting suitable targets for structure determination, we have recently developed several new protocols for classifying structures in the CATH domain database (http://www.biochem.ucl.ac.uk/bsm/cath). These aim to increase the speed of classification of new structures using fast algorithms for structure comparison (GRATH) and to improve the sensitivity in recognising distant structural relatives by incorporating sequence information from relatives in the genomes (DomainFinder). In order to ensure the integrity of the database given the expected increase in data, the CATH Protein Family Database (CATH-PFDB), which currently includes 25,320 structural domains and a further 160,000 sequence relatives has now been installed in a relational ORACLE database. This was essential for developing more rigorous validation procedures and for allowing efficient querying of the database, particularly for genome analysis. The associated Dictionary of Homologous Superfamilies [Bray,J.E., Todd,A.E., Pearl,F.M.G., Thornton,J.M. and Orengo,C.A. (2000) Protein Eng., 13, 153-165], which provides multiple structural alignments and functional information to assist in assigning new relatives, has also been expanded recently and now includes information for 903 homologous superfamilies. In order to improve coverage of known structures, preliminary classification levels are now provided for new structures at interim stages in the classification protocol. Since a large proportion of new structures can be rapidly classified using profile-based sequence analysis [e.g. PSI-BLAST: Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Nucleic Acids Res., 25, 3389-3402], this provides preliminary classification for easily recognisable homologues, which in the latest release of CATH (version 1.7) represented nearly three-quarters of the non-identical structures.

From structure to function: approaches and limitations

This review presents a summary of current approaches to extract functional information from structural data on proteins and their complexes. While structural homologs may reveal possible biochemical functions (which may be hidden at the sequence level), elucidating the exact biological role of a protein in vivo will only be possible by including other results, such as data on expression and localization.

Discriminating between homodimeric and monomeric proteins in the crystalline state

Scores calculated from intermolecular contacts of proteins in the crystalline state are used to differentiate monomeric and homodimeric proteins, by classification into two categories separated by a cut-off score value. The generalized classification error is estimated by using bootstrap re-sampling on a nonredundant set of 172 water-soluble proteins whose prevalent quaternary state in solution is known to be either monomeric or homodimeric. A statistical potential, based on atom-pair frequencies across interfaces observed with homodimers, is found to yield an error rate of 12.5%. This indicates a small but significant improvement over the measure of solvent accessible surface area buried in the contact interface, which achieves an error rate of 15.4%. A further modification of the latter parameter relating the two most extensive contacts of the crystal results in an even lower error rate of 11.1%.

Just noticeable and objectionable group delays in digital hearing aids

Group delay in a digital signal processing (DSP) hearing aid may be perceived as an echo in the sound heard by a wearer listening to his or her own voice, due to a combination of unprocessed sound received at the ear through head and air pathways and delayed sound reaching the eardrum through the hearing aid. Depending on the amount, this delay may be audible or objectionable and can even result in auditory confusion. This study presents results from 18 subjects listening to their own voices through a DSP hearing aid with a variable group delay. The subjects varied the length of the delay and determined the amounts that were noticeable and objectionable as compared to the undelayed condition, while listening to their own amplified voices. Results indicated that a delay of 3 to 5 msec was noticeable to the listeners in 76 percent of the trials, and a delay of longer than 10 msec was objectionable 90 percent of the time.

Comparison of functional annotation schemes for genomes

In this paper we survey a number of functional classification schemes applicable to genomes. We present the concepts of depth, breadth and resolution as descriptors of the schemes' scope and architecture and compare selected classifications according to these criteria. We also generate a 'Combined Scheme' against which we map six classifications which we believe are representative of the range currently available. The mapping allows the generation of 'FuncWheels', which are graphical representations of hierarchical classification schemes. They are used to illustrate similarities and differences in functional space coverage. This survey highlights many issues related to the design and implementation of gene product functional classifications, which are discussed in the light of emerging 'second-generation' schemes.

The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues

A consensus approach has been developed for identifying distant structural homologues. This is based on the CATH Dictionary of Homologous Superfamilies (DHS), a database of validated multiple structural alignments annotated with consensus functional information for evolutionary protein superfamilies (URL: http://www. biochem.ucl.ac.uk/bsm/dhs). Multiple structural alignments have been generated for 362 well-populated superfamilies in the CATH structural domain database and annotated with secondary structure, physicochemical properties, functional sequence patterns and protein-ligand interaction data. Consensus functional information for each superfamily includes descriptions and keywords extracted from SWISS-PROT and the ENZYME database. The Dictionary provides a powerful resource to validate, examine and visualize key structural and functional features of each homologous superfamily. The value of the DHS, for assessing functional variability and identifying distant evolutionary relationships, is illustrated using the pyridoxal-5'-phosphate (PLP) binding aspartate aminotransferase superfamily. The DHS also provides a tool for examining sequence-structure relationships for proteins within each fold group.

Protein domain interfaces: characterization and comparison with oligomeric protein interfaces

The physical and chemical properties of domain-domain interactions have been analysed in two-domain proteins selected from the protein classification, CATH. The two-domain structures were divided into those derived from (i) monomeric proteins, or (ii) oligomeric or complexed proteins. The size, polarity, hydrogen bonding and packing of the intra-chain domain interface were calculated for both sets of two-domain structures. The results were compared with inter-chain interface parameters from permanent and non-obligate protein-protein complexes. In general, the intra-chain domain and inter-chain interfaces were remarkably similar. Many of the intra-chain interface properties are intermediate between those calculated for permanent and non-obligate inter-chain complexes. Residue interface propensities were also found to be very similar, with hydrophobic residues playing a major role, together with positively charged arginine residues. In addition, the residue composition of the domain interfaces were found to be more comparable with domain surfaces than domain cores. The implications of these results for domain swapping and protein folding are discussed.

Using the CATH domain database to assign structures and functions to the genome sequences

The CATH database of protein structures contains approximately 18000 domains organized according to their (C)lass, (A)rchitecture, (T)opology and (H)omologous superfamily. Relationships between evolutionary related structures (homologues) within the database have been used to test the sensitivity of various sequence search methods in order to identify relatives in Genbank and other sequence databases. Subsequent application of the most sensitive and efficient algorithms, gapped blast and the profile based method, Position Specific Iterated Basic Local Alignment Tool (PSI-BLAST), could be used to assign structural data to between 22 and 36 % of microbial genomes in order to improve functional annotation and enhance understanding of biological mechanism. However, on a cautionary note, an analysis of functional conservation within fold groups and homologous superfamilies in the CATH database, revealed that whilst function was conserved in nearly 55% of enzyme families, function had diverged considerably, in some highly populated families. In these families, functional properties should be inherited far more cautiously and the probable effects of substitutions in key functional residues carefully assessed.

Analysis and prediction of carbohydrate binding sites

An analysis of the characteristic properties of sugar binding sites was performed on a set of 19 sugar binding proteins. For each site six parameters were evaluated: solvation potential, residue propensity, hydrophobicity, planarity, protrusion and relative accessible surface area. Three of the parameters were found to distinguish the observed sugar binding sites from the other surface patches. These parameters were then used to calculate the probability for a surface patch to be a carbohydrate binding site. The prediction was optimized on a set of 19 non-homologous carbohydrate binding structures and a test prediction was carried out on a set of 40 protein-carbohydrate complexes. The overall accuracy of prediction achieved was 65%. Results were in general better for carbohydrate-binding enzymes than for the lectins, with a rate of success of 87%.

An overview of the structures of protein-DNA complexes

On the basis of a structural analysis of 240 protein-DNA complexes contained in the Protein Data Bank (PDB), we have classified the DNA-binding proteins involved into eight different structural/functional groups, which are further classified into 54 structural families. Here we present this classification and review the functions, structures and binding interactions of these protein-DNA complexes.

Assigning genomic sequences to CATH

We report the latest release (version 1.6) of the CATH protein domains database (http://www.biochem.ucl. ac.uk/bsm/cath ). This is a hierarchical classification of 18 577 domains into evolutionary families and structural groupings. We have identified 1028 homo-logous superfamilies in which the proteins have both structural, and sequence or functional similarity. These can be further clustered into 672 fold groups and 35 distinct architectures. Recent developments of the database include the generation of 3D templates for recognising structural relatives in each fold group, which has led to significant improvements in the speed and accuracy of updating the database and also means that less manual validation is required. We also report the establishment of the CATH-PFDB (Protein Family Database), which associates 1D sequences with the 3D homologous superfamilies. Sequences showing identifiable homology to entries in CATH have been extracted from GenBank using PSI-BLAST. A CATH-PSIBLAST server has been established, which allows you to scan a new sequence against the database. The CATH Dictionary of Homologous Superfamilies (DHS), which contains validated multiple structural alignments annotated with consensus functional information for evolutionary protein superfamilies, has been updated to include annotations associated with sequence relatives identified in GenBank. The DHS is a powerful tool for considering the variation of functional properties within a given CATH superfamily and in deciding what functional properties may be reliably inherited by a newly identified relative.

Protein folds, functions and evolution

The evolution of proteins and their functions is reviewed from a structural perspective in the light of the current database. Protein domain families segregate unequally between the three major classes, the 32 different architectures and almost 700 folds observed to date. We find that the number of new topologies is still increasing, although 25 new structures are now determined for each new topology. The corresponding analysis and classification of function is only just beginning, fuelled by the genome data. The structural data revealed unexpected conservations and divergence of function both within and between families. The next five years will see the compilation of a definitive dictionary of protein families and their related functions, based on structural data which reveals relationships hidden at the sequence level. Such information will provide the foundation to build a better understanding of the molecular basis of biological complexity and hopefully to facilitate rational molecular design.

Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels

Automated methods for identifying and characterizing regular beta-barrels from coordinate data have been developed to analyze and classify various kinds of barrel structures based on geometric parameters such as the barrel strand number (n) and shear number (S). In total, we find 1,316 barrels in the January 1998 release of Protein Data Bank. Of 1,316 barrels, 1,277 barrels had an even shear number, corresponding to 50 nonhomologous families. The (beta alpha)8 triose phosphate isomerase (TIM) barrel (n = 8, S = 8) fold has the largest number of apparently nonhomologous entries, 16, although the trypsin like antiparallel (n = 6, S = 8) barrels (representing only three families) are the most common with 527 barrels. Of all the protein families that exhibit barrel structures, 68% are found to be various kinds of enzymes, the remainder being binding proteins and transport membrane proteins. In addition, the layers of side chains, which form the cores of barrels with S = n and S = 2n, are also analyzed. More sophisticated methods were developed for detecting TIM barrels specifically, including consideration of the amino acid propensities for the side chains that form the layers. We found that the residues on the outside of the eight stranded parallel beta-barrel, buried by the alpha-helices, are much more hydrophobic than the residues inside the barrel.

Evolution of protein function, from a structural perspective

The recent growth in structural data, and ensuing analyses, have revealed the structural and functional versatility of protein families. With respect to enzymes, local active-site mutations, variations in surface loops and recruitment of additional domains accommodate the diverse substrate specificities and catalytic activities observed within several superfamilies. Conversely, some functions have more than one structural solution, having evolved independently several times during evolution. Combined with the existence of multi-functional genes, which have arisen by gene recruitment, these phenomena must be considered in the process of genome annotation.

Polymerase chain reaction (PCR)-based typing analysis of atypical isolates of the fish pathogen Aeromonas salmonicida

Two hundred and five isolates of atypical Aeromonas salmonicida, recovered from a wide range of hosts and countries were characterized by polymerase chain reaction (PCR) targeting four genes. The chosen genes were those encoding the extracellular A-layer protein (AP), the serine protease (Sprot), the glycerophospholipid:cholestrol acetyltransferase protein (GCAT), and the 16S rRNA (16S rDNA). All the atypical A. salmonicida isolates could be assigned to 4 PCR groups. Group 1 comprised 45 strains which tested positive for PCR amplification, using the 16S rDNA, GCAT2, Sprot2, and AP primer-sets. Group 2 comprised 88 strains with produced PCR products using the 16S rDNA, GCAT2 and AP primer-sets. Group 3 comprised 21 strains which produced PCR products using 16S rDNA, GCAT2 and Sprot2 primer-sets, and group 4 comprised 51 strains which produced PCR products using the 16S rDNA and GCAT2 primer-sets only. A. salmonicida subsp. salmonicida isolates tested, belonged to group 1. The PCR primer-sets separated A. salmonicida from other reference strains of Aeromonas species and related bacteria with the exception of Aeromonas hydrophila. The results indicated that PCR typing is a useful framework for characterization of the increasing number of isolations of atypical A. salmonicida.

From protein structure to function

Several databases of protein structural families now exist-organised according to both evolutionary relationships and common folding arrangements. Although these lag behind sequence databases in size, the prospect of structural genomics initiatives means that they may soon include representatives of many of the sequence families. To some extent, functional information can be derived from structural similarity. For some structural families, their function is highly conserved, whereas, for others, it can only be inherited or derived on the basis of additional information (e.g. sequence patterns, common residue clusters and characteristic surface properties).

Protein side-chain conformation: a systematic variation of chi 1 mean values with resolution - a consequence of multiple rotameric states?

A systematic variation with resolution of the mean values of the gauche-, trans and gauche+ chi1 rotamers in protein structures determined by X-ray crystallography has been observed. Further analysis revealed that these correlations differ considerably between residue types, being highly significant for some residue types (e.g. Ser, Thr, Leu, Lys) and absent for others (e.g. aromatics). For the individual residue types which exhibited the trend most strongly, these changes were accompanied by corresponding systematic variations in the percentage relative populations in the three energy wells. Examination of a uniformly sized subset of monomers showed that this effect, while attenuated, was still present, and was thus not entirely a consequence of the change in size and surface area which also correlates with resolution. An analysis of B values in the disfavoured high-energy barrier region between the rotameric wells showed a pronounced tendency towards larger than average values. As a plausible hypothesis, it is suggested here that these observations can be accounted for by the presence of multiple rotameric states. The averaged electron density produced by dual occupancy at low resolution giving an averaged conformation is resolved at high resolution into its individual components.

Prediction of the location and type of beta-turns in proteins using neural networks

A neural network has been used to predict both the location and the type of beta-turns in a set of 300 nonhomologous protein domains. A substantial improvement in prediction accuracy compared with previous methods has been achieved by incorporating secondary structure information in the input data. The total percentage of residues correctly classified as beta-turn or not-beta-turn is around 75% with predicted secondary structure information. More significantly, the method gives a Matthews correlation coefficient (MCC) of around 0.35, compared with a typical MCC of around 0.20 using other beta-turn prediction methods. Our method also distinguishes the two most numerous and well-defined types of beta-turn, types I and II, with a significant level of accuracy (MCCs 0.22 and 0.26, respectively).

DOMPLOT: a program to generate schematic diagrams of the structural domain organization within proteins, annotated by ligand contacts

A program is described for automatically generating schematic linear representations of protein chains in terms of their structural domains. The program requires the co-ordinates of the chain, the domain assignment, PROSITE information and a file listing all intermolecular interactions in the protein structure. The output is a PostScript file in which each protein is represented by a set of linked boxes, each box corresponding to all or part of a structural domain. PROSITE motifs and residues involved in ligand interactions are highlighted. The diagrams allow immediate visualization of the domain arrangement within a protein chain, and by providing information on sequence motifs, and metal ion, ligand and DNA binding at the domain level, the program facilitates detection of remote evolutionary relationships between proteins.

COVOL: an interactive program for evaluating second virial coefficients from the triaxial shape or dimensions of rigid macromolecules

An interactive program is described for calculating the second virial coefficient contribution to the thermodynamic nonideality of solutions of rigid macromolecules based on their triaxial dimensions. The FORTRAN-77 program, available in precompiled form for the PC, is based on theory for the covolume of triaxial ellipsoid particles [Rallison, J. M., and S.E Harding. (1985). J. Colloid Interface Sci. 103:284-289]. This covolume has the potential to provide a magnitude for the second virial coefficient of macromolecules bearing no net charge. Allowance for a charge-charge contribution is made via an expression based on Debye-Hückel theory and uniform distribution of the net charge over the surface of a sphere with dimensions governed by the Stokes radius of the macromolecule. Ovalbumin, ribonuclease A, and hemoglobin are used as model systems to illustrate application of the COVOL routine.

Protein-DNA interactions: A structural analysis

A detailed analysis of the DNA-binding sites of 26 proteins is presented using data from the Nucleic Acid Database (NDB) and the Protein Data Bank (PDB). Chemical and physical properties of the protein-DNA interface, such as polarity, size, shape, and packing, were analysed. The DNA-binding sites shared common features, comprising many discontinuous sequence segments forming hydrophilic surfaces capable of direct and water-mediated hydrogen bonds. These interface sites were compared to those of protein-protein binding sites, revealing them to be more polar, with many more intermolecular hydrogen bonds and buried water molecules than the protein-protein interface sites. By looking at the number and positioning of protein residue-DNA base interactions in a series of interaction footprints, three modes of DNA binding were identified (single-headed, double-headed and enveloping). Six of the eight enzymes in the data set bound in the enveloping mode, with the protein presenting a large interface area effectively wrapped around the DNA.A comparison of structural parameters of the DNA revealed that some values for the bound DNA (including twist, slide and roll) were intermediate of those observed for the unbound B-DNA and A-DNA. The distortion of bound DNA was evaluated by calculating a root-mean-square deviation on fitting to a canonical B-DNA structure. Major distortions were commonly caused by specific kinks in the DNA sequence, some resulting in the overall bending of the helix. The helix bending affected the dimensions of the grooves in the DNA, allowing the binding of protein elements that would otherwise be unable to make contact. From this structural analysis a preliminary set of rules that govern the bending of the DNA in protein-DNA complexes, are proposed.

Correlation of observed fold frequency with the occurrence of local structural motifs

It is well known that some protein folds (superfolds) occur very frequently. We show that compared to other folds, most superfold structures have a higher proportion of their alpha-helical or beta-strand residues in one of three basic units of supersecondary structure (alpha-hairpin, beta-hairpin or betaalphabeta-unit). Furthermore, by taking into consideration two more complex motifs, the four-stranded Greek-key (beta4) and the betaalpha-Greek key (betaalphabetabeta), we demonstrate that the remaining superfold structures contain many of these higher order units of three-dimensional packing. The implications of these results for folding are discussed.