Graham J. L. Kemp

PROTEIN DOCKING USING SPHERICAL POLAR FOURIER CORRELATIONS

We present a new computational method of docking pairs of proteins by using spherical polar Fourier correlations to accelerate the search for candidate low‐energy conformations. Interaction energies are estimated using a hydrophobic excluded volume model derived from the notion of “overlapping surface skins,” augmented by a rigorous but “soft” model of electrostatic complementarity. This approach has several advantages over former three‐dimensional grid‐based fast Fourier transform (FFT) docking correlation methods even though there is no analogue to the FFT in a spherical polar representation. For example, a complete search over all six rigid‐body degrees of freedom can be performed by rotating and translating only the initial expansion coefficients, many infeasible orientations may be eliminated rapidly using only low‐resolution terms, and the correlations are easily localized around known binding epitopes when this knowledge is available. Typical execution times on a single processor workstation range from 2 hours for a global search (5 × 108 trial orientations) to a few minutes for a local search (over 6 × 107 orientations). The method is illustrated with several domain dimer and enzyme–inhibitor complexes and 20 large antibody–antigen complexes, using both the bound and (when available) unbound subunits. The correct conformation of the complex is frequently identified when docking bound subunits, and a good docking orientation is ranked within the top 20 in 11 out of 18 cases when starting from unbound subunits. Proteins 2000;39:178–194.

FAST COMPUTATION, ROTATION, AND COMPARISON OF LOW RESOLUTION SPHERICAL HARMONIC MOLECULAR SURFACES

A procedure that rapidly generates an approximate parametric representation of macromolecular surface shapes is described. The parametrization is expressed as an expansion of real spherical harmonic basis functions. The advantage of using a parametric representation is that a pair of surfaces can be matched by using a quasi‐Newton algorithm to minimize a suitably chosen objective function. Spherical harmonics are a natural and convenient choice of basis function when the task is one of search in a rotational search space. In particular, rotations of a molecular surface can be simulated by rotating only the harmonic expansion coefficients. This rotational property is applied for the first time to the 3‐dimensional molecular similarity problem in which a pair of similar macromolecular surfaces are to be maximally superposed. The method is demonstrated with the superposition of antibody heavy chain variable domains. Special attention is given to computational efficiency. The spherical harmonic expansion coefficients are determined using fast surface sampling and integration schemes based on the tessellation of a regular icosahedron. Low resolution surfaces can be generated and displayed in under 10 s and a pair of surfaces can be maximally superposed in under 3 s on a contemporary workstation. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 383–395, 1999

KRAFT: knowledge fusion from distributed databases and knowledge bases

The KRAFT project aims to investigate how a distributed architecture can support the transformation and reuse of a particular class of knowledge, namely constraints, and to fuse this knowledge so as to gain added value, by using it for constraint solving or data retrieval.

Rainbow trout cytokine and cytokine receptor genes

Summary: Transforming growth factor‐β (TGF‐β) and interleukin‐1β (IL‐1β) have been cloned from rainbow trout (Oncorhynchus mykiss) in our laboratory. The trout TGF‐β is typical of members of the cysteine knot cytokine family, and has highest homology to TGF‐β1, TGF‐β4 and TGF‐βs The gene organisation is different to other TGF‐β genes despite die presence of seven exons. Trout IL‐1β has less homology lo known IL‐1βs (49–56% amino acid similarity) but shows dear conservation of the secondary structure of the “mature peptide”. An interleukin‐converting enzyme cut site is not apparent however, and it remains to be determined whether fish IL‐1β must be cleaved for biological activity. The trout IL‐1β gene consists of six exons, one less than in mammals, with the missing exon at the 51 end of the gene. Two trout chemokine receptors have also been isolated in our laboratory, having high homology to CXC‐R4 and CC‐R7 (67% and 56% nucleotide identity respectively). With a view to studying the biological effects of fish cytokines we have also cloned the inducible nitric oxide (iNOS) and cyclooxygenase (COX‐2) genes in trout. Both have high homology to known mammalian and chicken genes, and have been shown to be inducible in trout.

Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation

BackgroundThe translational efficiency of an mRNA can be modulated by upstream open reading frames (uORFs) present in certain genes. A uORF can attenuate translation of the main ORF by interfering with translational reinitiation at the main start codon. uORFs also occur by chance in the genome, in which case they do not have a regulatory role. Since the sequence determinants for functional uORFs are not understood, it is difficult to discriminate functional from spurious uORFs by sequence analysis.ResultsWe have used comparative genomics to identify novel uORFs in yeast with a high likelihood of having a translational regulatory role. We examined uORFs, previously shown to play a role in regulation of translation in Saccharomyces cerevisiae, for evolutionary conservation within seven Saccharomyces species. Inspection of the set of conserved uORFs yielded the following three characteristics useful for discrimination of functional from spurious uORFs: a length between 4 and 6 codons, a distance from the start of the main ORF between 50 and 150 nucleotides, and finally a lack of overlap with, and clear separation from, neighbouring uORFs. These derived rules are inherently associated with uORFs with properties similar to the GCN4 locus, and may not detect most uORFs of other types. uORFs with high scores based on these rules showed a much higher evolutionary conservation than randomly selected uORFs. In a genome-wide scan in S. cerevisiae, we found 34 conserved uORFs from 32 genes that we predict to be functional; subsequent analysis showed the majority of these to be located within transcripts. A total of 252 genes were found containing conserved uORFs with properties indicative of a functional role; all but 7 are novel. Functional content analysis of this set identified an overrepresentation of genes involved in transcriptional control and development.ConclusionEvolutionary conservation of uORFs in yeasts can be traced up to 100 million years of separation. The conserved uORFs have certain characteristics with respect to length, distance from each other and from the main start codon, and folding energy of the sequence. These newly found characteristics can be used to facilitate detection of other conserved uORFs.

PROPHECY—a database for high-resolution phenomics

The rapid recent evolution of the field phenomics—the genome-wide study of gene dispensability by quantitative analysis of phenotypes—has resulted in an increasing demand for new data analysis and visualization tools. Following the introduction of a novel approach for precise, genome-wide quantification of gene dispensability in Saccharomyces cerevisiae we here announce a public resource for mining, filtering and visualizing phenotypic data—the PROPHECY database. PROPHECY is designed to allow easy and flexible access to physiologically relevant quantitative data for the growth behaviour of mutant strains in the yeast deletion collection during conditions of environmental challenges. PROPHECY is publicly accessible at http://prophecy.lundberg.gu.se.

A schema-based approach to building a bioinformatics database federation

Developments in our ability to integrate and analyse the data held in existing heterogeneous data resources can lead to an increase in our understanding of biological function at all levels. However, supporting ad-hoc queries across multiple data resources and correlating the data retrieved from these is still difficult. To address this, we are building a mediator based on the functional data model database, P/FDM, which integrates access to heterogeneous, distributed biological databases, while making use of existing search engines and indexes, without infringing on the autonomy of the underlying databases. Central to our design philosophy is the use of schemas. We have adopted a federated architecture with a five-level schema, arising from the use of the ANSI-SPARC three-level schema to describe both the existing autonomous data resources and the mediator itself. We describe the use of mapping functions and list comprehensions in query splitting, producing execution plans, code generation and result fusion. We give an example of cross-database querying involving data held locally in P/FDM systems and external data in the Sequence Retrieval System (SRS).

Analysis of Fish IL-1β and Derived Peptide Sequences Indicates Conserved Structures with Species-Specific IL-1 Receptor Binding: Implications for Pharmacological Design

A large number of IL-1 protein sequences have become available recently from a range of vertebrate species and especially from bony fish. However, 3D structures are still only known for mammalian IL-1. In this review, we use a multiple sequence alignment of all published non-mammalian vertebrate IL-1beta proteins to locate the structurally important residues critical for maintaining the beta-trefoil fold and we investigate the degree to which functionally important residues involved in receptor binding are conserved across vertebrate species. We find that although there is a high level of variability of positions involved in receptor binding, the mode of binding and overall shape of the ligand-receptor complex is probably maintained. This implies that each species has evolved its own unique interleukin-1 signalling system through ligand-receptor co-evolution. Nonetheless, the IL-1beta processing mechanism in non-mammalian vertebrates remains unclear because, with the exception of three bony fish, all non-mammalian IL-1beta sequences discovered so far lack an ICE (Interleukin Converting Enzyme) cut site. The IL-1 system has become an important drug target because of its significance in inflammatory diseases. Research on peptides derived from IL-1beta has identified peptides that possess agonist activity in humans and in trout, and peptides with antagonist activity. The agonist peptides map to two distinct loop regions of IL-1beta that are known to interact with the flexible domain III of the corresponding receptor. Further analysis of the IL-1 system may prove useful in engineering IL-1 with improved features and in suggesting new avenues for therapeutic intervention.

PROPHECY—a yeast phenome database, update 2006

Connecting genotype to phenotype is fundamental in biomedical research and in our understanding of disease. Phenomics—the large-scale quantitative phenotypic analysis of genotypes on a genome-wide scale—connects automated data generation with the development of novel tools for phenotype data integration, mining and visualization. Our yeast phenomics database PROPHECY is available at . Via phenotyping of 984 heterozygous diploids for all essential genes the genotypes analysed and presented in PROPHECY have been extended and now include all genes in the yeast genome. Further, phenotypic data from gene overexpression of 574 membrane spanning proteins has recently been included. To facilitate the interpretation of quantitative phenotypic data we have developed a new phenotype display option, the Comparative Growth Curve Display, where growth curve differences for a large number of mutants compared with the wild type are easily revealed. In addition, PROPHECY now offers a more informative and intuitive first-sight display of its phenotypic data via its new summary page. We have also extended the arsenal of data analysis tools to include dynamic visualization of phenotypes along individual chromosomes. PROPHECY is an initiative to enhance the growing field of phenome bioinformatics.

Using the functional data model to integrate distributed biological data sources

There is unavoidable heterogeneity in the databanks and databases currently used for biological data collections. The authors are aiming to develop a system that will provide uniform access to heterogeneous databases via a single high-level query language or graphical interface and will enable multi-database queries. They have taken an approach in which high-level code in an object-oriented database system (based on the functional data model) is used effectively as a mediator between distributed heterogeneous databases. The resulting system enables one to ask queries that combine, for example, geometric calculations on three-dimensional protein structures stored locally and access to databanks held at the European Bioinformatics Institute, while making use of existing search engines and indexes when accessing remote data.