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Robert B Russell

Publications and source records attributed to Robert B Russell.

At least 37 records · Page 2Linked to original sources
PubMed2004

Finding functional sites in structural genomics proteins.

Assigning function to structures is an important aspect of structural genomics projects, since they frequently provide structures for uncharacterized proteins. Similarities uncovered by structure alignment can suggest a similar function, even in the absence of sequence similarity. For proteins adopting novel folds or those with many functions, this strategy can fail, but functional clues can still come from comparison of local functional sites involving a few key residues. Here we assess the general applicability of functional site comparison through the study of 157 proteins solved by structural genomics initiatives. For 17, the method bolsters confidence in predictions made based on overall fold similarity. For another 12 with new folds, it suggests functions, including a putative phosphotyrosine binding site in the Archaeal protein Mth1187 and an active site for a ribose isomerase. The approach is applied weekly to all new structures, providing a resource for those interested in using structure to infer function.

Algorithms↗
PubMed2004

Ten thousand interactions for the molecular biologist.

Previous studies have suggested that nature is restricted to about 1,000 protein folds to perform a great diversity of functions. Here, we use protein interaction data from different sources and three-dimensional structures to suggest that the total number of interaction types is also limited, and estimate that most interactions in nature will conform to one of about 10,000 types. We currently know fewer than 2,000, and at the present rate of structure determination, it will be more than 20 years before we know a full representative set.

Cell Physiological Phenomena↗
PubMed2004

Geminate structures of African cassava mosaic virus.

Two types of geminate structures were purified from African cassava mosaic geminivirus (ACMV)-infected Nicotiana benthamiana plants and analyzed by electron cryomicroscopy and image reconstruction. After cesium sulfate density gradient centrifugation, they were separated into lighter top (T) and heavier bottom (B) components. T particles comigrated with host proteins, whereas B particles were concentrated in a cesium density typical for complete virions. Both particles were composed of two incomplete icosahedra of 11 capsomers each, but T particles were slightly larger (diameter, 22.5 nm) and less dense in the interior than B particles (diameter, 21.5 nm). T particles were frequently associated with small globules of approximately 14 nm diameter of unknown origin. The overall structure of ACMV, a begomovirus transmitted by whiteflies, was similar to that of Maize streak virus (MSV), a mastrevirus transmitted by leafhoppers, although the vertices of the icosahedra were less pronounced. Models of ACMV coat proteins based on Satellite tobacco necrosis virus support the exposure of parts of the molecule essential for transmission specificity by whiteflies and provide possible structural explanations for the smaller protrusion of the ACMV capsid relative to MSV. The differences of ACMV and MSV virion shapes are discussed with reference to their different animal vectors.

Amino Acid Sequence↗
PubMed2003

Identification of Drosophila MicroRNA targets.

MicroRNAs (miRNAs) are short RNA molecules that regulate gene expression by binding to target messenger RNAs and by controlling protein production or causing RNA cleavage. To date, functions have been assigned to only a few of the hundreds of identified miRNAs, in part because of the difficulty in identifying their targets. The short length of miRNAs and the fact that their complementarity to target sequences is imperfect mean that target identification in animal genomes is not possible by standard sequence comparison methods. Here we screen conserved 3' UTR sequences from the Drosophila melanogaster genome for potential miRNA targets. The screening procedure combines a sequence search with an evaluation of the predicted miRNA-target heteroduplex structures and energies. We show that this approach successfully identifies the five previously validated let-7, lin-4, and bantam targets from a large database and predict new targets for Drosophila miRNAs. Our target predictions reveal striking clusters of functionally related targets among the top predictions for specific miRNAs. These include Notch target genes for miR-7, proapoptotic genes for the miR-2 family, and enzymes from a metabolic pathway for miR-277. We experimentally verified three predicted targets each for miR-7 and the miR-2 family, doubling the number of validated targets for animal miRNAs. Statistical analysis indicates that the best single predicted target sites are at the border of significance; thus, target predictions should be considered as tentative until experimentally validated. We identify features shared by all validated targets that can be used to evaluate target predictions for animal miRNAs. Our initial evaluation and experimental validation of target predictions suggest functions for two miRNAs. For others, the screen suggests plausible functions, such as a role for miR-277 as a metabolic switch controlling amino acid catabolism. Cross-genome comparison proved essential, as it allows reduction of the sequence search space. Improvements in genome annotation and increased availability of cDNA sequences from other genomes will allow more sensitive screens. An increase in the number of confirmed targets is expected to reveal general structural features that can be used to improve their detection. While the screen is likely to miss some targets, our study shows that valid targets can be identified from sequence alone.

3' Untranslated Regions↗
PubMed2003

The relationship between sequence and interaction divergence in proteins.

There is currently a gap in knowledge between complexes of known three-dimensional structure and those known from other experimental methods such as affinity purifications or the two-hybrid system. This gap can sometimes be bridged by methods that extrapolate interaction information from one complex structure to homologues of the interacting proteins. To do this, it is important to know if and when proteins of the same type (e.g. family, superfamily or fold) interact in the same way. Here, we study interactions of known structure to address this question. We found all instances within the structural classification of proteins database of the same domain pairs interacting in different complexes, and then compared them with a simple measure (interaction RMSD). When plotted against sequence similarity we find that close homologues (30-40% or higher sequence identity) almost invariably interact the same way. Conversely, similarity only in fold (i.e. without additional evidence for a common ancestor) is only rarely associated with a similarity in interaction. The results suggest that there is a twilight zone of sequence similarity where it is not possible to say whether or not domains will interact similarly. We also discuss the rare instances of fold similarities interacting the same way, and those where obviously homologous proteins interact differently.

Amino Acid Sequence↗
PubMed2003

Crystal structure of an archaeal class I aldolase and the evolution of (betaalpha)8 barrel proteins.

Fructose-1,6-bisphosphate aldolase (FBPA) catalyzes the reversible cleavage of fructose 1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate in the glycolytic pathway. FBPAs from archaeal organisms have recently been identified and characterized as a divergent family of proteins. Here, we report the first crystal structure of an archaeal FBPA at 1.9-A resolution. The structure of this 280-kDa protein complex was determined using single wavelength anomalous dispersion followed by 10-fold non-crystallographic symmetry averaging and refined to an R-factor of 14.9% (Rfree 17.9%). The protein forms a dimer of pentamers, consisting of subunits adopting the ubiquitous (betaalpha)8 barrel fold. Additionally, a crystal structure of the archaeal FBPA covalently bound to dihydroxyacetone phosphate was solved at 2.1-A resolution. Comparison of the active site residues with those of classical FBPAs, which share no significant sequence identity but display the same overall fold, reveals a common ancestry between these two families of FBPAs. Structural comparisons, furthermore, establish an evolutionary link to the triosephosphate isomerases, a superfamily hitherto considered independent from the superfamily of aldolases.

Archaeal Proteins↗
PubMed2003

Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures.

The detection of local structural patterns in proteins (e.g. active sites) can provide insights into protein function in the absence of sequence or fold similarity. Methods to detect such similarities are key during structural annotation, for example with results from Structural Genomics initiatives. PINTS (Patterns in Non-homologous Tertiary Structures, http://pints.embl.de) performs database searches for such patterns and most importantly provides a measure of statistical significance for any similarity uncovered. To aid functional annotation of proteins, we allow comparisons of pre-defined patterns against databases of complete structures and of entire structures to databases of particular residues likely to be functionally important.

Binding Sites↗
PubMed2003

GlobPlot: Exploring protein sequences for globularity and disorder.

A major challenge in the proteomics and structural genomics era is to predict protein structure and function, including identification of those proteins that are partially or wholly unstructured. Non-globular sequence segments often contain short linear peptide motifs (e.g. SH3-binding sites) which are important for protein function. We present here a new tool for discovery of such unstructured, or disordered regions within proteins. GlobPlot (http://globplot.embl.de) is a web service that allows the user to plot the tendency within the query protein for order/globularity and disorder. We show examples with known proteins where it successfully identifies inter-domain segments containing linear motifs, and also apparently ordered regions that do not contain any recognised domain. GlobPlot may be useful in domain hunting efforts. The plots indicate that instances of known domains may often contain additional N- or C-terminal segments that appear ordered. Thus GlobPlot may be of use in the design of constructs corresponding to globular proteins, as needed for many biochemical studies, particularly structural biology. GlobPlot has a pipeline interface--GlobPipe--for the advanced user to do whole proteome analysis. GlobPlot can also be used as a generic infrastructure package for graphical displaying of any possible propensity.

Algorithms↗
PubMed2003

bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila.

Cell proliferation, cell death, and pattern formation are coordinated in animal development. Although many proteins that control cell proliferation and apoptosis have been identified, the means by which these effectors are linked to the patterning machinery remain poorly understood. Here, we report that the bantam gene of Drosophila encodes a 21 nucleotide microRNA that promotes tissue growth. bantam expression is temporally and spatially regulated in response to patterning cues. bantam microRNA simultaneously stimulates cell proliferation and prevents apoptosis. We identify the pro-apoptotic gene hid as a target for regulation by bantam miRNA, providing an explanation for bantam's anti-apoptotic activity.

3' Untranslated Regions↗
PubMed2003

A model for statistical significance of local similarities in structure.

Structural biology can provide three-dimensional structures for proteins of unknown function. When sequence or structure comparisons fail to suggest a function, insights can come from discovery of functionally important local structural patterns. Existing methods to detect such patterns lack rigorous statistics needed for widespread application. Here, we derive a formula to calculate statistical significance of the root-mean-square deviation between atoms in such patterns. When combined with a database search method, our statistics permit true functional or structural patterns in different folds to be discerned from noise. The approach is highly complementary to fold comparison for providing functional clues for new structures, and is key for the detection of recurrences of any new pattern.

Algorithms↗
PubMed2003

Predictions without templates: new folds, secondary structure, and contacts in CASP5.

We present the assessment of CASP5 predictions in the new fold category. For coordinate predictions, we considered five targets with new folds and eight lying on the fold recognition borderline. We performed detailed visual and numerical comparisons between predicted and experimental structures to assess prediction accuracy. The two procedures largely agreed, but the visual inspection identified instances where metrics, such as GDT_TS, ranked what we considered incorrect predictions highly. We found the quality of the best predictions to be very good: for nearly every target at least one group predicted a structure close to the correct one. However, selection of the best of five models is still problematic. The group of David Baker once again proved to be best overall, with many individual highlights. However, high quality and consistency were also seen from others, suggesting that the community is moving toward general procedures to predict accurate structures for proteins showing no resemblance to anything seen before. Predictions for secondary structure showed at best limited progress since CASP4. The number of targets is probably too small to spot differences in performance between methods, suggesting that such predictions might be better evaluated with schemes involving more proteins. For contact predictions, accuracies are still low, although there were several instances of accurate and useful contacts predicted de novo, and new approaches hint at future progress.

Algorithms↗
PubMed2003

Protein disorder prediction: implications for structural proteomics.

A great challenge in the proteomics and structural genomics era is to predict protein structure and function, including identification of those proteins that are partially or wholly unstructured. Disordered regions in proteins often contain short linear peptide motifs (e.g., SH3 ligands and targeting signals) that are important for protein function. We present here DisEMBL, a computational tool for prediction of disordered/unstructured regions within a protein sequence. As no clear definition of disorder exists, we have developed parameters based on several alternative definitions and introduced a new one based on the concept of "hot loops," i.e., coils with high temperature factors. Avoiding potentially disordered segments in protein expression constructs can increase expression, foldability, and stability of the expressed protein. DisEMBL is thus useful for target selection and the design of constructs as needed for many biochemical studies, particularly structural biology and structural genomics projects. The tool is freely available via a web interface (http://dis.embl.de) and can be downloaded for use in large-scale studies.

Circular Dichroism↗
PubMed2003

InterPreTS: protein interaction prediction through tertiary structure.

SUMMARY: InterPreTS (Interaction Prediction through Tertiary Structure) is a web-based version of our method for predicting protein-protein interactions (Aloy and Russell, 2002, PROC: Natl Acad. Sci. USA, 99, 5896-5901). Given a pair of query sequences, we first search for homologues in a database of interacting domains (DBID) of known three-dimensional complex structures. Pairs of sequences homologous to a known interacting pair are scored for how well they preserve the atomic contacts at the interaction interface. InterPreTS includes a useful interface for visualising molecular details of any predicted interaction. AVAILABILITY: http://www.russell.embl.de/interprets.

Databases, Protein↗
PubMed2002

Evolutionary relationship between the bacterial HPr kinase and the ubiquitous PEP-carboxykinase: expanding the P-loop nucleotidyl transferase superfamily.

Similarities between protein three-dimensional structures can reveal evolutionary and functional relationships not apparent from sequence comparison alone. Here we report such a similarity between the metabolic enzymes histidine phosphocarrier protein kinase (HPrK) and phosphoenolpyruvate carboxykinase (PCK), suggesting that they are evolutionarily related. Current structure classifications place PCK and other P-loop containing nucleotidyl-transferases into different folds. Our comparison of both HPrK and PCK to other P-loop containing proteins reveals that all share a common structural motif consisting of an alphabeta segment containing the P-loop flanked by an additional beta-strand that is adjacent in space, but far apart along the sequence. Analysis also shows that HPrK/PCK differ from other P-loop containing structures no more than they differ from each other. We thus suggest that HPrK and PCK should be classified with other P-loop containing proteins, and that all probably share a common ancestor that probably contained a simple P-loop motif with different protein segments being added or lost over the course of evolution. We used the structure-based sequence alignment containing residues specific to HPrK/PCK to identify additional members of this P-loop containing family.

Amino Acid Motifs↗