Characterization of the definitive classical calpain family of vertebrates using phylogenetic, evolutionary and expression analyses

Peer reviewedPublisher PD

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

DISOPRED3: Precise disordered region predictions with annotated protein binding activity

Motivation: A sizeable fraction of eukaryotic proteins contain intrinsically disordered regions (IDRs), which act in unfolded states or by undergoing transitions between structured and unstructured conformations. Over time, sequence-based classifiers of IDRs have become fairly accurate and currently a major challenge is linking IDRs to their biological roles from the molecular to the systems level. Results: We describe DISOPRED3, which extends its predecessor with new modules to predict IDRs and protein binding sites within them. Based on recent CASP evaluation results, DISOPRED3 can be regarded as state of the art in the identification of IDRs, and our self-assessment shows that it significantly improves over DISOPRED2 because its predictions are more specific across the whole board and more sensitive to IDRs longer than 20 amino acids. Predicted IDRs are annotated as protein binding through a novel SVM-based classifier, which uses profile data and additional sequence-derived features. Based on benchmarking experiments with full cross-validation, we show that this predictor generates precise assignments of disordered protein binding regions and that it compares well with other publicly available tools. Availability: http://bioinf.cs.ucl.ac.uk/disopred

Accurate contact predictions using covariation techniques and machine learning.

Here we present the results of residue-residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On a set of 40 target domains with a median family size of around 40 effective sequences, our server achieved an average top-L/5 long-range contact precision of 27%. MetaPSICOV method bases on a combination of classical contact prediction features, enhanced with three distinct covariation methods embedded in a two-stage neural network predictor. Some unique features of our approach are (1) the tuning between the classical and covariation features depending on the depth of the input alignment and (2) a hybrid approach to generate deepest possible multiple-sequence alignments by combining jackHMMer and HHblits. We discuss the CONSIP2 pipeline, our results and show that where the method underperformed, the major factor was relying on a fixed set of parameters for the initial sequence alignments and not attempting to perform domain splitting as a preprocessing step. Proteins 2015. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc

Computational Methods for Annotation Transfers from Sequence

Surveys of public sequence resources show that experimentally supported functional information is still completely missing for a considerable fraction of known proteins and is clearly incomplete for an even larger portion. Bioinformatics methods have long made use of very diverse data sources alone or in combination to predict protein function, with the understanding that different data types help elucidate complementary biological roles. This chapter focuses on methods accepting amino acid sequences as input and producing GO term assignments directly as outputs; the relevant biological and computational concepts are presented along with the advantages and limitations of individual approaches

The relationship between reductions in knee loading and immediate pain response whilst wearing lateral wedged insoles in knee osteoarthritis

Studies of lateral wedge insoles (LWIs) in medial knee osteoarthritis (OA) have shown reductions in the average external knee adduction moment (EKAM) but no lessening of knee pain. Some treated patients actually experience increases in the EKAM which could explain the overall absence of pain response. We examined whether, in patients with painful medial OA, reductions in the EKAM were associated with lessening of knee pain. Each patient underwent gait analysis whilst walking in a control shoe and two LWI's. We evaluated the relationship between change in EKAM and change in knee pain using Spearman Rank Correlation coefficients and tested whether dichotomizing patients into biomechanical responders (decreased EKAM) and non-responders (increased EKAM) would identify those with reductions in knee pain. In 70 patients studied, the EKAM was reduced in both LWIs versus control shoe (−5.21% and −6.29% for typical and supported wedges, respectively). The change in EKAM using LWIs was not significantly associated with the direction of knee pain change. Further, 54% were biomechanical responders, but these persons did not have more knee pain reduction than non-responders. Whilst LWIs reduce EKAM, there is no clearcut relationship between change in medial load when wearing LWIs and corresponding change in knee pain

Cassini detection of Enceladus' cold water-group plume ionosphere

This study reports direct detection by the Cassini plasma spectrometer of freshly-produced water-group ions (O+, OH+, H2O+, H3O+) and heavier water dimer ions (HxO(2))(+) very close to Enceladus where the plasma begins to emerge from the plume. The data were obtained during two close ( 52 and 25 km) flybys of Enceladus in 2008 and are similar to ion data in cometary comas. The ions are observed in detectors looking in the Cassini ram direction exhibiting energies consistent with the Cassini speed, indicative of a nearly stagnant plasma flow in the plume. North of Enceladus the plasma slowing commences about 4 to 6 Enceladus radii away, while south of Enceladus signatures of the plasma interaction with the plume are detected 22 Enceladus radii away. Citation: Tokar, R. L., R. E. Johnson, M. F. Thomsen, R. J. Wilson, D. T. Young, F. J. Crary, A. J. Coates, G. H. Jones, and C. S. Paty ( 2009), Cassini detection of Enceladus' cold water-group plume ionosphere, Geophys. Res. Lett., 36, L13203, doi:10.1029/2009GL038923

Caspase 8 activation independent of Fas (CD95/APO-1) signaling may mediate killing of B-chronic lymphocytic leukemia cells by cytotoxic drugs or gamma radiation.

Ligation of the cell-surface Fas molecule by its ligand (Fas-L) or agonistic anti-Fas monoclonal antibodies results in the cleavage and activation of the cysteine protease procaspase 8 followed by the activation of procaspase 3 and by apoptosis. In some leukemia cell lines, cytotoxic drugs induce expression of Fas-L, which may contribute to cell killing through the ligation of Fas. The involvement of Fas, Fas-L, and caspase 8 was studied in the killing of B-cell chronic lymphocytic leukemia (B-CLL) cells by chlorambucil, fludarabine, or gamma radiation. Spontaneous apoptosis was observed at 24-hour incubation, with additional apoptosis induced by each of the cytotoxic treatments. Although Fas mRNA expression was elevated after exposure to chlorambucil, fludarabine, or gamma radiation, Fas protein levels only increased after irradiation. Therefore, Fas expression may be regulated by multiple mechanisms that allow the translation of Fas mRNA only in response to restricted cytotoxic stimuli. None of the cytotoxic stimuli studied here induced Fas-L expression. An agonistic anti-Fas monoclonal antibody (CH-11) did not significantly augment apoptosis induction by any of the death stimuli. A Fas-blocking antibody (ZB4) did not inhibit spontaneous, chlorambucil-, fludarabine-, or radiation-induced apoptosis. However, procaspase 8 processing was induced by all cytotoxic stimuli. These data suggest that the Fas/Fas-L signaling system does not play a major role in the induction of apoptosis in B-CLL cells treated with cytotoxic drugs or radiation. However, Fas-independent activation of caspase 8 may play a crucial role in the regulation of apoptosis in these cells

Geldanamycin and herbimycin A induce apoptotic killing of B chronic lymphocytic leukemia cells and augment the cells' sensitivity to cytotoxic drugs.

We studied the actions of geldanamycin (GA) and herbimycin A (HMA), inhibitors of the chaperone proteins Hsp90 and GRP94, on B chronic lymphocytic leukemia (CLL) cells in vitro. Both drugs induced apoptosis of the majority of CLL isolates studied. Whereas exposure to 4-hour pulses of 30 to 100 nM GA killed normal B lymphocytes and CLL cells with similar dose responses, T lymphocytes from healthy donors as well as those present in the CLL isolates were relatively resistant. GA, but not HMA, showed a modest cytoprotective effect toward CD34+ hematopoietic progenitors from normal bone marrow. The ability of bone marrow progenitors to form hematopoietic colonies was unaffected by pulse exposures to GA. Both GA and HMA synergized with chlorambucil and fludarabine in killing a subset of CLL isolates. GA- and HMA-induced apoptosis was preceded by the up-regulation of the stress-responsive chaperones Hsp70 and BiP. Both ansamycins also resulted in down-regulation of Akt protein kinase, a modulator of cell survival. The relative resistance of T lymphocytes and of CD34+ bone marrow progenitors to GA coupled with its ability to induce apoptosis following brief exposures and to synergize with cytotoxic drugs warrant further investigation of ansamycins as potential therapeutic agents in CLL

Scalable web services for the PSIPRED Protein Analysis Workbench

Here, we present the new UCL Bioinformatics Group’s PSIPRED Protein Analysis Workbench. The Workbench unites all of our previously available analysis methods into a single web-based framework. The new web portal provides a greatly streamlined user interface with a number of new features to allow users to better explore their results. We offer a number of additional services to enable computationally scalable execution of our prediction methods; these include SOAP and XML-RPC web server access and new HADOOP packages. All software and services are available via the UCL Bioinformatics Group website at http://bioinf.cs.ucl.ac.uk/