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At least 19 recordsLinked to original sources

PubMed1997

CASP, a novel, highly conserved alternative-splicing product of the CDP/cut/cux gene, lacks cut-repeat and homeo DNA-binding domains, and interacts with full-length CDP in vitro.

Human CDP/cut and its murine counterpart, cux1/CDP are homeodomain repressor proteins in the family of Drosophila Cut. Northern blot analysis reveals complex alternative splicing, including forms too small to encode the full 1505 amino acid protein. We have characterized a CDP/cut alternatively spliced cDNA (CASP) of 3.4 kb. Human CASP, a predicted 678 amino acid polypeptide, shares 400 amino acids with CDP, but has an alternate N terminal exon of 20 aa, and the C-terminal 258 amino acids diverge from CDP/cut entirely. As the unique C-terminus of CASP lacks the three 'cut-repeats' and homeodomain of CDP/cut, we predict it does not bind DNA. Murine CASP, 96% similar to human, shares these features. Database searches identify homologs in chicken (86% identical to human CASP) and yeast (29% identical to human). Murine CASP mRNA is ubiquitous in mouse tissues and in tissue-culture cell lines. We generated a specific antiserum against the unique C-terminus of CASP, and used this reagent to demonstrate that CASP protein is expressed as an approx. 80 kDa protein in human and murine cells. Co-translation of in vitro-translated CDP and CASP mRNA, followed by immunoprecipitation with specific anti-CASP IgG, shows that CASP polypeptide can from a complex with CDP. Studies of the intron/exon structure of the murine cux/CDP/mCASP locus (>> 100 kb) reveal that the unique 3' exons of CASP are interposed between cut-repeats 2 and 3 of the cux gene. We speculate that a primordial CASP-like gene captured a cut-repeat-homeobox gene to give rise to the eukaryotic Cut/CDP family of proteins.

Alternative Splicing↗

PubMed1998

Upregulation of CASP genes in human tumor cells undergoing etoposide-induced apoptosis.

Caspases are aspartate-specific cysteine proteases that play a pivotal role in drug-induced cell death. We designed RT-PCR assays to analyse the expression of CASP-3, CASP-4, CASP-6 and the long and short isoforms of CASP-2 genes in human cells. These genes heterogeneously coexpress in leukemic cell lines and bone marrow samples from patients with de novo acute myelogenous leukemia at diagnosis. Treatment of U937 and HL60 leukemic cells and HT29 colon carcinoma cells with the topoisomerase II inhibitor etoposide upregulates CASP-2 and CASP-3 genes in these cells before inducing their apoptosis. This effect of etoposide is not observed in K562 cells and bcl-2-transfected U937 cells which are less sensitive to drug-induced apoptosis. Nuclear run-on experiments demonstrate that etoposide increases CASP gene transcription in U937 cells, an effect that is prevented by Bcl-2 overexpression. Upregulation of CASP genes is associated with an enhanced synthesis of related procaspases that precedes the appearance of apoptosis markers including caspase-3 activation, poly(ADP-ribose) polymerase cleavage and internucleosomal DNA fragmentation. These results suggest that the ability of tumor cells to upregulate CASP-2 and CASP-3 genes in response to cytotoxic drugs could be predictive of their sensitivity to drug-induced apoptosis.

Apoptosis↗

PubMed2002

The N-terminal coiled coil domain of the cytohesin/ARNO family of guanine nucleotide exchange factors interacts with the scaffolding protein CASP.

Cytohesin is a guanine nucleotide exchange factor that regulates members of the ADP-ribosylation factor (ARF) family of small GTPases. All of the members of the cytohesin family (including ARNO, ARNO3, and the newly characterized cytohesin-4) have a similar domain distribution consisting of a Sec7 homology domain, a pleckstrin homology domain, and an N-terminal coiled coil. In this study, we attempt to identify proteins that interact specifically with the coiled coil motif of cytohesin. Yeast two-hybrid screening of a B cell library using the cytohesin N terminus as bait, identified CASP, a scaffolding protein of previously unknown function, as a binding partner. CASP contains an internal coiled coil motif that is required for cytohesin binding both in vitro and in COS-1 cells. The specificity of the coiled coil of CASP is not restricted to cytohesin, however, because it is also capable of interacting with other members of the cytohesin/ARNO family, ARNO and ARNO3. In immunofluorescence experiments, CASP localizes to perinuclear tubulovesicular structures that are in close proximity to the Golgi. These structures remain relatively undisturbed when the cells are treated with brefeldin A. In epidermal growth factor-stimulated COS-1 cells overexpressing cytohesin and CASP, cytohesin recruits CASP to membrane ruffles, revealing a functional interaction between the two proteins. These observations collectively suggest that CASP is a scaffolding protein that facilitates the function of at least one member of the cytohesin/ARNO family in response to specific cellular stimuli.

Amino Acid Sequence↗

PubMed1985

Catheter aspiration for simple pneumothorax (CASP) in the outpatient management of simple traumatic pneumothorax.

Catheter aspiration for simple pneumothorax (CASP) was evaluated prospectively in the outpatient management of simple traumatic pneumothorax in 17 patients and compared to conventional tube thoracostomy (CTT) in 17 matched control patients. In 16 of the 17 consecutive study patients CASP maintained lung reexpansion without complications. Pneumothorax was due to needle puncture for drug abuse in 11 patients, stab wounds in five patients, and blunt trauma in one patient. The CASP patients were not hospitalized, whereas the control CTT patients averaged 4.9 days' hospitalization. CTT was associated with complications in two patients versus none for CASP. Parenteral analgesics were utilized for greater than 48 hours in CTT patients but were not needed for CASP patients. Costs averaged +310 for CASP compared to +3,030 for CTT. This ongoing pilot study data indicates that CASP is a reasonable alternative to CTT in selected patients with simple traumatic pneumothorax.

Adolescent↗

PubMed1999

Some measures of comparative performance in the three CASPs.

Performance in the three Critical Assessment of protein Structure Prediction (CASP) experiments has been compared in the areas of alignment accuracy for models based on homology and three-dimensional accuracy for models produced by using ab initio prediction methods. The homologous models span the comparative modeling and fold-recognition regimes. Each CASP target is assigned a relative difficulty based on the extent of sequence identity and the degree of structural overlap with the best available template. There is a clear improvement in alignment accuracy between CASP1 and CASPs 2 and 3 over much of the difficulty scale but no apparent improvement between CASP2 and CASP3. Encouragingly, the best ab initio models of small targets are clearly more accurate in CASP3 than in CASPs 1 and 2.

Algorithms↗

PubMed1992

Effect of aspirin on photodynamic therapy utilizing chloroaluminum sulfonated phthalocyanine (CASP).

The efficacy of photodynamic therapy (PDT) is mediated through a direct vascular effect. Interference with platelet function and resulting vascular stasis have been recently demonstrated utilizing the photosensitizer dihematoporphyrin ether (DHE). We examined the effect of aspirin, a known inhibitor of both cyclooxygenase and platelet activity, on PDT using chloroaluminum sulfonated phthalocyanine (CASP). Thirty-six rats implanted with a window chamber were given either 0.1 mg/kg (low dose) or 10 mg/kg (high dose) aspirin immediately before, immediately after, or 6 hours after the completion of CASP-PDT. Aspirin in either dosage did not appear to have any effect on the window vasculature when given immediately after light exposure. A moderate inhibition of vascular response was seen in animals treated with aspirin pre-PDT, whereas high-dose aspirin completely abrogated the CASP-PDT vascular response when given 6 hours post-PDT. These data indicate that aspirin can effect CASP-PDT in both time-dependent and dose-dependent fashions.

Animals↗

PubMed2002

CASP, the alternatively spliced product of the gene encoding the CCAAT-displacement protein transcription factor, is a Golgi membrane protein related to giantin.

Large coiled-coil proteins are being found in increasing numbers on the membranes of the Golgi apparatus and have been proposed to function in tethering of transport vesicles and in the organization of the Golgi stack. Members of one class of Golgi coiled-coil protein, comprising giantin and golgin-84, are anchored to the bilayer by a single C-terminal transmembrane domain (TMD). In this article, we report the characterization of another mammalian coiled-coil protein, CASP, that was originally identified as an alternatively spliced product of the CUTL1 gene that encodes CCAAT-displacement protein (CDP), the human homologue of the Drosophila homeodomain protein Cut. We find that the Caenorhabditis elegans homologues of CDP and CASP are also generated from a single gene. CASP lacks the DNA binding motifs of CDP and was previously reported to be a nuclear protein. Herein, we show that it is in fact a Golgi protein with a C-terminal TMD and shares with giantin and golgin-84 a conserved histidine in its TMD. However, unlike these proteins, CASP has a homologue in Saccharomyces cerevisiae, which we call COY1. Deletion of COY1 does not affect viability, but strikingly restores normal growth to cells lacking the Golgi soluble N-ethylmaleimide-sensitive factor attachment protein receptor Gos1p. The conserved histidine is necessary for Coy1p's activity in cells lacking Gos1p, suggesting that the TMD of these transmembrane Golgi coiled-coil proteins is directly involved in their function.

Alternative Splicing↗

PubMed1999

Photodynamic modulation of wound healing with BPD-MA and CASP.

BACKGROUND AND OBJECTIVE: Wound healing is an intricate process requiring the orchestration of cells, growth factors, cytokines, and the extracellular matrix. Cytokines, specifically TGF-beta, are believed to be instrumental in sustaining the fibrotic process, which leads to scarring. Photodynamic therapy (PDT) uses potent photosensitizers, which induce a wide range of effects on cells and the extracellular matrix. The influences of PDT on wound healing are not well known. STUDY DESIGN/MATERIALS AND METHODS: Seven full-thickness incisional wounds were placed on each of 24 hairless Sprague Dawly rats, three wounds on one flank serving as dark controls and four on the contralateral side treated with PDT. Wounds were created two days before, one hour before, or one hour after red light exposure with an argon ion pumped dye laser. Twelve rats were injected with 0.25 mg/kg or 0.5 mg/kg of the PDT drug, BPD-MA, and the other 12 with 5 mg/kg or 10 mg/kg of the PDT drug, CASP, 3 and 24 hours prior to irradiation of light, respectively. At low doses of both photosensitizers, animals were irradiated with 1, 5, 10, and 20 J/cm2. At higher doses of BPD-MA and CASP animals were treated with 10, 20, 50, and 100 J/cm2 of light. Wounds were examined each day for 14 days and noted for edema, erythema, inflammation, necrosis, and quality of scarring. Wounds were also photographed at day 0, 2, 5, 8, and 14 post-irradiation. All animals were sacrificed 14 days after irradiation and the wounds were evaluated by light microscopy. RESULTS: Grossly, animals treated with 0.25 mg/kg BPD-MA showed no effect with PDT. Animals treated with 0.5 mg/kg BPD, and 5 and 10 mg/kg CASP showed responses that varied with both light and drug dose. Erythema, edema, inflammation, and necrosis attributed to PDT were all observed, but there was no apparent influence of PDT on either the rate or final appearance of wound healing. Histologically, there were no apparent differences between treated and untreated sites, regardless of the drug, dose of light, or time of irradiation. CONCLUSION: A single PDT treatment given before or after skin wounds does not apparently alter wound healing even when PDT caused brisk inflammatory reactions. PDT may have effects that were not detected. We conclude that PDT does not greatly influence incisional skin wound healing in the rat model.

Aluminum↗

PubMed2001

Comparison of performance in successive CASP experiments.

As the number of completed CASP (Critical Assessment of Protein Structure Prediction) experiments grows, so does the need for stable, standard methods for comparing performance in successive experiments. It is critical to develop methods for determining the areas in which there is progress and in which areas are static. We have added an analysis of the CASP4 results to that previously published for CASPs 1, 2, and 3. We again use a unified difficulty scale to permit comparison of performance as a function of target difficulty in the different CASPs. The scale is used to compare performance in aligning target sequences to a structural template. There was a clear improvement in alignment quality between CASP1 (1994) and CASP2 (1996). No change is apparent between CASP2 and CASP3 (1998). There is a small barely detectable improvement between CASP3 and the latest experiment (CASP4, 2000). Alignment remains the major source of error in all models based on less than about 30% sequence identity. Comparison of performance in the new fold modeling regime is complicated by issues in devising an objective target difficulty scale. We have found limited numerical support for significant progress between CASP3 and CASP4 in this area. More subjectively, most observers are convinced that there has been substantial progress. Progress is dominated by a single group.

Models, Molecular↗

PubMed2002

Metallo-beta-lactamase fold within nucleic acids processing enzymes: the beta-CASP family.

A separate family of enzymes within the metallo-beta-lactamase fold comprises several important proteins acting on nucleic acid substrates, involved in DNA repair (Artemis, SNM1 and PSO2) and RNA processing [cleavage and polyadenylation specificity factor (CPSF) subunit]. Proteins of this family, named beta-CASP after the names of its representative members, possess specific features relative to those of other metallo-beta-lactamases, that are concentrated in the C-terminal part of the domain. In this study, using sensitive methods of sequence analysis, we identified highly conserved amino acids specific to the beta-CASP family, some of which were unidentified to date, that are predicted to play critical roles in the enzymatic function. The identification and characterisation of all the extant, detectable beta-CASP members within sequence databases and genome data also allowed us to unravel particular sequence features which are likely to be involved in substrate specificity, as well as to describe new but as yet uncharacterised members which may play critical roles in DNA and RNA metabolism.

Amino Acid Motifs↗

PubMed2003

CASP and CAFASP experiments and their findings.

This short introductory chapter is intended simply to introduce a sense of the progress, limitations, challenges, and likely future developments in the field of protein structure prediction through what seems to be a unique scientific process. CASP and CAFASP represent a direct challenge and careful assessment of a field of study that has captured the interest of many scientists. Three of the best scientists in the field and their colleagues provide a more detailed description of the field and how it is developing in Chapters 25, 26, and 27. As prediction methods have advanced the distinction between comparative modeling, fold recognition, and novel fold recognition have blurred somewhat. It is a testament to the community that as the knowledge of the algorithms evolved, World Wide Web servers providing access to these algorithms appeared. Thus, making it relatively straightforward for any investigator to apply a melting pot of methods to the prediction process. What all approaches need are more targets and a continued refinement to the evaluation process. The first need is being met in part by the PDB, which is, with depositors' approval, releasing sequences ahead of structure release (see http://www.rcsb.org/pdb/status.html). Further, the structural genomics projects are reporting their progress for all targets on a weekly basis (see http://targetdb.pdb.org/). While there is no indication that the sequences of the latter will lead to a structure, it is a rich source of targets (17,000 in October 2002). Not only do CASP and CAFASP measure progress, they help define where efforts should be directed to move the field forward. It is a testament to how far the field has come that investigators are now turning to the unknown. Although attempting to predict a structure that will appear experimentally helps improve the methods applied to structure prediction, it does not further our understanding of living systems directly. Attempts at defining the "The Most Wanted" (Abbott, 2001)--the structures most in need of prediction to help further our understanding of the biology, and the efforts to make those predictions, speak to a healthy future for the field of protein structure prediction. To the many individuals who help define the CASP and CAFASP processes, serve the community as assesors and compete in the experiments this is a tribute.

Computational Biology↗

PubMed2003

Assessment of progress over the CASP experiments.

The quality of structure models produced in the CASP5 experiment has been compared with that in earlier CASPs. The most significant progress is in the fold recognition regime, where the development of meta-servers has allowed more accurate consensus models to be generated. In contrast to this, there is little evidence of progress in producing more accurate comparative models, particularly those based on sequence identities > 30%. For comparative models based on low-sequence identity and for fold recognition models, accuracy depends primarily on the fraction of the target structure that is similar to an available template, and the quality of the alignment. Overall, these results indicate that there are still no effective methods of improving model quality beyond that obtained by successfully copying a template structure. For models of proteins with previously unknown folds, there appears to be a pause in the previous consistent improvement. There is some evidence that more groups are producing top-quality models, however. Although specific progress between successive experiments is sometimes difficulty to identify, over the history of all the CASPs there has been steady, if sometimes slow, progress in all modeling regimes.

Algorithms↗

PubMed2003

Critical assessment of methods of protein structure prediction (CASP)-round V.

This article provides an introduction to the special issue of the journal Proteins dedicated to the fifth CASP experiment to assess the state of the art in protein structure prediction. The article describes the conduct, the categories of prediction, and the evaluation and assessment procedures of the experiment. A brief summary of progress over the five CASP experiments is provided. Related developments in the field are also described.

Computational Biology↗

PubMed2005

Critical assessment of methods of protein structure prediction (CASP)--round 6.

This article is an introduction to the special issue of the journal Proteins, dedicated to the sixth CASP experiment to assess the state of the art in protein structure prediction. The article describes the conduct of the experiment and the categories of prediction included, and outlines the evaluation and assessment procedures. A brief summary of progress over the decade of CASP experiments is also provided.

Algorithms↗

PubMed2005

Progress over the first decade of CASP experiments.

CASP has now completed a decade of monitoring the state of the art in protein structure prediction. The quality of structure models produced in the latest experiment, CASP6, has been compared with that in earlier CASPs. Significant although modest progress has again been made in the fold recognition regime, and cumulatively, progress in this area is impressive. Models of previously unknown folds again appear to have modestly improved, and several mixed alpha/beta structures have been modeled in a topologically correct manner. Progress remains hard to detect in high sequence identity comparative modeling, but server performance in this area has moved forward.

Algorithms↗

PubMed1999

Ab initio protein structure prediction of CASP III targets using ROSETTA.

To generate structures consistent with both the local and nonlocal interactions responsible for protein stability, 3 and 9 residue fragments of known structures with local sequences similar to the target sequence were assembled into complete tertiary structures using a Monte Carlo simulated annealing procedure (Simons et al., J Mol Biol 1997; 268:209-225). The scoring function used in the simulated annealing procedure consists of sequence-dependent terms representing hydrophobic burial and specific pair interactions such as electrostatics and disulfide bonding and sequence-independent terms representing hard sphere packing, alpha-helix and beta-strand packing, and the collection of beta-strands in beta-sheets (Simons et al., Proteins 1999;34:82-95). For each of 21 small, ab initio targets, 1,200 final structures were constructed, each the result of 100,000 attempted fragment substitutions. The five structures submitted for the CASP III experiment were chosen from the approximately 25 structures with the lowest scores in the broadest minima (assessed through the number of structural neighbors; Shortle et al., Proc Natl Acad Sci USA 1998;95:1158-1162). The results were encouraging: highlights of the predictions include a 99-residue segment for MarA with an rmsd of 6.4 A to the native structure, a 95-residue (full length) prediction for the EH2 domain of EPS15 with an rmsd of 6.0 A, a 75-residue segment of DNAB helicase with an rmsd of 4.7 A, and a 67-residue segment of ribosomal protein L30 with an rmsd of 3.8 A. These results suggest that ab initio methods may soon become useful for low-resolution structure prediction for proteins that lack a close homologue of known structure.

Algorithms↗

PubMed2003

Automated prediction of CASP-5 structures using the Robetta server.

Robetta is a fully automated protein structure prediction server that uses the Rosetta fragment-insertion method. It combines template-based and de novo structure prediction methods in an attempt to produce high quality models that cover every residue of a submitted sequence. The first step in the procedure is the automatic detection of the locations of domains and selection of the appropriate modeling protocol for each domain. For domains matched to a homolog with an experimentally characterized structure by PSI-BLAST or Pcons2, Robetta uses a new alignment method, called K*Sync, to align the query sequence onto the parent structure. It then models the variable regions by allowing them to explore conformational space with fragments in fashion similar to the de novo protocol, but in the context of the template. When no structural homolog is available, domains are modeled with the Rosetta de novo protocol, which allows the full length of the domain to explore conformational space via fragment-insertion, producing a large decoy ensemble from which the final models are selected. The Robetta server produced quite reasonable predictions for targets in the recent CASP-5 and CAFASP-3 experiments, some of which were at the level of the best human predictions.

Algorithms↗

PubMed2005

A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction.

For the past ten years, CASP (Critical Assessment of Structure Prediction) has monitored the state of the art in modeling protein structure from sequence. During this period, there has been substantial progress in both comparative modeling of structure (using information from an evolutionarily related structural template) and template-free modeling. The quality of comparative models depends on the closeness of the evolutionary relationship on which they are based. Template-free modeling, although still very approximate, now produces topologically near correct models for some small proteins. Current major challenges are refining comparative models so that they match experimental accuracy, obtaining accurate sequence alignments for models based on remote evolutionary relationships, and extending template-free modeling methods so that they produce more accurate models, handle parts of comparative models not available from a template and deal with larger structures.

Algorithms↗