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L-aspartate association contributes to rate limitation and induction of the T-->R transition in Escherichia coli aspartate transcarbamoylase. Equilibrium exchanges and kinetic isotope effects with a Vmax-enhanced mutant, Asp-236-->Ala.

Equilibrium isotope exchange kinetics (EIEK) and kinetic isotope effects have been used to determine the mechanistic basis for the altered kinetic characteristics of a mutant version of Escherichia coli aspartate transcarbamylase in which Asp-236 of the catalytic chain is replaced by alanine (Asp-236-->Ala). The [14C]Asp<--> N-carbamyl-L-aspartate (CAsp) and [14C]CP<-->CAsp exchange rates, observed as a function of various reactant-product pairs, exhibited dramatic increases in maximal rates, along with decreases in substrate half-saturation values and cooperativity. The carbon kinetic isotope effect, 13C versus 12C at the carbonyl group of carbamoyl phosphate, for the Asp-236-->Ala enzyme decreased toward unity as [Asp] increased, as observed for the wild-type enzyme. Both the kinetic isotope effects and EIEK results indicate that the Asp-236-->Ala enzyme operates by the same ordered kinetic mechanism as the wild-type enzyme. Although activation effects by ATP and N-phosphonacetyl-L-aspartate are lost, inhibition by CTP was apparent in equilibrium exchanges. Simulation of the EIEK data indicated that the best fit to the observed changes in saturation curves was obtained by preferentially increasing the rate of the T-->R transition, kappa T-->R, thereby destabilizing the T-state and increasing the equilbrium constant for the T<-->R transition. A multistep model for Asp bindng to aspartate transcarbamoylase is proposed, in which Asp induces the initial conformational changes that in turn trigger the T-->R transition, followed by stepwise filling of the remaining active sites.

Alanine↗

ATP-dependent rotation of mutant ATP synthases defective in proton transport.

During ATP hydrolysis, the gammaepsilon c10 complex (gamma and epsilon subunits and a c subunit ring formed from 10 monomers) of F0F1 ATPase (ATP synthase) rotates relative to the alpha3beta3delta ab2 complex, leading to proton transport through the interface between the a subunit and the c subunit ring. In this study, we replaced the two pertinent residues for proton transport, cAsp-61 and aArg-210 of the c and a subunits, respectively. The mutant enzymes exhibited lower ATPase activities than that of the wild type but exhibited ATP-dependent rotation in planar membranes, in which their original assemblies are maintained. The mutant enzymes were defective in proton transport, as shown previously. These results suggest that proton transport can be separated from rotation in ATP hydrolysis, although rotation ensures continuous proton transport by bringing the cAsp-61 and aArg-210 residues into the correct interacting positions.

Adenosine Triphosphate↗

The metallo-beta-lactamase/beta-CASP domain of Artemis constitutes the catalytic core for V(D)J recombination.

The V(D)J recombination/DNA repair factor Artemis belongs to the metallo-beta-lactamase (beta-Lact) superfamily of enzymes. Three regions can be defined within the Artemis protein sequence: (a) the beta-Lact homology domain, to which is appended (b) the beta-CASP region, specific of members of the beta-Lact superfamily acting on nucleic acids, and (c) the COOH-terminal domain. Using in vitro mutagenesis, here we show that the association of the beta-Lact and the beta-CASP regions suffices for in vivo V(D)J recombination of chromosome-integrated substrates. Single amino acid mutants point to critical catalytic residues for V(D)J recombination activity. The results presented here define the beta-Lact/beta-CASP domain of Artemis as the minimal core catalytic domain needed for V(D)J recombination and suggest that Artemis uses one or two Zn(II) ions to exert its catalytic activity, like bacterial class B beta-Lact enzymes hydrolyzing beta-lactam compounds.

Amino Acid Sequence↗

What are the baselines for protein fold recognition?

MOTIVATION: What constitutes a baseline level of success for protein fold recognition methods? As fold recognition benchmarks are often presented without any thought to the results that might be expected from a purely random set of predictions, an analysis of fold recognition baselines is long overdue. Given varying amounts of basic information about a protein-ranging from the length of the sequence to a knowledge of its secondary structure-to what extent can the fold be determined by intelligent guesswork? Can simple methods that make use of secondary structure information assign folds more accurately than purely random methods and could these methods be used to construct viable hierarchical classifications? EXPERIMENTS PERFORMED: A number of rapid automatic methods which score similarities between protein domains were devised and tested. These methods ranged from those that incorporated no secondary structure information, such as measuring absolute differences in sequence lengths, to more complex alignments of secondary structure elements. Each method was assessed for accuracy by comparison with the Class Architecture Topology Homology (CATH) classification. Methods were rated against both a random baseline fold assignment method as a lower control and FSSP as an upper control. Similarity trees were constructed in order to evaluate the accuracy of optimum methods at producing a classification of structure. RESULTS: Using a rigorous comparison of methods with CATH, the random fold assignment method set a lower baseline of 11% true positives allowing for 3% false positives and FSSP set an upper benchmark of 47% true positives at 3% false positives. The optimum secondary structure alignment method used here achieved 27% true positives at 3% false positives. Using a less rigorous Critical Assessment of Structure Prediction (CASP)-like sensitivity measurement the random assignment achieved 6%, FSSP-59% and the optimum secondary structure alignment method-32%. Similarity trees produced by the optimum method illustrate that these methods cannot be used alone to produce a viable protein structural classification system. CONCLUSIONS: Simple methods that use perfect secondary structure information to assign folds cannot produce an accurate protein taxonomy, however they do provide useful baselines for fold recognition. In terms of a typical CASP assessment our results suggest that approximately 6% of targets with folds in the databases could be assigned correctly by randomly guessing, and as many as 32% could be recognised by trivial secondary structure comparison methods, given knowledge of their correct secondary structures.

Computational Biology↗

The role of cell death in regulating the size and shape of the mammalian forebrain.

The size of the cerebral cortex is determined by the rate of production of neurons and glial cells in the proliferative ventricular and subventricular zones. Recent studies from targeted mutations of different death-effector gene families indicate that programmed cell death (PCD) plays an important role in cell production and early morphogenesis of the mammalian forebrain before the formation of neuronal connections. For example, disruption of the c/Jun N-kinase signaling pathway by double-targeted mutation of both Jnk1 and Jnk2 results in increased PCD in the forebrain leading to precocious degeneration of cerebral precursors. In contrast, disturbance of the caspase cascade by targeted disruption of either casp-9 or casp-3 leads to decreased PCD causing expansion and exencephaly of the forebrain as well as supernumerary neurons in the cerebral cortex. The supernumerary neurons in these knockout mice align radially and form an expanded cortical plate which begins to form cerebral convolutions. Thus, the precise coordination of different apoptotic signaling pathways during early stages of neurogenesis is crucial for regulation of the proper cortical size and shape.

Animals↗

Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines.

Intrinsically disordered proteins have long stretches of their polypeptide chain, which do not adopt a single native structure composed of stable secondary and tertiary structure in the absence of binding partners. The prediction of intrinsically disordered regions in proteins from sequence is increasingly becoming of interest, as the presence of many such regions in the complete genome sequences are discovered and important functional roles are associated with them. We have developed a machine learning approach based on two support vector machines (SVM) to discriminate disordered regions from sequence. The SVM are trained and benchmarked on two sets, representing long and short disordered regions. A preliminary version of Spritz was shown to perform consistently well at the recent biannual CASP-6 experiment [Critical Assessment of Techniques for Protein Structure Prediction (CASP), 2004]. The fully developed Spritz method is freely available as a web server at http://distill.ucd.ie/spritz/ and http://protein.cribi.unipd.it/spritz/.

Artificial Intelligence↗

The 2002 Olympic Games of protein structure prediction.

The summer of every even year is considered by the protein structure prediction community as the Olympic Games season, because in addition to a number of continuous benchmarking experiments such as LiveBench, much effort is invested in the blind prediction experiments CASP and CAFASP. Here we report the major advances registered in the field since the last Games of 2000, as measured by the recently completed LiveBench-4 experiment. These results provide a timely measure of the capabilities of current methods and of their expected performance in the upcoming CASP-5 and CAFASP-3 experiments. We also describe the initiation of the two new, community-wide experiments, PDB-CAFASP and MR-CAFASP. These new experiments extend the scope of previous efforts and may have important implications for structural genomics.

Computational Biology↗

The 2000 Olympic Games of protein structure prediction; fully automated programs are being evaluated vis-à-vis human teams in the protein structure prediction experiment CAFASP2.

In this commentary, we describe two new protein structure prediction experiments being run in parallel with the CASP experiment, which together may be regarded as the 2000 Olympic Games of structure prediction. The first new experiment is CAFASP, the Critical Assessment of Fully Automated Structure Prediction. In CAFASP, the participants are fully automated programs or Internet servers, and here the automated results of the programs are evaluated, without any human intervention. The second new experiment, named LiveBench, follows the CAFASP ideology in that it is aimed towards the evaluation of automatic servers only, while it runs on a large set of prediction targets and in a continuous fashion. Researchers will be watching the 2000 protein structure prediction Olympic Games, to be held in December, in order to learn about the advances in the classical 'human-plus-machine' CASP category, the fully automated CAFASP category, and the comparison between the two.

Amino Acid Sequence↗

Rigorous performance evaluation in protein structure modelling and implications for computational biology.

In principle, given the amino acid sequence of a protein, it is possible to compute the corresponding three-dimensional structure. Methods for modelling structure based on this premise have been under development for more than 40 years. For the past decade, a series of community wide experiments (termed Critical Assessment of Structure Prediction (CASP)) have assessed the state of the art, providing a detailed picture of what has been achieved in the field, where we are making progress, and what major problems remain. The rigorous evaluation procedures of CASP have been accompanied by substantial progress. Lessons from this area of computational biology suggest a set of principles for increasing rigor in the field as a whole.

Computational Biology↗

The V(D)J recombination/DNA repair factor artemis belongs to the metallo-beta-lactamase family and constitutes a critical developmental checkpoint of the lymphoid system.

V(D)J recombination constitutes a critical checkpoint in the development of the immune system as shown in several animal models as well as severe combined immune deficiency (SCID) condition in humans. We recently cloned the Artemis gene, whose mutations are responsible for RS-SCID, a condition characterized by an absence of both B and T lymphocytes and associated with increased sensitivity to ionizing radiations. Artemis is ubiquitously expressed and is localized in the nucleus. Artemis belongs to the metallo-beta-lactamase superfamily and defines a new group, beta-CASP, within this family. beta-CASP proteins are beta-lactamases acting on nucleic acids. While RS-SCID patients harbor Artemis loss-of-function mutations, we identified four patients with a combined immunodeficiency characterized by a low but detectable number of both B and T lymphocytes caused by hypomorphic mutations in the Artemis gene. Two of these patients developed aggressive B cell lymphomas, a condition that suggests Artemis may be considered a "caretaker" factor, similarly to the other V(D)J recombination/DNA repair actors.

DNA Nucleotidyltransferases↗

Golgin tethers define subpopulations of COPI vesicles.

Coiled-coil proteins of the golgin family have been implicated in intra-Golgi transport through tethering coat protein complex I (COPI) vesicles. The p115-golgin tether is the best studied, and here we characterize the golgin-84-CASP tether. The vesicles bound by this tether were strikingly different from those bound by the p115-golgin tether in that they lacked members of the p24 family of putative cargo receptors and contained enzymes instead of anterograde cargo. Microinjected golgin-84 or CASP also inhibited Golgi-enzyme transport to the endoplasmic reticulum, further implicating this tether in retrograde transport. These and other golgins may modulate the flow patterns within the Golgi stack.

Animals↗

Antifungal susceptibility of Candida biofilms: unique efficacy of amphotericin B lipid formulations and echinocandins.

Biofilms, likely the predominant mode of device-related microbial infection, exhibit resistance to antimicrobial agents. Evidence suggests that Candida biofilms have dramatically reduced susceptibility to antifungal drugs. We examined antifungal susceptibilities of Candida albicans and Candida parapsilosis biofilms grown on a bioprosthetic model. In addition to conventional agents, we determined if new antifungal agents (triazoles, amphotericin B lipid formulations, and echinocandins) have activities against Candida biofilms. We also explored effects of preincubation of C. albicans cells with subinhibitory concentrations (sub-MICs) of drugs to see if they could modify subsequent biofilm formation. Finally, we used confocal scanning laser microscopy (CSLM) to image planktonic- and biofilm-exposed blastospores to examine drug effects on cell structure. Candida biofilms were formed on silicone elastomer and quantified by tetrazolium and dry weight (DW) assays. Susceptibility testing of fluconazole, nystatin, chlorhexidine, terbenafine, amphotericin B (AMB), and the triazoles voriconazole (VRC) and ravuconazole revealed resistance in all Candida isolates examined when grown as biofilms, compared to planktonic forms. In contrast, lipid formulations of AMB (liposomal AMB and AMB lipid complex [ABLC]) and echinocandins (caspofungin [Casp] and micafungin) showed activity against Candida biofilms. Preincubation of C. albicans cells with sub-MIC levels of antifungals decreased the ability of cells to subsequently form biofilm (measured by DW; P < 0.0005). CSLM analysis of planktonic and biofilm-associated blastospores showed treatment with VRC, Casp, and ABLC resulted in morphological alterations, which differed with each agent. In conclusion, our data show that Candida biofilms show unique susceptibilities to echinocandins and AMB lipid formulations.

Amphotericin B↗

Quality of life at older ages: evidence from the English longitudinal study of aging (wave 1).

OBJECTIVES: To investigate whether longstanding illnesses, social context, and current socioeconomic circumstances predict quality of life. DESIGN: Secondary analysis of wave 1 of the English longitudinal study of aging. Missing data were imputed and multiple regression analyses conducted. SETTING: England, 2002 PARTICIPANTS: Nationally representative sample of non-institutionalised adults living in England (n = 11 234, 54.5% women, age 65.1 (SD 10.2) years). MAIN OUTCOME MEASURE: Quality of life as measured by CASP-19, a 19 item Likert scaled index. RESULTS: The quality of life was reduced by depression (beta -0.265), poor perceived financial situation (beta -0.157), limitations in mobility (beta -0.124), difficulties with everyday activities (beta -0.112), and limiting longstanding illness (beta -0.112). The quality of life was improved by trusting relationships with family (beta 0.105) and friends (beta 0.078), frequent contacts with friends (beta 0.059), living in good neighbourhoods (beta 0.103), and having two cars (beta 0.066). The regression models explained 48% variation in CASP-19 scores. There were slight differences between age groups and between men and women. CONCLUSIONS: Efforts to improve quality of life in early old age need to address financial hardships, functionally limiting disease, lack of at least one trusting relationship, and inability to move out of a disfavoured neighbourhood. There is the potential for improved quality of life in early old age (the third age) if these factors are controlled.

Aged↗

Overexpression of caspase-3s splice variant in locally advanced breast carcinoma is associated with poor response to neoadjuvant chemotherapy.

PURPOSE: CASP-3 gene gives rise, by alternative splicing to a caspase-3s variant, to the antagonist apoptotic property of caspase-3. Deregulation of splicing in tumor cells favoring the expression of antiapoptotic variants has been reported to contribute to both tumorigenesis and chemoresistance. Thus, we investigated the role of caspase-3 and its splice variant in breast cancer cells. EXPERIMENTAL DESIGN: Breast tumor cell lines deficient (MCF-7) and proficient (HBL100) for CASP-3 gene were transfected with each transcript and were characterized for their apoptotic response to cyclophosphamide. Expression of the two transcripts were measured by reverse transcription-PCR in 130 breast carcinomas, including 90 locally advanced tumors treated with neoadjuvant chemotherapy containing cyclophosphamide, epirubicine, and 5-fluorouracil. RESULTS: Overexpression of caspase-3s variant in caspase-3-transfected cell lines significantly inhibits apoptosis induced by cyclophosphamide (P < 0.0001 for both cell lines). In breast tissues, only caspase-3 levels were higher in carcinomas than in corresponding adjacent normal tissues (P = 0.0396). Locally advanced carcinomas with high levels of caspase-3 (P < 0.0001) and weak levels of caspase-3s (P = 0.0248) were more sensitive to treatment. Therefore, increase in caspase-3s/caspase3 ratio expression was significantly associated with chemoresistance (P = 0.01). Logistic univariate and multivariate analyses realized according to pathologic response confirm that increased caspase-3s expression was indicative of chemoresistance (P = 0.012 and P = 0.026, respectively). CONCLUSIONS: The results agree with an antagonist function between the two transcripts of caspase-3 and show that their ratio of expression levels may define a subset of locally advanced breast cancer patients who are more likely to benefit from neoadjuvant cyclophosphamide-containing chemotherapy.

Alternative Splicing↗

Midline cerebral malformations and schizophrenia.

To investigate a possible association of midline cerebral malformations with psychotic disorders, MRI and CT scans were blindly evaluated for 52 patients with schizophrenia, 9 with schizoaffective disease, and 79 consecutive nonpsychotic control subjects. Midline abnormalities were present in 10 of 61 patients (16.4%) versus 4 of 79 control subjects (5.1%; P < 0.05, chi-square). Of 52 schizophrenic patients, 8 had abnormalities of the septum pellucidum (SP): 5 had cavum vergae (CaV), 2 had cavum septum pellucidum (CaSP), and 1 had agenesis of the corpus callosum and SP. Of 9 schizoaffective patients, 2 had SP abnormalities: 1 CaV and 1 CaSP. Abnormalities of the SP, especially CaV, were significantly more frequent in women than in men (P < 0.02, chi-square).

Adult↗

Social and language skills in adolescent boys with Asperger syndrome.

Twenty-one adolescent boys with Asperger syndrome and 21 boys matched on age and an estimate of IQ were assessed using standardized measures of social perception (Child and Adolescent Social Perception Measure, CASP), social skills (parent, teacher, and student forms of the Social Skills Rating System, SSRS), number of close friends and frequency of contact (Child Behavior Checklist) and expressive and receptive language (Clinical Evaluation of Language Fundamentals-Revised). There were significant differences between groups on CASP scores, SSRS scores, number of friends, frequency of contact and social competence. There was also a significant difference on receptive language. The clinically and statistically significant differences between the groups on the measures of social skills help us understand the nature of the social deficits in Asperger syndrome and suggest the need to focus on specific deficits. These findings are discussed in relation to diagnostic criteria and intervention.

Adolescent↗

Citrus Reticulata blanco induces apoptosis in human gastric cancer cells SNU-668.

Citrus fruits have been known to reduce the proliferation of many cancer cells. The antiproliferative effects of Citrus reticulata Blanco (CR) extract, the immature tangerine peel, on human gastric cancer cell line SNU-668 were evaluated using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, 4,6-diamidineo-2-phenylindole staining, terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling assay, reverse transcription-polymerase chain reaction expressions of BCL-2, BAX and CASP-3 genes, caspase-3 activity, and immunocytochemistry of caspase-3. From the results of the morphological and biochemical assays, CR (50 microg/ml) increased the apoptosis of human gastric cancer cells with typical apoptotic characteristics, including morphological changes of chromatin condensation and apoptotic body formation. CR (50 microg/ml) reduced the expression of BCL-2, whereas the expression of BAX and CASP-3 was increased compared with the control group. Furthermore, caspase-3 activity and caspase-3 protein expression in the CR-treated group was significantly increased compared with that in control group. These results suggest that CR may induce the apoptosis through the caspase-3 pathway in human gastric cancer cells.

Antineoplastic Agents↗

Pathogenesis of six pigeon-origin isolates of Newcastle disease virus for domestic chickens.

The pathogenesis of six pigeon-origin isolates of Newcastle disease virus (NDV) was investigated in chickens. Four isolates were previously defined as the variant pigeon paramyxovirus 1 (PPMV-1), and two isolates were classified as avian paramyxovirus 1 (APMV-1). Birds inoculated with PPMV-1 isolates were euthanatized, and tissue samples were collected at 2, 5, and 10 days postinoculation (DPI). Birds inoculated with APMV-1 isolates died or were euthanatized, and tissue samples were collected at 2, 4, and 5 DPI. Tissues were examined by histopathology, immunohistochemistry (IHC) for the presence of NDV nucleoprotein, and in situ hybridization (ISH) for the presence of viral mRNA for the matrix gene. Spleen sections were stained by the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) assay and by IHC using an anti-active caspase-3 antibody (IHC-Casp) to detect apoptotic cells. Brain sections of PPMV-1-infected birds were examined by IHC to detect T and B lymphocytes and glial fibrillary acidic protein (GFAP). Histologically, birds inoculated with PPMV-1 isolates had marked lesions in the heart and brain. Presence of viral nucleoprotein and viral mRNA in the affected tissues was confirmed by IHC and ISH, respectively. Numerous reactive astrocytes were observed in brain sections stained for GFAP Among all the isolates, the IHC-Casp demonstrated that apoptosis was very prominent in the ellipsoid-associated cells of the spleen at 2 DPI. Results of the TUNEL assay indicated that apoptotic cells were prominent at 5 DPI and were more randomly distributed. The clinical signs and gross and histopathologic changes observed in the APMV-1-infected birds were characteristic of an extensive infection with highly virulent NDV evident by IHC.

Animals↗