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Biomedical subjects

A Valencia

Publications and source records attributed to A Valencia.

At least 19 recordsLinked to original sources
PubMed2000

Practical limits of function prediction.

The widening gap between known protein sequences and their functions has led to the practice of assigning a potential function to a protein on the basis of sequence similarity to proteins whose function has been experimentally investigated. We present here a critical view of the theoretical and practical bases for this approach. The results obtained by analyzing a significant number of true sequence similarities, derived directly from structural alignments, point to the complexity of function prediction. Different aspects of protein function, including (i) enzymatic function classification, (ii) functional annotations in the form of key words, (iii) classes of cellular function, and (iv) conservation of binding sites can only be reliably transferred between similar sequences to a modest degree. The reason for this difficulty is a combination of the unavoidable database inaccuracies and the plasticity of protein function. In addition, analysis of the relationship between sequence and functional descriptions defines an empirical limit for pairwise-based functional annotations, namely, the three first digits of the six numbers used as descriptors of protein folds in the FSSP database can be predicted at an average level as low as 7.5% sequence identity, two of the four EC digits at 15% identity, half of the SWISS-PROT key words related to protein function would require 20% identity, and the prediction of half of the residues in the binding site can be made at the 30% sequence identity level.

Amino Acid Sequence↗
PubMed2000

[Compliance with inhalation treatment of patients with chronic obstructive pulmonary disease].

OBJECTIVES: To evaluate patient compliance with inhaled medication therapy in chronic obstructive pulmonary disease (COPD), to identify determining factors and to propose corrective measures to improve compliance. METHODS: This was an open, observational, cross-sectional, non-comparative, single-measurement, non-random study. The inhalers were the Serevent Accuhaler, the Serevent Inhalador and the Flixotide Inhaler. Compliance was measured in four ways: a) difference in weight at the beginning and end of the study for all devices; b) dose counter reading for the Accuhaler; c) information from patient diaries (by days and by applications); and d) information from patient interviews using the Morinsky-Green Test. Compliance was rated as follows: poor: < 50%, fair 51%-79%, good 80%-119%, or "hypercompliant" > 120%. RESULTS: Seventy-two patients (mean age 65 years) were enrolled. Compliance measured by weight was good in 77.1%, fair in 11.5%, poor in 1.4% and hypercompliant in 10%. Compliance was good for the Accuhaler according to both weight (75%) and counted doses (83.3%). According to patient diaries, compliance was good when assessed by applications (98.8%) and by days (98.3%). According to the Morinksky-Green test, compliance was good for 87.9%. CONCLUSIONS: Compliance was good as assessed by the methods used in this study. Patients who live in families, who enjoy a high socioeconomic level, have simple therapeutic regimens and have a good understanding of their disease and inhaler tend to have good compliance. Careful patient follow-up and good patient-physician communication has improved compliance. However, follow-up studies are needed to check these results.

Administration, Inhalation↗
PubMed2000

[The internal consistency and content validity of the Spanish version of the Asthma Autonomy Questionnaire].

The Asthma Autonomy Questionnaire (AAQ) was designed to evaluate asthmatics' desire to learn about their disease and to make decisions. The AAQ consists of 26 items distributed in two scales: Preferences in the Search for Information (PSI, 8 items) and Preferences in Decision Making (PDM, 6 general items and 12 related to 3 scenarios depicting asthma in stable phase, during mild exacerbation and during severe exacerbation). The aim of this study was to analyze the internal consistency (Cronbach's-coefficient) and content validity (factorial analysis of principal components) of the AAQ. After translation and back translation, the Spanish version of the AAQ was administered to 115 adult asthmatics of both sexes and differing levels of severity. The alpha coefficients for the two scales and 3 scenarios ranged from 0.42 (PSI) to 0.73 (stable phase scenario); only for the stable-phase scenario were values high or statistically acceptable. Factorial analysis reproduced the content of the scales only approximately, with some items proving to relate to factors that were different from the scale they originally belonged to. These results indicate that, in its current formulation, the AAQ presents important measurement problems and revision is advisable.

Adult↗
PubMed2000

Alpha-amylases of the coffee berry borer (Hypothenemus hampei) and their inhibition by two plant amylase inhibitors.

The adult coffee berry borer (Hypothenemus hampei Ferrari [Coleoptera: Scolytidae]), a major insect pest of coffee, has two major digestive alpha-amylases that can be separated by isoelectric focusing. The alpha-amylase activity has a broad pH optimum between 4.0 and 7.0. Using pH indicators, the pH of the midgut was determined to be between 4.5 and 5.2. At pH 5.0, the coffee berry borer alpha-amylase activity is inhibited substantially (80%) by relatively low levels of the amylase inhibitor (alphaAI-1) from the common bean, Phaseolus vulgaris L., and much less so by the amylase inhibitor from Amaranthus. We used an in-gel zymogram assay to demonstrate that seed extracts can be screened to find suitable inhibitors of amylases. The prospect of using the genes that encode these inhibitors to make coffee resistant to the coffee berry borer via genetic engineering is discussed.

Animals↗
PubMed1999

Effective use of sequence correlation and conservation in fold recognition.

Protein families are a rich source of information; sequence conservation and sequence correlation are two of the main properties that can be derived from the analysis of multiple sequence alignments. Sequence conservation is related to the direct evolutionary pressure to retain the chemical characteristics of some positions in order to maintain a given function. Sequence correlation is attributed to the small sequence adjustments needed to maintain protein stability against constant mutational drift. Here, we showed that sequence conservation and correlation were each frequently informative enough to detect incorrectly folded proteins. Furthermore, combining conservation, correlation, and polarity, we achieved an almost perfect discrimination between native and incorrectly folded proteins. Thus, we made use of this information for threading by evaluating the models suggested by a threading method according to the degree of proximity of the corresponding correlated, conserved, and apolar residues. The results showed that the fold recognition capacity of a given threading approach could be improved almost fourfold by selecting the alignments that score best under the three different sequence-based approaches.

Amino Acid Sequence↗
PubMed1999

Model of the ran-RCC1 interaction using biochemical and docking experiments.

RCC1, the regulator of chromosome condensation, is the guanine nucleotide exchange factor (GEF) for the nuclear Ras-like GTP-binding protein Ran. Its structure was solved by X-ray crystallography and revealed a seven-bladed beta-propeller, one side of which was proposed to be the interaction site with Ran. To gain more insight into this interaction, alanine mutagenesis studies were performed on conserved residues on the surface of the structure. Purified mutant proteins were analysed by steady-state kinetic analysis of their GEF activities towards Ran. A number of residues were identified whose mutation affected either the KMor kcatof the overall reaction, or had no effect. Mutants were further analysed by plasmon surface resonance in order to get more information on individual steps of the complex reaction pathway. Ran-GDP was coupled to the sensor chip and reacted with RCC1 mutants to categorise them into different groups, demonstrating the usefulness of plasmon surface resonance in the study of complex multi-step kinetic processes. A docking solution of Ran-RCC1 structures in combination with sequence analysis allows prediction of the site of interaction between RCC1 and Ran and proposes a model for the Ran-RCC1 structure which corresponds to and extends the biochemical data. Three invariant residues which most severely affect the kcatof the reaction, D128, D182 and H304, are located in the centre of the Ran-RCC1 interface and interfere with switch II and the phosphate binding area. The structural model suggests that different guanine nucleotide exchange factors use a similar interaction site on their respective GTP-binding proteins, but that the molecular mechanisms for the release of nucleotides are likely to be different.

Alanine↗
PubMed1999

Effector recognition by the small GTP-binding proteins Ras and Ral.

The Ral effector protein RLIP76 (also called RIP/RalBP1) binds to Ral.GTP via a region that shares no sequence homology with the Ras-binding domains of the Ser/Thr kinase c-Raf-1 and the Ral-specific guanine nucleotide exchange factors. Whereas the Ras-binding domains have a similar ubiquitin-like structure, the Ral-binding domain of RLIP was predicted to comprise a coiled-coil region. In order to obtain more information about the specificity and the structural mode of the interaction between Ral and RLIP, we have performed a sequence space and a mutational analysis. The sequence space analysis of a comprehensive nonredundant assembly of Ras-like proteins strongly indicated that positions 36 and 37 in the core of the effector region are tree-determinant positions for all subfamilies of Ras-like proteins and dictate the specificity of the interaction of these GTPases with their effector proteins. Indeed, we could convert the specific interaction with Ras effectors and RLIP by mutating these residues in Ras and Ral. We therefore conclude that positions 36 and 37 are critical for the discrimination between Ras and Ral effectors and that, despite the absence of sequence homology between the Ral-binding and the Ras-binding domains, their mode of interaction is most probably similar.

ATP-Binding Cassette Transporters↗
PubMed1999

Molecular analysis of HIV-1 gp120 antibody response using isotype IgM and IgG phage display libraries from a long-term non-progressor HIV-1-infected individual.

To characterize the variable heavy chain (VH)3 antibody response to HIV-1 gp120, we analyzed a panel of IgM and IgG1 Fab fragments from phage display isotype libraries from a long-term, non-progressor HIV-1-infected individual. The IgM Fab antibodies isolated had low affinity for gp120, were not restricted to a particular VH3 germ-line gene, and consisted mainly of unmutated VH genes. In contrast, IgG Fab fragments were gp120 specific, with high affinity and extensive somatic mutation; all were clonally related and were derived from a single VH3 germ-line gene (DP50). One IgG Fab (S8) has DP50 VH region nucleotide substitutions identical to those of IgM Fab M025 and uses similar DH and JH segments, suggesting that S8 arose from M025 by isotype switching. In addition, somatic mutation in the IgG heavy chain third complementarity-determining region results in a 100-fold affinity increase for gp120, which correlates with a similar increase in neutralization capacity. These results imply that in vivo IgM to IgG isotype switch and affinity maturation may be important for protection and long-term survival in certain HIV-1-infected individuals.

Amino Acid Sequence↗
PubMed1999

Functional classes in the three domains of life.

The evolutionary divergence among the three major domains of life can now be addressed through the first set of complete genomes from representative species. These model species from the three domains of life, Haemophilus influenzae for Bacteria, Saccharomyces cerevisiae for Eukarya, and Methanococcus jannaschii for Archaea, provide the basis for a universal functional classification and analysis. We have chosen 13 functional classes and three superclasses (ENERGY, COMMUNICATION and INFORMATION) as global descriptors of protein function. Compositional comparison of the three complete genomes reveals that functional classes are ubiquitous yet diverse in the three domains of life. Proteins related with ENERGY processes are generally represented in all three domains, while those related with COMMUNICATION represent the most distinctive functional feature of each single domain. Finally, functions related with INFORMATION processing (translation, transcription, and replication) show a complex behaviour. In Archaea, proteins in this superclass are related with proteins in either Eukarya or Bacteria, as recognized previously. The distribution of functional classes in the three domains accurately reflects the principal characteristics of cellular life forms.

Archaeal Proteins↗
PubMed1999

[Information seeking and decision making in asthmatic patients].

Patient cooperation in controlling asthma is a key element for achieving the most efficient therapy possible according to current guidelines. Cooperation requires that the patient be adequately informed about his disease and able to make certain decisions. The aim of this study was to analyze whether patients really desire information about asthma and to what point they are disposed to cooperate actively in managing their disease. Ninety-five adult asthmatics with different levels of severity of disease were studied in stable condition. All responded to the Spanish version of the questionnaire on autonomy in asthma, an instrument with a scoring range of 0 to 100 and 26 items grouped in two subscales: preferences in the search for information (PSI) and preferences in decision making (PDM). The second subscale was based on three scenarios describing stable asthma, slight exacerbation and severe exacerbation. The results obtained indicate that although patients are greatly interested in receiving information (PSI scores of 86.4 +/- 8.7) they express substantially less desire to make decisions (PDM 45 +/- 10.2) (p < 0.01). Attitudes did not change in relation to education, number of exacerbations during the last year, duration of disease or severity as assessed by the patient. Only patient age (with older patients scoring higher on PSI) and presence of severe asthma (according to consensus guidelines) increased the desire for information (but not the preference for decision making). These data indicate the need to implement educational programs about asthma, components of which promote effective desire for self-management.

Adult↗
PubMed1999

Effect of NMDA antagonists on the activity of glutaminase and aspartate aminotransferase in the developing rat cerebellum.

Chronic treatment of rats from postnatal day 6 to 25 with drugs that interact with the N-methyl-D-aspartate (NMDA) receptor induced a differential effect on the activity of some enzymes involved in neurotransmitter synthesis. Two of these drugs ((5R,10S)-(+)-5-methyl-10,11 -dihydro-5H-dibenzo(a,d)cyclohepten-5,10-imine hydrogen maleate (MK-801) and 3-(2-carboxypiperazin-4-yl)propyl-1phosphonic acid (CPP)) caused a marked reduction (20-40%) of glutaminase and aspartate aminotransferase activity in the cerebellum. These changes were observed only at a very precise time of development (i.e. 10 to 19 postnatal day). The competitive antagonist, amino phosphonovaleric acid (APV), did not affect any of the enzymes studied at all tested ages. When animals were treated with NMDA only a slight, but significant, increase in the activity of glutaminase was observed at 9-11 postnatal day only. Any of the agonists or antagonists tested significantly affected the activity of lactate dehydrogenase as compared to control animals. Histologic observations of cerebella treated with the indicated drugs showed that only MK-801, and CPP to a lesser extent, induced a small reduction in the width of the internal granule layer. The body weight of animals treated with MK-801 was clearly reduced, but only in more mature rats (> 16 postnatal day), when animals did not show any alteration in the enzymes tested. These results support the suggestion that presynaptic influences, particularly from glutamatergic neurons, are critical to promote cerebellar granule neurons differentiation during critical periods of the cerebellar development.

2-Amino-5-phosphonovalerate↗
PubMed1999

Identification of a mammalian homologue of the fungal Tom70 mitochondrial precursor protein import receptor as a thyroid hormone-regulated gene in specific brain regions.

Thyroid hormone is an important regulator of mammalian brain maturation. By differential display PCR, we isolated a cDNA clone (S2) that is specifically up-regulated in the striatum of neonatal hypothyroid rats. S2 was identified as KIAA0719, the first human gene distantly homologous to the fungal Tom70, which encodes a member of the translocase mitochondrial outer membrane complex involved in the import of preproteins into the mitochondria. By northern and in situ hybridization studies, KIAA0719 was found to be up-regulated in the striatum, nucleus accumbens, and discrete cortical layers of 15-day-old hypothyroid rats. In contrast, lower expression was found in the olfactory tubercle, whereas no differences were detected in other brain regions. Significantly, treatment of hypothyroid animals with single injections of thyroxine restored the normal levels of KIAA0719 expression. Moreover, treatment of control animals with thyroxine led to a reduced expression, demonstrating a negative hormonal regulation in vivo. Thus, KIAA0719 gene expression is regulated by thyroid hormone in the neonatal rat brain in a region-specific fashion. Given the role of the homologous Tom70 gene, the alteration of KIAA0719 expression may contribute to the changes in mitochondrial morphology and physiology caused by hypothyroidism in the developing rat brain.

Amino Acid Sequence↗
PubMed1999

Automated genome sequence analysis and annotation.

MOTIVATION: Large-scale genome projects generate a rapidly increasing number of sequences, most of them biochemically uncharacterized. Research in bioinformatics contributes to the development of methods for the computational characterization of these sequences. However, the installation and application of these methods require experience and are time consuming. RESULTS: We present here an automatic system for preliminary functional annotation of protein sequences that has been applied to the analysis of sets of sequences from complete genomes, both to refine overall performance and to make new discoveries comparable to those made by human experts. The GeneQuiz system includes a Web-based browser that allows examination of the evidence leading to an automatic annotation and offers additional information, views of the results, and links to biological databases that complement the automatic analysis. System structure and operating principles concerning the use of multiple sequence databases, underlying sequence analysis tools, lexical analyses of database annotations and decision criteria for functional assignments are detailed. The system makes automatic quality assessments of results based on prior experience with the underlying sequence analysis tools; overall error rates in functional assignment are estimated at 2.5-5% for cases annotated with highest reliability ('clear' cases). Sources of over-interpretation of results are discussed with proposals for improvement. A conservative definition for reporting 'new findings' that takes account of database maturity is presented along with examples of possible kinds of discoveries (new function, family and superfamily) made by the system. System performance in relation to sequence database coverage, database dynamics and database search methods is analysed, demonstrating the inherent advantages of an integrated automatic approach using multiple databases and search methods applied in an objective and repeatable manner. AVAILABILITY: The GeneQuiz system is publicly available for analysis of protein sequences through a Web server at http://www.sander.ebi.ac. uk/gqsrv/submit

Amino Acid Sequence↗
PubMed1999

Automatic extraction of biological information from scientific text: protein-protein interactions.

We describe the basic design of a system for automatic detection of protein-protein interactions extracted from scientific abstracts. By restricting the problem domain and imposing a number of strong assumptions which include pre-specified protein names and a limited set of verbs that represent actions, we show that it is possible to perform accurate information extraction. The performance of the system is evaluated with different cases of real-world interaction networks, including the Drosophila cell cycle control. The results obtained computationally are in good agreement with current biological knowledge and demonstrate the feasibility of developing a fully automated system able to describe networks of protein interactions with sufficient accuracy.

Algorithms↗
PubMed1998

Mutations in the DnaK chaperone affecting interaction with the DnaJ cochaperone.

Hsp70 chaperones assist protein folding by ATP-controlled cycles of substrate binding and release. ATP hydrolysis is the rate-limiting step of the ATPase cycle that causes locking in of substrates into the substrate-binding cavity of Hsp70. This key step is strongly stimulated by DnaJ cochaperones. We show for the Escherichia coli Hsp70 homolog, DnaK, that stimulation by DnaJ requires the linked ATPase and substrate-binding domains of DnaK. Functional interaction with DnaJ is affected by mutations in an exposed channel located in the ATPase domain of DnaK. It is proposed that binding to this channel, possibly involving the J-domain, allows DnaJ to couple substrate binding with ATP hydrolysis by DnaK. Evolutionary conservation of the channel and the J-domain suggests conservation of the mechanism of action of DnaJ proteins.

Adenosine Triphosphatases↗
PubMed1998

Structural model for family 32 of glycosyl-hydrolase enzymes.

A structural model is presented for family 32 of the glycosyl-hydrolase enzymes based on the beta-propeller fold. The model is derived from the common prediction of two different threading methods, TOPITS and THREADER. In addition, we used a correlated mutation analysis and prediction of active-site residues to corroborate the proposed model. Physical techniques (circular dichroism and differential scanning calorimetry) confirmed two aspects of the prediction, the proposed all-beta fold and the multi-domain structure. The most reliable three-dimensional model was obtained using the structure of neuraminidase (1nscA) as template. The analysis of the position of the active site residues in this model is compatible with the catalytic mechanism proposed by Reddy and Maley (J. Biol. Chem. 271:13953-13958, 1996), which includes three conserved residues, Asp, Glu, and Cys. Based on this analysis, we propose the participation of one more conserved residue (Asp 162) in the catalytic mechanism. The model will facilitate further studies of the physical and biochemical characteristics of family 32 of the glycosyl-hydrolases.

Amino Acid Sequence↗
PubMed1998

Distribution and functional diversification of the ras superfamily in Saccharomyces cerevisiae.

The recent availability of the full Saccharomyces cerevisiae genome sequence offers a first opportunity to analyze the composition, function and evolution of GTPases in the ras-p21 superfamily. This superfamily in yeast is composed of 29 proteins divided into five families: ras with four sequences implicated in cell signalling; rho, six genes related to the cell shape machinery; ypt-rab, ten proteins with different roles in intracellular trafficking; arf-sar, seven proteins related to vesicular trafficking in secretory pathways; and ran, two proteins acting as components of the nuclear transport system. The superfamily covers a wide range of cellular functions from signalling to intracellular trafficking, while conserving the structural framework and a common mechanism of GTP hydrolysis.

Evolution, Molecular↗