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Alfonso Valencia

Publications and source records attributed to Alfonso Valencia.

79 records · Page 5Linked to original sources
PubMed2002

Clustering of proximal sequence space for the identification of protein families.

MOTIVATION: The study of sequence space, and the deciphering of the structure of protein families and subfamilies, has up to now been required for work in comparative genomics and for the prediction of protein function. With the emergence of structural proteomics projects, it is becoming increasingly important to be able to select protein targets for structural studies that will appropriately cover the space of protein sequences, functions and genomic distribution. These problems are the motivation for the development of methods for clustering protein sequences and building families of potentially orthologous sequences, such as those proposed here. RESULTS: First we developed a clustering strategy (Ncut algorithm) capable of forming groups of related sequences by assessing their pairwise relationships. The results presented for the ras super-family of proteins are similar to those produced by other clustering methods, but without the need for clustering the full sequence space. The Ncut clusters are then used as the input to a process of reconstruction of groups with equilibrated genomic composition formed by closely-related sequences. The results of applying this technique to the data set used in the construction of the COG database are very similar to those derived by the human experts responsible for this database. AVAILABILITY: The analysis of different systems, including the COG equivalent 21 genomes are available at http://www.pdg.cnb.uam.es/GenoClustering.html.

Algorithms↗
PubMed2002

Molecular and structural analysis of the panallergen profilin B cell epitopes defined by monoclonal antibodies.

Interactions of five mouse mAb (10A4, 5F2, 9A7, 9G4 and 3H8) and sunflower profilin were characterized using synthetic overlapping peptides. All the continuous B cell epitopes analyzed in this work were 6-10 amino acids in length, and clustered at the N- and C-terminal alpha-helices and a two-stranded segment composed of residues 40-50. Mutational analysis of the epitopes revealed that single amino acid changes within these peptides had dramatic effects on IgG-binding characteristics. A three-dimensional molecular model of sunflower profilin was generated by homology modeling based on the crystal structure of Arabidopsis thaliana profilin. All but one of the murine B cell epitopes defined in this work were located on the surface of the profilin molecule in the alpha-helices (10A4 and 3H8) or in the turns (5F2 and 9G4). In contrast, 9A7 epitope was located in the profilin core and partially buried by the C-terminal. Two mAb (5F2 and 10A4) inhibited the binding of anti-profilin human IgE up to 52%. In contrast, mAb 3H8 seemed to enhance the binding of anti-profilin IgE of sera from allergic patients.

Allergens↗
PubMed2002

Automatic ontology construction from the literature.

Detailed classifications, controlled vocabularies and organised terminology are widely used in different areas of science and technology. Their relatively recent introduction in molecular biology has been crucial for progress in the analysis of genonics and massive proteomics experiments. Unfortunately the construction of the ontologies, including terminology, classification and entity relations requires considerable effort, including the analysis of massive amounts of literature. We propose here a method that automatically generates classifications of gene-product functions using bibliographic information. The corresponding classification structures mirror the ones constructed by human experts. The analysis of a large structure built for yeast gene-products, and the detailed inspection of various examples, show encouraging properties. In particular, the comparison with the well accepted GO ontology points to different situations in which the automatically derived classification can be useful for assisting human experts in the annotation of ontologies.

Computational Biology↗
PubMed2001

Functional interaction between the Ser/Thr kinase PKL12 and N-acetylglucosamine kinase, a prominent enzyme implicated in the salvage pathway for GlcNAc recycling.

PKL12 (STK16) is a ubiquitously expressed Ser/Thr kinase, not structurally related to the well known subfamilies, with a putative role in cell adhesion control. Yeast two-hybrid protein interaction screening was used to search for proteins that associate with PKL12 and to delineate signaling pathways and/or regulatory circuits in which this kinase participates. One positive clone contained an open reading frame highly similar to N-acetylglucosamine kinase (GlcNAcK) of several species. The PKL12/GlcNAcK interaction was further confirmed both in vitro and in vivo. Protein expression analysis of GlcNAcK using a specific rabbit antiserum displayed a ubiquitous pattern in cell lines and animal tissues. Subcellular localization studies showed that GlcNAcK is a cytoplasmic protein with a dual subcellular localization, distributed between the perinuclear and peripheral cell reservoirs. After overexpression, GlcNAcK localizes in vesicular structures associated mainly with the cell membrane and colocalizes with the PKL12 protein. GlcNAcK is not otherwise a substrate for PKL12 activity and PKL12 does not appear to influence GlcNAcK activity either in vitro or in vivo. In vitro kinase assays have nonetheless revealed that functional GlcNAcK, although not able to modulate autophosphorylation of PKL12, greatly influences PKL12 kinase activity on a defined substrate protein. These results are interpreted to indicate a potential in vivo role for GlcNAcK in PKL12 translocation and a tentative regulatory role for PKL12-mediated phosphorylation on substrate proteins.

3T3 Cells↗