RESUMEN
BACKGROUND: Protein-protein interactions (PPIs) are fundamental in many biological processes and understanding these interactions is key for a myriad of applications including drug development, peptide design and identification of drug targets. The biological data deluge demands efficient and scalable methods to characterize and understand protein-protein interfaces. In this paper, we present ppiGReMLIN, a graph based strategy to infer interaction patterns in a set of protein-protein complexes. Our method combines an unsupervised learning strategy with frequent subgraph mining in order to detect conserved structural arrangements (patterns) based on the physicochemical properties of atoms on protein interfaces. To assess the ability of ppiGReMLIN to point out relevant conserved substructures on protein-protein interfaces, we compared our results to experimentally determined patterns that are key for protein-protein interactions in 2 datasets of complexes, Serine-protease and BCL-2. RESULTS: ppiGReMLIN was able to detect, in an automatic fashion, conserved structural arrangements that represent highly conserved interactions at the specificity binding pocket of trypsin and trypsin-like proteins from Serine-protease dataset. Also, for the BCL-2 dataset, our method pointed out conserved arrangements that include critical residue interactions within the conserved motif LXXXXD, pivotal to the binding specificity of BH3 domains of pro-apoptotic BCL-2 proteins towards apoptotic suppressors. Quantitatively, ppiGReMLIN was able to find all of the most relevant residues described in literature for our datasets, showing precision of at least 69% up to 100% and recall of 100%. CONCLUSIONS: ppiGReMLIN was able to find highly conserved structures on the interfaces of protein-protein complexes, with minimum support value of 60%, in datasets of similar proteins. We showed that the patterns automatically detected on protein interfaces by our method are in agreement with interaction patterns described in the literature.
Asunto(s)
Mapeo de Interacción de Proteínas/métodos , Animales , Gráficos por Computador , Minería de Datos , Complejos Multiproteicos/química , Proteínas Proto-Oncogénicas c-bcl-2/química , Proteínas Proto-Oncogénicas c-bcl-2/metabolismo , Tripsina/química , Tripsina/metabolismoRESUMEN
El presente trabajo constituye un artículo de reflexión, en torno a conflictos vecinales presentados a una Oficina Municipal de Relaciones Vecinales y Defensa del Consumidor en Buenos Aires (Argentina). Se intenta reflexionar sobre algunos patrones de interacción vinculados al género, que aparecen en tales situaciones. En el proceso de mediación comunitaria, que es el dispositivo elegido por la Oficina Municipal para abordar estas situaciones, se utilizan diarios de campo y entrevistas domiciliarias. Se analizan dos disputas vecinales entre un hombre y una mujer, en las cuales se ponen de manifiesto posibles expectativas mutuas de comportamiento, relacionadas con una atribución de vulnerabilidad hacia la mujer, así como la consiguiente pérdida de la posición de interlocutora válida al momento del diálogo para abordar el conflicto en el que participan.
This paper focuses on some interaction patterns related to gender in Neighborhood Dispute Cases, submitted to a Local Neighborhood Consumer Protection Office. Community mediation using field research logs and home interviews were the schemes relied on by the Local Office to handle these situations. To deal with the conflict situation, a dispute between a man and a woman is discussed in which mutual behavioral expectations as they related to women vulnerability and consequent loss of the mediating position during the dialogue are analyzed.