Search results for "PROTEIN INTERACTION"

PINCoC: a Co-Clustering based Method to Analyze Protein-Protein Interaction Networks

2007

Anovel technique to search for functionalmodules in a protein-protein interaction network is presented. The network is represented by the adjacency matrix associated with the undirected graph modelling it. The algorithm introduces the concept of quality of a sub-matrix of the adjacency matrix, and applies a greedy search technique for finding local optimal solutions made of dense submatrices containing the maximum number of ones. An initial random solution, constituted by a single protein, is evolved to search for a locally optimal solution by adding/removing connected proteins that best contribute to improve the quality function. Experimental evaluations carried out on Saccaromyces Cerevis…

Protein interactions with ordered lipid films: Specific and unspecific binding

1991

Data Sources and Models

2017

Biological networks rely on the storage and retrieval of data associated to the physical interactions and/or functional relationships among different actors. In particular, the attention may be on the interactions among cellular components, such as proteins, genes, RNA, or for example on phenotype–genotype associations. Data from which biological networks are built are usually stored in public databases, and we provide here a brief summary of the main types of both data and associations, publicly available. Moreover, we also explain how it is possible to construct suitable network models from these associations, focusing on protein–protein interaction networks, gene–disease networks and net…

Protein Interaction Networks and Disease: Highlights of the 3rd Challenges in Computational Biology Meeting

2017

Cellular functions are managed by a complex network of protein interactions, the malfunction of which may derive in disease phenotypes. In spite of the incompleteness and noise present in our current protein interaction maps, computational biologists are making strenuous efforts to extract knowledge from these intricate networks and, through their integration with other types of biological data, expedite the development of novel and more effective treatments against human disorders. The 3rd Challenges in Computational Biology meeting revolved around the Protein Interaction Networks and Disease subject, bringing expert network biologists to the city of Mainz, Germany to debate the current st…

A Coclustering Approach for Mining Large Protein-Protein Interaction Networks

2012

Several approaches have been presented in the literature to cluster Protein-Protein Interaction (PPI) networks. They can be grouped in two main categories: those allowing a protein to participate in different clusters and those generating only nonoverlapping clusters. In both cases, a challenging task is to find a suitable compromise between the biological relevance of the results and a comprehensive coverage of the analyzed networks. Indeed, methods returning high accurate results are often able to cover only small parts of the input PPI network, especially when low-characterized networks are considered. We present a coclustering-based technique able to generate both overlapping and nonove…

Production and characterisation of recombinant forms of human pulmonary surfactant protein C (SP-C):Structure and surface activity

2006

  Udgivelsesdato: 2006-Apr Surfactant protein C (SP-C) is an essential component for the surface tension-lowering activity of the pulmonary surfactant system. It contains a valine-rich alpha helix that spans the lipid bilayer, and is one of the most hydrophobic proteins known so far. SP-C is also an essential component of various surfactant preparations of animal origin currently used to treat neonatal respiratory distress syndrome (NRDS) in preterm infants. The limited supply of this material and the risk of transmission of infectious agents and immunological reactions have prompted the development of synthetic SP-C-derived peptides or recombinant humanized SP-C for inclusion in new prepar…

Interaction of Bacillus thuringiensis Cry1 and Vip3A Proteins with Spodoptera frugiperda Midgut Binding Sites

2009

ABSTRACT Vip3Aa, Vip3Af, Cry1Ab, and Cry1Fa were tested for their toxicities and binding interactions. Vip3A proteins were more toxic than Cry1 proteins. Binding assays showed independent specific binding sites for Cry1 and Vip3A proteins. Cry1Ab and Cry1Fa competed for the same binding sites, whereas Vip3Aa competed for those of Vip3Af.

Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling p…

2014

One of the most important physiological platelet inhibitors is endothelium-derived prostacyclin which stimulates the platelet cyclic adenosine monophosphate/protein kinase A (cAMP/PKA)-signaling cascade and inhibits virtually all platelet-activating key mechanisms. Using quantitative mass spectrometry, we analyzed time-resolved phosphorylation patterns in human platelets after treatment with iloprost, a stable prostacyclin analog, for 0, 10, 30, and 60 seconds to characterize key mediators of platelet inhibition and activation in 3 independent biological replicates. We quantified over 2700 different phosphorylated peptides of which 360 were significantly regulated upon stimulation. This com…

Meox2/Tcf15 Heterodimers Program the Heart Capillary Endothelium for Cardiac Fatty Acid Uptake

2015

Background— Microvascular endothelium in different organs is specialized to fulfill the particular needs of parenchymal cells. However, specific information about heart capillary endothelial cells (ECs) is lacking. Methods and Results— Using microarray profiling on freshly isolated ECs from heart, brain, and liver, we revealed a genetic signature for microvascular heart ECs and identified Meox2/Tcf15 heterodimers as novel transcriptional determinants. This signature was largely shared with skeletal muscle and adipose tissue endothelium and was enriched in genes encoding fatty acid (FA) transport–related proteins. Using gain- and loss-of-function approaches, we showed that Meox2/Tcf15 media…

Subcellular localization of bacteriophage PRD1 proteins in Escherichia coli

2014

Bacteria possess an intricate internal organization resembling that of the eukaryotes. The complexity is especially prominent at the bacterial cell poles, which are also known to be the preferable sites for some bacteriophages to infect. Bacteriophage PRD1 is a well-known model serving as an ideal system to study structures and functions of icosahedral internal membrane-containing viruses. Our aim was to analyze the localization and interactions of individual PRD1 proteins in its native host Escherichia coli. This was accomplished by constructing a vector library for production of fluorescent fusion proteins. Analysis of solubility and multimericity of the fusion proteins, as well as their …