Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form in a biologically functional way. Proteinprotein interactions are intrinsic to virtually every cellular process. Interactions between proteins have been studied through a number of high-throughput experiments and have also been predicted through an array of computational me...

The solution structure of the 48 kDa IIAHPr complex of the mannose branch of the E. coli phosphotransferase system (PTS) has been solved by NMR using conjoined rigid body/torsion angle simulated annealing on the basis of intermolecular nuclear Overhauser enhancement data and residual dipolar couplings. IIA is dimeric and has two symmetrically related binding sites per dimer for HPr. A convex su...

The use of process calculi to represent biological systems has led to the design of different calculi such as brane calculi [1] and κ-calculus [3]. Both have proved to be useful to model different types of biological systems. As an attempt to unify the two directions, we introduce the bioκ-calculus, a simple calculus for describing proteins and cells, in which bonds are represented by means of ...

The study of proteomics reached unexpected levels of interest, as a direct consequence of its discovered influence over some complex biological phenomena, such as problematic diseases like cancer. This paper presents the latest authors’ achievements regarding the analysis of the networks of proteins (interactome networks), by computing more efficiently the betweenness centrality measure. The pa...

Members of the Toll-like receptor (TLR) and interleukin-1 receptor (IL-1R) family play important roles in immunity and inflammation. They initiate common intracellular signalling cascades leading to the activation of nuclear factor-?B (NF-?B) and other transcription factors that stimulate the expression of a variety of genes that shape an appropriate immune response. TLR/IL-1R signalling involv...

Community detection plays a key role in such important fields as biology, sociology and computer science. For example, detecting the communities in proteinprotein interactions networks helps in understanding their functionalities. Most existing approaches were devoted to community mining in undirected social networks (either weighted or not). In fact, despite their ubiquity, few proposals were ...

Coordination between sequential steps in synaptic vesicle endocytosis, including clathrin coat formation, fission, and uncoating, appears to involve proteinprotein interactions. Here, we show that compounds that disrupt interactions of the SH3 domain of endophilin with dynamin and synaptojanin impair synaptic vesicle endocytosis in a living synapse. Two distinct endocytic intermediates accumula...

The subject of protein-protein interactions represents a vast ensemble of results from biological, biochemical and biophysical studies carried out to date and cannot be treated in its entirety in any reasonable fashion. The following chapter will focus therefore on particular aspects of protein-protein interactions. It will begin with an overview of some classes of protein-protein interactions ...

interpretation is a theory of abstraction and constructive approximation of the mathematical structures used in the formal description of complex or infinite systems and the inference or verification of their combinatorial or undecidable properties. Developed in the late seventies with Radhia Cousot, it has been since then applied to many aspects of computer science (such as static analysis and...