Related papers: Length, Protein-Protein Interactions, and Complexi…
Proteins participating in a protein-protein interaction network can be grouped into homology classes following their common ancestry. Proteins added to the network correspond to genes added to the classes, so that the dynamics of the two…
Understanding the molecular determinants of specificity in protein-protein interaction is an outstanding challenge of postgenome biology. The availability of large protein databases generated from sequences of hundreds of bacterial genomes…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
The function of proteins arises from cooperative interactions and rearrangements of their amino acids, which exhibit large-scale dynamical modes. Long-range correlations have also been revealed in protein sequences, and this has motivated…
We employed the random graph theory approach to analyze the protein-protein interaction database DIP (Feb. 2004), for seven species (S. cerevisiae, H. pylori, E. coli, C. elegans, H. sapiens, M. musculus and D. melanogaster). Several global…
We investigate a model protein interaction network whose links represent interactions between individual proteins. This network evolves by the functional duplication of proteins, supplemented by random link addition to account for…
Biological systems have evolved to amazingly complex states, yet we do not understand in general how evolution operates to generate increasing genetic and functional complexity. Molecular recognition sites are short genome segments or…
Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…
Protein-DNA interactions are critical for the successful functioning of all natural systems. The key role in these interactions is played by processes of protein search for specific sites on DNA. Although it has been studied for many years,…
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that…
Motivation: With the aim to amplify and make sense of interactions of virus-human proteins in the case of SARS-CoV-2, we performed a structural analysis of the network of protein interactions obtained from the integration of three sources:…
Mutations in proteins can have deleterious effects on a protein's stability and function, which ultimately causes particular diseases. Genetically inherited muscular dystrophies (MDs) include several genetic diseases, which cause increasing…
Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these…
Many fundamental biological processes are regulated by protein-DNA complexes called {\it synaptosomes}, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation remain not…
Understanding why some cellular components are conserved across species, while others evolve rapidly is a key question of modern biology. Here we demonstrate that in S. cerevisiae proteins organized in cohesive patterns of interactions are…
A fundamental question for evolutionary biology is why rates of evolution vary dramatically between proteins. Perhaps surprisingly, it is controversial how much a protein's functional importance affects its rate of evolution. In most…
Topological analysis of large scale protein-protein interaction networks (PINs) is important for understanding the organisational and functional principles of individual proteins. The number of interactions that a protein has in a PIN has…
Determining which proteins interact together is crucial to a systems-level understanding of the cell. Recently, algorithms based on Direct Coupling Analysis (DCA) pairwise maximum-entropy models have allowed to identify interaction partners…
The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such…