Related papers: Deep-time consistency in proteome elemental compos…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
Differentiating structural evolution from structural development or formation opens many avenues of research. The study particularly advances the chemical and physical sciences, material science, energy science, and chemical engineering. By…
Proteins have regular tertiary structures but irregular amino acid sequences. This made it very difficult to decode the structural information in the protein sequences. Here we demonstrate that many small alpha protein domains have hidden…
The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistently from several…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
Evolution of genetic code is studied as the change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states…
Proteins, chain molecules of amino acids, behave in ways which are similar to each other yet quite distinct from standard compact polymers. We demonstrate that the Flory theorem, derived for polymer melts, holds for compact protein native…
Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is,…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
Viruses and their hosts are involved in an 'arms race' where they continually evolve mechanisms to overcome each other. It has long been proposed that intrinsic disorder provides a substrate for the evolution of viral hijack functions and…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…
Protein-fragment seqlets typically feature about 10 amino acid residue positions that are fixed to within conservative substitutions but usually separated by a number of prescribed gaps with arbitrary residue content. By quantifying a…
Proteins encoded by genes containing regions of variable number tandem repeats (VNTRs) are known to be polymorphic within species but the influence of their instability in molecular interactions remains unclear. VNTRs are overrepresented in…
Nucleosome organization in eukaryotic genomes has a deep impact on gene function. Although progress has been recently made in the identification of various concurring factors influencing nucleosome positioning, it is still unclear whether…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
In this Communication we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein…
Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing…