Related papers: Is the unfoldome widespread in proteomes?
Integrative modeling enables structure determination for large macromolecular assemblies by combining data from multiple sources of experiment data with theoretical and computational predictions. Recent advancements in AI-based structure…
Transcriptional and post-transcriptional regulation shape tissue-type-specific proteomes, but their relative contributions remain contested. Estimates of the factors determining protein levels in human tissues do not distinguish between (i)…
Cancer complexome comprises a heterogeneous and multifactorial milieu that varies in cytology, physiology, signaling mechanisms and response to therapy. The combined framework of network theory and spectral graph theory along with the…
Although machine learning has transformed protein structure prediction of folded protein ground states with remarkable accuracy, intrinsically disordered proteins and regions (IDPs/IDRs) are defined by diverse and dynamical structural…
Introduction: While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and…
Sub-diffusion in biological systems is conventionally treated as anomalous, requiring fractional derivatives, heavy-tailed waiting times, or fitted memory kernels. We argue that this anomaly is an artifact of an incomplete phase space.…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
We present a geometrical analysis of the protrusion statistics of side chains in more than 4,000 high-resolution protein structures. We employ a coarse-grained representation of the protein backbone viewed as a linear chain of C{\alpha}…
Function of proteins or a network of interacting proteins often involves communication between residues that are well separated in sequence. The classic example is the participation of distant residues in allosteric regulation.…
The evolutionary reason for the increase in gene length from archaea to prokaryotes to eukaryotes observed in large scale genome sequencing efforts has been unclear. We propose here that the increasing complexity of protein-protein…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
The budding yeast {\it Saccharomyces cerevisiae} is the first eukaryote whose genome has been completely sequenced. It is also the first eukaryotic cell whose proteome (the set of all proteins) and interactome (the network of all mutual…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…
Intrinsically disordered proteins (IDPs) play a significant role in intracellular phenomena and are known to exist in an ensemble of inter-converting conformations in solution. Accurately modeling the conformations of IDPs in solution poses…
It is becoming clear that traditional, single-structure models of proteins are insufficient for understanding their biological function. Here, we outline one method for inferring, from experiments, not only the most common structure a…
A mathematico-physically valid formulation is required to infer properties of disordered protein conformations from single-molecule F\"orster resonance energy transfer (smFRET). Conformational dimensions inferred by conventional approaches…
Unfolded proteins may contain native or non-native residual structure, which has important implications for the thermodynamics and kinetics of folding as well as for misfolding and aggregation diseases. However, it has been universally…
Characterization of proteins with intrinsic or unfolded state disorder comprises a new frontier in structural biology, requiring the characterization of diverse and dynamic structural ensembles. We introduce a comprehensive Bayesian…
We show that in experimental atomic force microscopy studies of the lifetime distribution of mechanically stressed folded proteins the effects of externally applied fluctuations can not be distinguished from those of internally present…