生物大分子
Channels are Catalysts for Diffusion and in that sense are Enzymes. This idea is useful for the design and interpretation of experiments.
Because organisms synthesize component molecules at rates that reflect those molecules' adaptive utility, we expect a population of biota to leave a distinctive chemical signature on their environment that is anomalous given the local…
Considering all available non-redundant protein structures across different structural classes, present study identified the probabilistic characteristics that describe several facets of the occurrence of 3(10) and Pi-helices in proteins.…
Changes in the extent of local concavity along with changes in surface roughness of binding sites of proteins have long been considered as useful markers to identify functional sites of proteins. However, an algorithm that describes the…
The tertiary structure of protein, as well as the local secondary structure organization are fully determined by the angles of the peptidic bound. The backbone dihedral angles not only determine the global fold of the protein, but also the…
The consequences of recent experimental finding that hydrogen bonds of the anti-parallel $\beta $-sheet in nonspecific binding site of serine proteases become significantly shorter and stronger synchronously with the catalytic act are…
Complex hierarchical structures composed of simple nanoscale building blocks form the basis of most biological materials. Here we demonstrate how analogies between seemingly different fields enable the understanding of general principles by…
Energetically responsive residues of the 173 amino acid N-terminal domain of the cardiac Ryanodine receptor RyR2 are identified by a simple elastic net model. Residues that respond in a correlated way to fluctuations of spatially…
Quantitative understanding of the principles regulating nucleosome occupancy on a genome-wide level is a central issue in eukaryotic genomics. Here, we address this question using budding yeast, Saccharomyces cerevisiae, as a model…
This paper has been withdrawn by the author due to a missing figure
We investigate the folding mechanism of the WW domain Fip35 using a realistic atomistic force field by applying the Dominant Reaction Pathways (DRP) approach. We find evidence for the existence of two folding pathways, which differ by the…
Transcription factors (TFs) are regulatory proteins that bind DNA in promoter regions of the genome and either promote or repress gene expression. Here we predict analytically that enhanced homo-oligonucleotide sequence correlations, such…
We analyze publicly available data on Affymetrix microarrays spike-in experiments on the human HGU133 chipset in which sequences are added in solution at known concentrations. The spike-in set contains sequences of bacterial, human and…
In eukaryotic genes the protein coding sequence is split into several fragments, the exons, separated by non-coding DNA stretches, the introns. Prokaryotes do not have introns in their genome. We report the calculations of stability domains…
Considering a basic enzyme-catalysed reaction, in which the rate of input of the substrate varies periodically in time, we give a necessary and sufficient condition for the existence of a periodic solution of the reaction equations. The…
In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo…
Using magnetic tweezers to investigate the mechanical response of single chromatin fibers, we show that fibers submitted to large positive torsion transiently trap positive turns, at a rate of one turn per nucleosome. A comparison with the…
Proteins are known to locate their specific targets on DNA up to two orders of magnitude faster than predicted by the Smoluchowski three-dimensional diffusion rate. One of the mechanisms proposed to resolve this discrepancy is termed…
We introduce a topology-based nonlinear network model of protein dynamics with the aim of investigating the interplay of spatial disorder and nonlinearity. We show that spontaneous localization of energy occurs generically and is a…
Many biological electron transfer (ET) reactions are mediated by metal centres in proteins. NADH:ubiquinone oxidoreductase (complex I) contains an intramolecular chain of seven iron-sulphur (FeS) clusters, one of the longest chains of metal…