Entanglement and knots occur across all aspects of the physical world. Despite the common belief that knots are too complicated for incorporation into proteins, knots have been identified in the native fold of a growing number of proteins. The discovery of proteins with this unique backbone characteristic has challenged the preconceptions about the complexity of biological structures, as well a...

The mechanisms behind length regulation of prokaryotic surface structures has long eluded microbiologists. The recent identification of a protein that functions as a 'molecular ruler' to determine the physical length of a bacterial extracellular needle advances our understanding of surface structure biogenesis.

The backbone structure of a protein is largely determined by the phi and psi torsion angles. Thus, knowing these angles, even if approximately, will be very useful for protein-structure prediction. However, in a previous work, a sequence-based, real-value prediction of psi angle could only achieve a mean absolute error of 54 degrees (83 degrees, 35 degrees, 33 degrees for coil, strand, and heli...

We study the statistical properties of contact vectors, a construct to characterize a protein's structure. The contact vector of an N-residue protein is a list of N integers n(i), representing the number of residues in contact with residue i. We study analytically (at mean-field level) and numerically the amount of structural information contained in a contact vector. Analytical calculations re...

A lot of research revolves around molecules, resulting in very different ways to visualize the corresponding molecular data, focused on showing relevant properties. For proteins, in particular, people tend to use some very different representations.The goal of this research is to provide researchers with a tool in which they can intuitively and interactively explore the structure of a protein, ...

The structure of crotapotin, a protein extracted, from the venom of the Crotalus durissus terrificus, in solution at pH = 1.5, was studied by SAXS. The experimental results yield structural parameter values of the molecular radius of gyration Rg = 13.6 A, volume v = 16.2 x 10(3) A3 A3 and maximal dimension Dmax = 46 A. The distance distribution function deduced from the scattering measurements ...

Cross-linking in combination with mass spectrometry can be used as a tool for structural modeling of protein complexes and multidomain proteins. Although cross-links represent only weak structural constraints, the combination of a limited set of experimental cross-links with molecular docking/modeling is often sufficient to determine the structure of a protein complex or multidomain protein at ...

A simple, five-element descriptor, derived from the Delaunay tessellation of a protein structure in a single point per residue representation, can be assigned to each residue in the protein. The descriptor characterizes main-chain topology and connectivity in the neighborhood of the residue and does not explicitly depend on putative hydrogen bonds or any geometric parameter, including bond leng...

Inside individual cells, expression of genes is stochastic across organisms ranging from bacterial to human cells. A ubiquitous feature of stochastic expression is burst-like synthesis of gene products, which drives considerable intercellular variability in protein levels across an isogenic cell population. One common mechanism by which cells control such stochasticity is negative feedback regu...

Orientation dependence of single-fluorophore intensity was exploited in order to videotape conformational changes in a protein machine in real time. The fluorophore Cy3 attached to the central subunit of F(1)-ATPase revealed that the subunit rotates in the molecule in discrete 120 degrees steps and that each step is driven by the hydrolysis of one ATP molecule. These results, unlike those from ...