While figures of speech are often useful and even educational, flashy titles combined with hyperbolae and imprecise language can mislead or deceive non-specialist readers and should therefore be avoided. The possibility of such confusion exists when poorly defined terms like ;structure quality' or ;super-resolution' are used to describe a protein structure.

Single-domain allostery has been postulated to occur through intramolecular pathways of signaling within a protein structure. We had previously investigated these pathways by introducing a local thermal perturbation and analyzed the anisotropic propagation of structural changes throughout the protein. Here, we develop an improved approach, the Rotamerically Induced Perturbation (RIP), that iden...

When spreading onto a protein microlattice living cells spontaneously acquire simple shapes determined by the lattice geometry. This suggests that, on a lattice, living cells' shapes are in thermodynamic metastable states. Using a model at thermodynamic equilibrium we are able to reproduce the observed shapes. We build a phase diagram based on two adimensional parameters characterizing essentia...

Proteins have evolved to use water to help guide folding. A physically motivated, nonpairwise-additive model of water-mediated interactions added to a protein structure prediction Hamiltonian yields marked improvement in the quality of structure prediction for larger proteins. Free energy profile analysis suggests that long-range water-mediated potentials guide folding and smooth the underlying...

Utilization of primary and secondary structure elements to predict a protein's propensity to form amyloids.

Gold nanoclusters with five discrete sizes (Au4, Au8, Au10, Au13, and Au25) are synthesized in a protein template with predefined conformation via a CO-mediated synthesis.

Single-molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different phase diagrams. The simple model proposed here indicates that in one case the system undergoes a transition akin to the unzipping of a beta sheet, while in the o...

The sorption of a protein pair on carboxylic cation exchangers with various contents of ionogenic groups is examined. The bi-Langmuir isotherm calculation is carried out from sorption data for single-component systems. It is shown that good agreement of calculated and experimental data is reached only when protein-sorbent interaction weakens because of implementation of the competitive sorption...

Protein shedding, or the proteolytic cleavage of a protein from the surface of a cell, is emerging as an important mechanism in the regulation of cellular activity but it is poorly understood. Growing evidence suggesting that protein shedding and protein function are closely linked may lead to new strategies for the treatment of a wide range of diseases.

It is well known that an important step toward understanding the functions of a protein is to determine its subcellular location. Although numerous prediction algorithms have been developed, most of them typically focused on the proteins with only one location. In recent years, researchers have begun to pay attention to the subcellular localization prediction of the proteins with multiple sites...