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In this study, we propose an analytic statistical mechanics approach to solve a fundamental problem in biological physics called protein design. Protein design is inverse of structure prediction, and its solution the amino acid sequence that best stabilizes given conformation. Despite recent rapid progress using deep learning, challenge exploring principles remains. Contrary previous computatio...

G-protein signaling pathways mediate communication across cell membranes. The first steps of this occur at the membrane, where upon receiving an external signal –the binding agonist ligand– membrane-embedded G-Protein Coupled Receptor adopts a conformation recognized by cytoplasmatic G protein. Whereas specialized GPCRs sense protons from extracellular milieu, thus acting as pH sensors in cells...

The Raman spectrum of cyclosporin-A has been recorded in the solid phase. The conformation of the molecule has been discussed on the basis of Raman data. It has been concluded that in agreement with X-ray data, cyclosporin-A molecule has an antiparallel P- pleated sheet conformation. It may have some reverse P- turn structure in what has been assigned to a random coil conformation.

Persistent alteration of protein conformation due to interaction with isoflurane may be a novel molecular aspect of preconditioning. We preincubated human serum albumin with isoflurane, dialyzed to release agent, and assessed protein conformation. Susceptibility to chemical modification by methylglyoxal and nitrophenylacetate was also examined. Isoflurane had a persistent effect on protein conf...

In the otherwise highly conserved NMR structures of cellular prion proteins (PrP(C)) from different mammals, species variations in a surface epitope that includes a loop linking a β-strand, β2, with a helix, α2, are associated with NMR manifestations of a dynamic equilibrium between locally different conformations. Here, it is shown that this local dynamic conformational polymorphism in mouse P...

Herein, we assessed the effect of full native peptide amyloid-beta (Aβ) (1-42) and its fragments (25-35 35-25) on tissue transglutaminase (TG2) isoforms (TG2-Long TG2-Short) expression levels olfactory ensheathing cells (OECs). Vimentin glial fibrillary acid protein (GFAP) were also studied. The pre-treatment with indicaxanthin from Opuntia ficus-indica fruit TG2 isoforms, cell viability, total...

A model to describe the mechanism of conformational dynamics in secondary protein based on matter interactions is proposed. The approach deploys the lagrangian method by imposing certain symmetry breaking. The protein backbone is initially assumed to be nonlinear and represented by the Sine-Gordon equation, while the nonlinear external bosonic sources is represented by φ interaction. It is argu...

A simple method for finding conformational substates of proteins is presented and realized through computer simulations. It is based on a procedure in which the amino acids in a protein take the places of the cities in the three-dimensional travelling salesman prob lem. Optimization by simulated annealing was employed in the computer simulations to obtain conformational substates originating fr...