Estimation of protein stability is important for many reasons: first providing an understanding of the basic thermodynamics of the process of folding, protein engineering, and protein stability plays important role in biotechnology especially in food and protein drug design. Today, proteins are used in many branches, including industrial processes, pharmaceutical industry, and medical fields. A...

The hybrid density functional theory (B3LYP) and ab initio molecular orbital (HF) based methods and Natural Bond Orbital (NBO) interpretation were used to analyze the conformational behaviors of 2,5,5-trimethyl-1,3,2-dioxaphosphinane 2-selenide (compound 1), 2,5,5-trimethyl-1,3,2-dithiaphosphinane 2-selenide (compound 2) and 2,5,5-trimethyl-1,3,2-diselena phosp...

Conformational heterogeneity leads to different excited state relaxation pathways in flexibly-linked DPP-dimers.

The mitotic checkpoint complex (MCC) coordinates proper chromosome biorientation on the spindle with ubiquitination activities of CDC20-activated anaphase-promoting complex/cyclosome (APC/C(CDC20)). APC/C(CDC20) and two E2s, UBE2C and UBE2S, catalyze ubiquitination through distinct architectures for linking ubiquitin (UB) to substrates and elongating polyUB chains, respectively. MCC, which cont...

BACKGROUND Biomolecules or other complex macromolecules undergo conformational transitions upon exposure to an external perturbation such as ligand binding or mechanical force. To follow fluctuations in pairwise forces between atoms or residues during such conformational changes as observed in Molecular Dynamics (MD) simulations, we developed Time-Resolved Force Distribution Analysis (TRFDA). ...

Serum albumin is the most abundant protein in the circulatory system. The ability of albumins to undergo a reversible conformational transition, observed with changes in pH, is conserved in distantly related species, suggesting for it a major physiological role possibly related to the transport of small molecules including drugs. We have followed changes of bovine serum albumin (BSA) in volume ...

Free energy calculations of the potential of mean force (PMF) based on the combination of targeted molecular dynamics (TMD) simulations and umbrella samplings as a function of physical coordinates have been applied to explore the detailed pathways and the corresponding free energy profiles for the conformational transition processes of the butane molecule and the 35-residue villin headpiece sub...

In recent experiments, the conformational change of proteins has been monitored by means of electrical measurements. In this paper we propose a model able to reproduce the variation of some conductive features of a protein resulting by its morphological transformations. To this purpose we map each protein into a network of interacting elementary impedances. The biological root (the kind of amin...

Raman spectroscopy is used to examine the effects of temperature, surface coverage, nature of the alkylsilane precursor (octadecyltrichlorosilane, methyloctadecyldichlorosilane, or dimethyloctadecylchlorosilane), and surface grafting method (surface or solution polymerized) on alkyl chain conformational order in a series of high-density octadecylsilane stationary phases ranging in surface cover...

Cytochrome (cyt) P450s hydroxylate a variety of substrates that can differ widely in their chemical structure. The importance of these enzymes in drug metabolism and other biological processes has motivated the study of the factors that enable their activity on diverse classes of molecules. Protein dynamics have been implicated in cyt P450 substrate specificity. Here, 2D IR vibrational echo spe...