We study the conformational freedom of a protein made by two rigid domains connected by a flexible linker. The conformational freedom is represented as an unknown probability distribution on the space of allowed states. A new algorithm for the calculation of the Maximum Allowable Probability is proposed, which can be extended to any type of measurements. In this paper we use Pseudo Contact Shif...

neuroserpin, a member of the serine proteinase inhibitor (serpin) superfamily, is known to be a neuroprotective factor in the focal ischemic stroke followed by reducing the microglial activation. neuroserpin is a protein rich of methionine residues that can scavenge the free radical species which may increase its neuroprotective effect. on the other hand, the oxidative modifications of the amin...

introduction: congenital long qt syndrome (lqts) is a cardiac disorder characterized by qt interval prolongation at basal ecg. different lqts genes encode ion channel subunits or proteins involved in regulating cardiac ionic currents. long qt syndrome type 6 (lqt6) is caused by mutation in the kcne2 gene. our research aimed to analyze genetic variants of kcne2 gene causing the disease in irania...

As established by several groups over the last 20 years, amino acid residues in unfolded peptides and proteins do not exhibit the unspecific random distribution as assumed by the classical random coil model. Individual amino acid residues in small peptides were found to exhibit different conformational preferences. Here, we utilize recently obtained conformational distributions of guest amino a...

Although the importance of protein dynamics in protein function is generally recognized, the role of protein fluctuations in allosteric effects scarcely has been considered. To address this gap, the Kullback-Leibler divergence (Dx) between protein conformational distributions before and after ligand binding was proposed as a means of quantifying allosteric effects in proteins. Here, previous ap...

Conformational fluctuations of a molecule are important to its function since such intrinsic fluctuations enable the molecule to respond to the external environmental perturbations. For extracting large conformational fluctuations, which predict the primary conformational change by the perturbation, principal component analysis (PCA) has been used in molecular dynamics simulations. However, sev...

In single-molecule FRET experiments with pulsed lasers, not only the colors of the photons but also the fluorescence lifetimes can be monitored. Although these quantities appear to be random, they are modulated by conformational dynamics. In order to extract information about such dynamics, we develop the theory of the joint distribution of FRET efficiencies and fluorescence lifetimes determine...

Reexamining experimental data of single-molecule fluorescence correlation spectroscopy for cholesterol oxidase, we find that the existing Michaelis-Menten models with dynamical disorder cannot explain strong correlations between subsequent turnover cycles revealed in the diagonal feature in the joint statistical distribution of adjacent "on" times of this enzyme. We suggest that functional conf...

the conformational behavior of monosubstituted tri-methylsilyle ethynyl derivative of cal ix[4]arene as a newgeneration of caliarene was compared with tetra alkylated calyx[4]arene. the most important conformationalphenomena in these compounds which are pinched cone interconversion process were done by semi-empiricalmethod and ab initio calculations with gaussian 98w programming.