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.

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...

Molecular genetics selection on individual genes is a promising method to genetically improve economically important traits in livestock. The insulin like growth factor-I (IGF-I) gene may play important roles in growth of multiple tissues, including muscle cells, cartilage and bone. The objectives of the present study were the estimate the haplotype frequencies of the IGF-I gene polymorphisms i...

A quantitative study of the variation of the conformational equilibria of 7-benzyl-2-iodo-9-oxa-7-azabicyclo[4.3.0]nonan-8-one 1 in 10 solvents has been carried out. The experimental composition in each solvent has been obtained from experimental NMR vicinal H-H coupling constants together with molecular modeling. The solvent properties, particularly polarity and hydrogen bonding ability, were ...

We perform a statistical and energetic analysis of atomic polarizabilities obtained with the LoProp approach for all atoms in the avidin tetramer for 70 snapshots from molecular dynamics simulations with seven different biotin analogues, and from the crystal structure of the photosynthetic reaction center (in total 560 698 individual polarizabilities). Dynamic effects give a variation of the po...

Abstract Particle fusion for single molecule localization microscopy improves signal-to-noise ratio and overcomes underlabeling, but ignores structural heterogeneity or conformational variability. We present a-priori knowledge-free unsupervised classification of structurally different particles employing the Bhattacharya cost function as dissimilarity metric. achieve 96% accuracy on mixtures up...

Experimental conditions or the presence of interacting components can lead to variations in the structural models of macromolecules. However, the role of these factors in conformational selection is often omitted by in silico methods to extract dynamic information from protein structural models. Structures of small peptides, considered building blocks for larger macromolecular structural models...

Cyclophilins are ubiquitous enzymes that are involved in protein folding, signal transduction, viral proliferation, oncogenesis, and regulation of the immune system. Cyclophilin A is the prototype of the cyclophilin family. We use molecular dynamics to describe the catalytic mechanism of cyclophilin A in full atomistic detail by sampling critical points along the reaction coordinate, and use ac...

The interaction between bovine serum albumin (BSA) and methyl cinnamate (MC), an strawberry flavor compound, was investigated. We found that BSA and MC form complex with stoichiometry (n) equal 1, driven by system’s entropy increase and enthalpy reduce at pH 7.4, 5.0 and 3.5, with binding constants (Kb) in magnitude of 10 5 L.mol -1 . There was difference in variation of standard enthalpy of co...

We analyzed the correlation between the conformational strain and the binding kinetics in antigen-antibody interactions. The catalytic antibodies 6D9, 9C10, and 7C8 catalyze the hydrolysis of a nonbioactive chloramphenicol monoester derivative to generate a bioactive chloramphenicol. The crystal structure of 6D9 complexed with a transition-state analog (TSA) suggests that 6D9 binds the substrat...