A novel approach for the modeling of coiled coils through molecular dynamics is described and applied to the dimerization region of the yeast transcriptional activator GCN4. Initially, a model is created consisting of C alpha atoms only, representing an idealized coiled coil with infinite pitch. Human bias in the placing of the other atoms is reduced by an automatic building procedure using sim...

Leucine zippers are alpha helical monomers dimerized to a coiled coil structure. Various scenarios for dimerization span interaction of unstructured monomers that form alpha helices in the process of dimerization to preformed alpha helical monomers dimerizing.Another suggested possibility, a trigger sequence hypothesis (M. O. Steinmetz et al., Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 7062-706...

Volume changes associated with protein folding reactions contain valuable information about the folding mechanism and the nature of the transition state. However, meaningful interpretation of such data requires that overall volume changes be deconvoluted into individual contributions from different structural components. Here we focus on one type of structural element, the α-helix, and measure ...

We have investigated the process of the assembly of the Dictyostelium discoideum cortexillin I oligomerization domain (Ir) into a tightly packed, two-stranded, parallel coiled-coil structure using a variety of recombinant polypeptide chain fragments. The structures of these Ir fragments were analyzed by circular dichroism spectroscopy, analytical ultracentrifugation and electron microscopy. Del...

Polar residues lying between adjacent α-helical chains of coiled-coils often contribute to coiled-coil curvature and flexibility, while more typical core hydrophobic residues anneal the chains together. In tropomyosins, ranging from smooth and skeletal muscle to cytoplasmic isoforms, a highly conserved Asp at residue 137 places negative charges within the tropomyosin coiled-coil core in a posit...

The effect of a solvation on the thermodynamics and kinetics of polyalanine (Ala(12)) is explored on the basis of its energy landscapes in vacuum and in an aqueous solution. Both energy landscapes are characterized by two basins, one associated with alpha-helical structures and the other with coil and beta-structures of the peptide. In both environments, the basin that corresponds to the alpha-...

As a result of cultivation of A. laidlawii PG8 cells on the deficient medium during 480 days, the mycoplasma culture adapted in vitro to unfavorable growth conditions was obtained. The culture consisted of cells with sizes less than 0.2 μm and features of A. laidlawii PG8 ultramicroforms, nanocells. A. laidlawii PG8 culture adapted in vitro to unfavorable growth conditions shows more evident ph...

This study investigates cold thermal energy storage (CTES) using a helical coil heat exchanger modified with bubble injection. One of the effective methods for increasing transfer rate in exchangers is A immersed inside cylindrical water tank, where evaporator vapor compression refrigeration cycle (VCRC) and provides designed cooling. Experimental studies were carried out to examine impact inje...