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The effect of sample size on the results of solvent extraction measurements for detecting cocontinuity in polymer blends was investigated. Poly(ethylene oxide)/polystyrene (PEO/PS) blend samples of several thicknesses were analyzed by removing the PEO phase using water extraction. The experimental degree of continuity was shown to have a linear dependence on the reciprocal of sample thickness. A model...
A new generation of polyurethane thermoplastic elastomers were synthesized via the reaction of NCO-terminated polyurethane with 2,2'-pyromellitdiimidodisuccinic anhydride chain extender. The starting materials and polymers were characterized by conventional methods and physical, mechanical and thermal properties were studied. In comparison to typical polyurethanes, these polymers exhibited improved...
X-ray powder diffraction and molecular modeling are used to identify the crystal structure and chain conformation of poly(trimethylene 2,6-naphthalate) (PTN) β-form crystal. The unit cell of PTN β-form crystal was determined to be a triclinic with dimensions of a=0.4665nm, b=0.7014nm, c=2.2177nm, α=100.85 o , β=88.78 o and γ=120.63 o , and the space group of the crystal is...
The fluctuations of residues of proteins about their equilibrium configurations are analyzed by the Langevin equation. Residue pairs that are covalently bonded and those that are within a given cutoff distance of each other are assumed to be connected by linear springs. The actions of the solvent and intramolecular interactions on each residue are treated as random noise. The correlations of fluctuations...
The vinylidene structures in polypropylenes produced by ethylenebis(indenyl)zirconiumdichloride (En(Ind) 2 ZrCl 2 ), 1, and isopropyl(cyclopentadienyl)(fluorenyl)zirconiumdichloride (iPr(Cp)(Flu)ZrCl 2 ), 2, were analyzed by 1 H NMR. The vinylidene group adjacent to the chain end was clearly distinguished from other internal vinylidene structures for the first time...
We perform a mixed coarse-graining approach in a normal mode analysis of protein motions, which enables the modeling of a protein's native conformation with different regions having low and high resolution. As a result, the dynamics of the interesting functional parts within a supramolecular assemblage can be analyzed at high resolution, while the remainder of the structure is represented at poorer...
The respective roles of local and nonlocal interactions in the thermodynamic cooperativity of proteins are investigated using continuum (off-lattice) native-centric Go-like models with a coarse-grained C α chain representation. We study a series of models in which the (local) bond- and torsion-angle terms have different strengths relative to the (nonlocal) pairwise contact energy terms. Conformational...
Protein-DNA recognition plays a crucial role in gene expression and regulation. In this work, we have analyzed the influence of cation-π interactions to the stability of 62 protein-DNA complexes. A new criterion has been formulated to delineate the cation-π interactions based on (i) the distribution of atoms in the π system (5 and 6-member rings) of DNA bases around the positive charged atoms of Lys...
In this article we review and discuss the state-of-the-art methods using minimalist models in the context of energy landscape theory to study protein folding. As good agreement between computational/theoretical studies and experimental observations in vitro continues to emerge, many research groups are asking how this structural and dynamical information can be used to understand proteins in vivo...
We analyze the dependence of thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, N. Using lattice Go models we show that ΔT/T F ~N -1 , where T F is the folding transition temperature and ΔT is the transition width computed using the temperature dependence of the order parameter that distinguishes between the unfolded...
Computational studies of protein folding have implicitly assumed that folding occurs from a denatured state comprised of the entire protein. Cotranslational folding accounts for the linear production and release of a protein from the ribosome, allowing part of the protein to explore its conformation space before other parts have been synthesized. This gradual 'extrusion' from the ribosome can yield...
We describe a gapped structural threading method starting from aligning the query protein sequence to the dominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural...
We present results obtained for anisotropic potentials for protein simulations extracted from the continually growing databases of protein structures. This work is based on the assumption that the detailed information on molecular conformations can be used to derive statistical (a.k.a. 'knowledge-based') potentials that can describe on a coarse-grained level the side chain-side chain interactions...
Reduced computer modeling of proteins now has a history of about 30 years. In spite of the enormous increase in computing abilities, reduced models are still very important tools for theoretical studies of protein structure, dynamics and thermodynamics. Very simple, highly idealized lattice (and recently also off-lattice) models could be studied in great detail, providing valuable insight into the...
The amount of structural information encoded in secondary structure can be measured by its ability to specify the correct peptide backbone conformation of protein chains. Using methodology derived from information theory, we generate optimized distributions of backbone phi-psi dihedral angle pairs given either correct or predicted three-state secondary structure. Entropy measurements on these distributions...
The folded (alpha helical) and unfolded (non-alpha helical) ensembles of the 21 amino acid peptide Ace-A21-Nme are characterized structurally. The replica exchange molecular dynamics approach is used to generate these ensembles at 46 different temperatures ranging from 278 to 487 K. Each replica system is simulated in explicit solvent for a period of 10ns/replica, for a total of 460ns. In addition...
New atomic pair contacts with considering the coordinates of each atom in a residue are introduced here. We analyze the ability of all the 20 amino acid residues to form long-range and short-range contacts by calculating the average numbers of short- and long-range contacts between different amino acid pairs. It is concluded that Phe-Phe, Leu-Phe and Leu-Leu have a high tendency to form contacts....
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