Chain entropy

Estimated side chain entropies TSppn for each residue simulated that possesses a mobile side chain are given in Table II along with entropy estimates, TSoisorderecb f°r side chains in a tripeptide model for disordered states taken from Creamer (2000), and the difference in entropy, TAS. In all cases, Y .Sppn in the peptides restricted to the PPII conformation is higher than that in disordered states, leading to positive values... 

Fig. 12 Chain entropy leads to thermodynamic stabilization of finite lamellar thickness...

The onset of glass formation in a polymer melt is associated with the development of orientational correlations that arise from chain stiffness. At the temperature Ta, there is a balance between the energetic cost of chain bending and the increased chain entropy, and below this temperature orientational correlations are appreciable while the melt still remains a fluid. Such a compensation temperature has been anticipated based on a field theoretic description of semiflexible polymers by Bascle et al. [120]. The temperature 7a is important for describing liquid dynamics since the orientational correlations (and dynamic fluid heterogeneities associated with these correlations) should alter the polymer dynamics for T < Ta from the behavior at higher... 

As a result of the branched chain architecture, TASP molecules exhibit some unique conformational properties)5 12-14 47 75 76 148 For example, the folding to a compact state proceeds via two distinct steps the onset of secondary structure in the attached peptide blocks followed by their template-directed self-assembly to a three-dimensional packing topology. Due to its characteristic branched chain connectivity, the conformational space accessible in the unfolded state is considerably reduced compared to a linear chain of similar size (excluded volume effect), resulting in a smaller chain entropy. Thus, folded TASP molecules are expected to show higher thermodynamic stability compared to unbranched polypeptides of comparable size. 

The disulfide bond differs from other types of interactions in folded proteins, such as hydrogen bonds and hydrophobic, electrostatic and van der Waals interactions. The disulfide bond is a covalent bond that is able to significantly stabilize folded conformations by 2-5 kcal/ mol for each disulfide.11 The effect is presumed to be due mainly to a decrease in the configurational chain entropy of the unfolded polypeptide.21 On the other hand, another view is that the disulfide bond destabilizes folded structures entropically, but stabilizes them enthalpically to a greater extent.31... 

The mechanical properties of polymer chains that do not exhibit interactions between the side chains and the backbone, or one part of the backbone and another part of the backbone, are related to the number of available conformations and hence the chain entropy. As we discuss later, the stiffness of a polymer chain that does not exhibit bonding with other parts of the chain is related to the change in the number of available conformations. It turns out this refers to random chain polymers of which elastin, poly(ethylene) at high temperatures, and natural rubber are discussed in this text. As we stretch a polymeric chain we reduce the number... 

Real chains in good solvents have the same universal features as self-avoiding walks on a lattice. These features are described by two "critical" exponents y and v. The first is related to chain entropy, the second to chain size a real chain has a size that is much larger than that of an ideal chain (Nv instead of N1/2, where v 3/5 in good solvents) in good solvents the conformation of the chain is "swollen". 

Several factors compensate the protein-solvent system for the loss of chain entropy required by folding ... 

Loh, A. P., Pawley, N., Nicholson, L. K., and Oswald, R. E. (2001). An increase in side chain entropy facilitates effector binding NMR characterization of the side chain methyl group dynamics in Cdc42Hs. Biochem. 40, 4590-4600. 

It was found basing on TGA data that initial destruction temperature raises for all prepared nanocomposites containing up to 5%. In contrast to original PET all nanocomposites decompose producing coke residue, which number increases with higher content of layered silicate. Nanocomposite presence indicates on more complex behavior of nanocomposite thermodestruction process. It is likely that the layered silicate addition is an initiator of coking as a result of barrier effects to volatile products, formed in process of thermal destruction and other processes, concerned with change of macromolecular chains entropy in near-surface nanocomposite layers. 

The position of minimum free energy will be determined by the balance between chain end electrostatic attraction and chain entropy. An increase in the dielectric constant of the medium will lead to a fall in chain end attraction, an increase in the average end to end distance and a rise in entropy. Fewer macrocycles will be formed. 

Lee AL, Kinnear SA, Wand AJ. Redistribution and loss of side chain entropy upon formation of a calmodulin-peptide complex. 

Amino acid Accessibility of side-chain to solvent" Solvent transfer relative to methionine, AG (kcal/mol) Side-chain entropy relative to alanine, TAS (kcal/mol) Volume of amino acid relative to alanine (Ay Volume available for substitution relative to alanine (Ay... 

It is expected that loss of stability will occur for methionine replacements of Leu, lie and Phe because of a reduction in solvent transfer free energy (Table I). In addition, methionine has one or more rotatable bonds than leucine, isoleucine, valine and phenylalanine which may entail a greater loss of side-chain entropy upon folding (Table I). Strain may also be introduced in some cases. The range of destabilization that is observed for the single substitutions (-0.4 to -1.9 kcal/mol) (Table II) shows how the characteristics of the local site of substitution can contribute. 

The dominant contribution to the free energy of lengthy (rubbery) polymer chains is entropy. This is known to accoimt for rubber elasticity, which can be satisfactorily modelled by the entropy of the cross-linked pol3rmer chains alone. A simple illustrative model of copolymer self-assembly can be developed by extending rubber elasticity theory to include bending as well as stretching deformations, to calculate chain entropy as a function of interfacial curvatures in diblock aggregates. 

Creamer, T. P., and Rose, G. D. (1992) Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities. Proc. Natl. Acad. Sci. U.S.A. 89, 5937-5941. 

On the other hand, the chain entropy (per link) is, of course, smaller than that of small molecules nevertheless, the entropy of very flexible chains remains large. In brief, the chains are less soluble than the corresponding monomers and their solubility diminishes when their molecular mass increases. 

P.F.W, and Kroemer, R.T. (2004) Novel scoring functions comprising QXP, SASA, and protein side-chain entropy terms. Journal of Chemical Information and Computer Sciences, 44, 882—893. 

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