Configurational entropy proteins

Ensembles 600 Enterokinase 480 Enthalpy 55 activation 56, 545-547 protein folding 509 -512 specific heat effects 511, 545 - 547 Enthalpy-entropy compensation 346 Enthalpy versus entropy in protein folding 509-512, 587, 599 Entropy 55, 68-72 activation 56, 545 -547 binding 324, 345 Boltzmann equation 510 chelate effect 345 configurational 510 configurational entropy of loops 535 effective concentration 68-72 equilibria on enzyme surface 118 hydrogen bond 338 hydrophobic bond 332, 510 importance in enzyme catalysis 72 importance in enzyme-substrate binding 72... 

Chang CE, Chen W, Gilson MK. Ligand configurational entropy 43. and protein binding. Proc. Natl. Acad. Sci. U.S.A. 2007 104 1534-1539. 

The complexity and diversity of structures in the native proteins eluded any attempt to produce some simple conformation that accounted for their interfacial properties. The study of synthetic polypeptides with non-polar side chains has provided good evidence to support the view that the a-helix can be stable at the air-water interface (5), and it is therefore possible that the interfacial denaturation of proteins is mainly a loss of the tertiary structure (6, 7, 8). Since for a typical protein an a-helix takes up about the same area per residue as the p conformation, it can be accommodated as easily. Moreover, like the p conformation but unlike a more randomly coiled structure, it is linear and therefore compatible with a plane surface without loss of configurational entropy (5). In this respect a plane surface may favor an ordered over a more random structure. The loss of solubility of the spread protein can then be attributed to intermolecular association between hydrophobic side chains exposed as a result of the action of the interface on the polar exterior of the molecules. 

Also, Schellman s work is pertinent (1809). From studies on heats of dilution of urea in water he concludes that the N—H 0=C bond has an enthalpy of 1.5 kcal/mole in aqueous solution, and he carries this value over to proteins and polypeptides. Among these complicated materials he is forced to approximate—but he deduces relations which show the stability of helices and sheets in terms of H bond enthalpy and configurational entropy. From this he draws the important conclusion that H bonds, taken by themselves, give a marginal stability to ordered structures which may be enhanced or disrupted by the interactions of the side chains. Schellman ends his papers with a discussion of experimental tests needed to eliminate some of the assumptions in his theoretical analysis. 

The 5 1 rule may be justified on thermodynamic grounds. Thus, Doig and Williams [12] addressed the inconsistencies in I lory s treatment of the entropic contribution to protein denaturation, calculating AAG for denaturation for a cross-linked protein versus its non-cross-linked counterpart. At physiological temperature of 300 K, they estimated A AG 4.4 kcal/mol. This value is essentially independent of protein length and loop size and best represents the insensitivity of experimental values to loop size-dependent configurational entropies [13]. 

B. Tidor and M. Karplus, Proteins, 15, 71 (1993). The Contribution of Cross-Links to Protein Stability A Normal Mode Analysis of the Configurational Entropy of the Native State. 

R. M. Levy, M. Karplus, J. Kushick, and D. Perahia, Macromolecules, 17, 1370 (1984). Evaluation of Configurational Entropy for Proteins Application to Molecular Dynamics Simulations of ct-Helix. 

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