Hydrophobic effect contributions

Beal, R. E., Toscano-Cantaffa, D., Young, P., Rechsteiner, M., and PiCKART, C. M. The hydrophobic effect contributes to polyubiquitin chain recognition. Biochemistry, 1998, 37, 2925-34. 

T. Beal et al.. The hydrophobic effect contributes to polyubiquitin chain recognition. Biochemistry 37(1998)2925-2934. 

The hydrophobic effect contributes between 25 to 50 cal/mol. A2 of nonpolar surface area that is freed from water. 

Water-soluble globular proteins usually have an interior composed almost entirely of non polar, hydrophobic amino acids such as phenylalanine, tryptophan, valine and leucine witl polar and charged amino acids such as lysine and arginine located on the surface of thi molecule. This packing of hydrophobic residues is a consequence of the hydrophobic effeci which is the most important factor that contributes to protein stability. The molecula basis for the hydrophobic effect continues to be the subject of some debate but is general considered to be entropic in origin. Moreover, it is the entropy change of the solvent that i... 

Niek Buurma and Theo Rispens are most gratefully acknowledged for the inspiring discussions on hydrophobic effects. These discussions have contributed significantly to a better understanding of this topic and form the basis of what is described in Section 1.3. 

Modem understanding of the hydrophobic effect attributes it primarily to a decrease in the number of hydrogen bonds that can be achieved by the water molecules when they are near a nonpolar surface. This view is confirmed by computer simulations of nonpolar solutes in water [15]. To a first approximation, the magnimde of the free energy associated with the nonpolar contribution can thus be considered to be proportional to the number of solvent molecules in the first solvation shell. This idea leads to a convenient and attractive approximation that is used extensively in biophysical applications [9,16-18]. It consists in assuming that the nonpolar free energy contribution is directly related to the SASA [9],... 

Prevost, M. Wodak, S. J. Tidor, B. Karplus, M., Contribution of the hydrophobic effect to protein stability — analysis based on simulations of the Ile-96- Ala mutation in barnase, Proc. Natl Acad. Sci. USA 1991, 88,10880-10884. 

Organic modifier Solvent strength Solvent strength generally increases with the volume percent of organic modifier. Its effect is most important when hydrophobic mechanisms contribute significantly to retention. In this case, changing... 

When the urea and thiol are removed by dialysis (see p. 78), secondary and tertiary structures develop again spontaneously. The cysteine residues thus return to a suf ciently close spatial vicinity that disulfide bonds can once again form under the oxidative effect of atmospheric oxygen. The active center also reestablishes itself In comparison with the denatured protein, the native form is astonishingly compact, at 4.5 2.5 nm. In this state, the apolar side chains (yellow) predominate in the interior of the protein, while the polar residues are mainly found on the surface. This distribution is due to the hydrophobic effect (see p. 28), and it makes a vital contribution to the stability of the native conformation (B). 

Cantor and SchimmeP provide a lucid description of the thermodynamics of the hydrophobic effect, and they stress the importance of considering both the unitary and cratic contributions to the partial molal entropy of solute-solvent interactions. Briefly, the partial molal entropy (5a) is the sum of the unitary contribution (5a ) which takes into account the characteristics of solute A and its interactions with water) and the cratic term (-R In Ca, where R is the universal gas constant and ( a is the mole fraction of component A) which is a statistical term resulting from the mixing of component A with solvent molecules. The unitary change in entropy 5a ... 

Part of the motivation behind so straightforward an approach derives from its ready application to certain simple systems, such as the solvation of alkanes in water. Figure 11.8 illustrates the remarkably good linear relationship between alkane solvation free energies and their exposed surface area. Insofar as the alkane data reflect cavitation, dispersion, and the hydrophobic effect, this seems to provide some support for the notion that these various terms, or at least their sum, can indeed be assumed to contribute in a manner proportional to solvent-accessible surface area (SASA). 

Thus, if we examine the variation in -RT In Kld for a series of alkyl amines participating in ion exchange, we should see how R groups affect the value of-RTln Kiex while the product, z,FT, remains constant. Since this hydrophobic effect appears to regularly increase with the size of the nonpolar part of the chemical structure (Cowan and White, 1958 Somasundaran et al., 1984), we may reasonably propose this energy term is composed of excess free energy of solution in water contributions from each of the nonpolar parts of the structure. Consequently, we expect for the alkyl ammonium ions studied by Cowan and White (1958) ... 

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