Hydrophobic free energy contribution

The hydrophobic free energy contribution to the stability of protein-protein complexes can also be estimated making similar assumptions to the ones described above (9). In this case as well (Table V) it appears that hydrophobic interactions contribute greatly to the overall stability of the complexes. This is particularly interesting in the case of the trypsin-pancreatic trypsin inhibitor complex since very few residues are involved in the interaction of the two molecules. 

Table IV. Hydrophobic Free Energy Contribution to Protein Stability (5)...

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],... 

The partitioning of free energy contributions in the explanation (and for design, the prediction) of binding constants is a subjective matter. Different workers choose different definitions, e.g. of hydrophobic binding, which may or may not include dispersion interaction, and different approaches to factorization of enthalpic and entropic components. 

Despite the fact that the neural network literature increasingly contains examples of radial basis function network applications, their use in genome informatics has rarely been -reported—not because the potential for applications is not there, but more likely due to a lag time between development of the technology and applications to a given field. Casidio et al. (1995) used a radial basis function network to optimally predict the free energy contributions due to hydrogen bonds, hydrophobic interactions and the unfolded state, with simple input measures. 

Fig. 7. Schematic diagram of the contributions of various types of interactions to the free energy of the native conformations of a hypothetical protein or a DNA molecule in aqueous solution. Fs, Fb, Fi/b, and Fm represent the free energy contributions of conformational entropy, electrostatic interactions, hydrogen bonding, and hydrophobic interactions, respectively. The magnitude oi Fg may vary considerably with the pH and ionic strength of the aqueous solution.

Reduction in the area of exposed hydrophobic surfaces can also enhance thermodynamic stability. Chothia has estimated a proportionality constant of 24 cal/ mol of hydrophobic free energy per square angstrom of solvent-exposed surface area (32). Substitutions at Ile-3 of T4 lysozyme enhance the stability by amounts that agree surprisingly well with this prediction (33). However, there is some debate over the choice of the proper hydrophobicity scale to quantitate the contributions of each hydrophobic residue, and it is perhaps an oversimplification to expect such a simple relationship to hold for all amino acids (34). 

The hydrophobic free energy associated with the transfer of the hydrocarbon tail from water to the hydrocarbon mixture in the micellar core. This contribution can be obtained from available solubility data. 

Therefore, it is only the copying of the results derived in Section 2.5, with the substitution of Weff for w that needs to be done to derive the dependence of polymer size on Bjerrum length, Debye length, and chain length. By adding the free energy contributions from the chain connectivity and the sum of excluded volume effects from hydrophobicity and electrostatic repulsion, we rewrite Equation 2.71 as... 

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