Solvent-exposed surface area

SPT provides a conceptual basis relating the nonpolar free energy contribution to the solvent-exposed surface area. An attractive approximation is to ignore curvature effects and write... 

Figure 1.21 Comparison of the solvent exposed surface area of amino acids in proteins. Data are plotted as a percentage of each amino acid in a protein having greater than a 30 A2 exposure to the aqueous environment. Charged and polar amino acids are seen to have the most solvent exposure, while uncharged, aromatic, or aliphatic amino acids have the least exposure.

Structural and energetic properties of studied molecules strongly depend on the solvent membrane-mimetic media significantly promote formation of a-helices capable of traversing the bilayer, whereas a polar environment destabilizes a-helical conformation via reduction of solvent-exposed surface area and packing. 

Given the somewhat ad hoc nature of most specific schemes for evaluating the non-electrostatic components of the solvation free energy, a reliance on a simpler, if somewhat more empirical, scheme has become widely accepted within available continuum models. In essence, the more empirical approach assumes that the free energy associated with the non-electrostatic solvation of any atom will be characteristic for that atom (or group) and proportional to its solvent-exposed surface area. Thus, the molecular Geos may be computed simply as... 

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). 

Paraffin wax vapor barriers are used in water rinse removers that can disperse the wax without coating the substrate. In soak tank applications, water is sometimes doated on top of an ad-solvent, neutral pH, nonwater rinse remover to prevent evaporation. Flotation devices that cover the exposed surface area may be used with other formulas. 

Dendrimer-protected colloids are capable of adsorbing carbon monoxide while suspended in solution, but upon removal from solution and support on a high surface area metal oxide, CO adsorption was nil presumably due to the collapse of the dendrimer [25]. It is proposed that a similar phenomena occurs on PVP-protected Pt colloids because removal of solvent molecules from the void space in between polymer chains most likely causes them to collapse on each other. Titration of the exposed surface area of colloid solution PVP-protected platinum nanoparticles demonstrated 50% of the total metal surface area was available for reaction, and this exposed area was present as... 

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). 

The magnitude of the classical hydrophobic effect is proportional to the amount of hydrophobic surface area buried on formation of the hydrophobic interaction, A A hp (Chapter 11). Changes in energy on mutation of Ala — Gly in the solvent exposed surfaces of a helixes are proportional to AAHP, and so these energetics are presumably driven by hydrophobicity.34,35 On the other hand, the correlation of energy changes in the core with packing density indicates that the interactions are dominated by the van der Waals term, because van der Waals interactions are... 

KUbanov [30] and co-workers [31, 32] showed that the tertiary structure of subtilisin Carlsberg was nearly the same in water, acetonitrile, and dioxane and that the differences observed were of the same magnitude as those observed between structures in different aqueous systems. In particular the active site stractures were essentially the same in all three solvents, but also the solvents did not substantially affect the exposed surface area of the enzyme, which was prepared from slightly cross-hnked crystals. 

In this equation, is the exposed surface area (perhaps the exposed solvent accessible surface area) of atom k, and is the surface tension of the atom k. This... 

Following the original work by Kauzmann on hydrophobic interactions and the determinations of the structures of myoglobin and hemoglobin, it was stated, and is still stated frequently (despite evidence to the contrary), that hydrophobic residues are buried in the interior of proteins and hydrophilic residues are exposed to solvent water. It was first shown by Klotz (1970 see also Lee and Richards, 1971) that a substantial proportion of the exposed solvent-accessible surface area of proteins is composed of nonpolar groups. This matter has been stressed in lectures for many years by one of the authors (H. McK.) (for a discussion of various approaches to this problem, see Edsall and McKenzie, 1983). In the case of lysozyme, a substantial proportion of the hydrophobic residues Leu, Val, He, Ala, Gly, Phe, Tyr, Trp, Met, and Pro are either fully exposed to solvent or at least have some atoms that are solvent accessible. Examples of hydrophobic residues that are surface exposed are Val-2, Phe-3, Leu-17, Phe-34, Leu-75, Trp-123, Pro-70, and Pro-79, with Trp-62, Trp-63, Ile-98, Trp-108, and Val-109 being on the surface of the cleft. Examples of the least-exposed ionizable side chains are Asp-66, Asp-52, Tyr-53, His-15, and Glu-35. 

The choice of exactly what surface area to calculate is, however, not entirely unambiguous. Although one might consider constructing a surface from standard atomic van der Waals radii, the more typical approach is to use the so-called solvent-accessible surface area (SASA)." 23,125 solvent-accessible surface is defined as that generated by the center of a spherical solvent molecule rolling on the van der Waals surface of the solute. A moment s reflection shows that this is the same as the exposed surface obtained by placing spheres at each of the atomic centers, where each sphere has a radius equal to the van der Waals radius of the atom plus the radius of a solvent molecule. For water, which is reasonably well approximated as a spherical solvent, the radius is usually taken as 1.4... 

The total S AS A calculated for both CT and CTWAT are lower relative to the X-ray structure while in CTMONO the SASA is increased relative to the X-ray structure.(Table 1) The protein, when placed in a non-aqueous media, have repositioned its solvent exposed side chains which results in a net reduction of SASA. Thus, the exposed surface area for the hydrophobic residues increased, while that of the polar residues decreased significantly. Both the CT and CTWAT systems experienced about 5% increase while CTMONO experiences a 4% increase for the SASA of the hydrophobic residues. This is in accord with the expectation of "like dissolves like". The hydrophobic side chains of CT reorient themselves on the surface and become more exposed to hexane, while the charged residues fold inward. 

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