Solvent contact surface area

The solvent accessible surface area (SASA) method is built around the assumption that the greatest amount of interaction with the solvent is in the area very close to the solute molecule. This is accounted for by determining a surface area for each atom or group of atoms that is in contact with the solvent. The free energy of solvation AG° is then computed by... 

Hydrophobic binding. The hydrophobic effect can have both enthalpic and entropic components, although the classical hydrophobic effect is entropic in origin (Section 1.9.1). Studies on the associations between planar aromatic molecules show an approximately linear relationship between the interaction energy and their mutual contact surface area with slope 64 dyn cm-1, very close to the macroscopic surface tension of water (72 dyn cm-1). Hence, in the absence of specific host or guest interactions with the solvent the hydrophobic effect can be calculated solely from the energy required to create a free surface of 1 A2 which amounts to 7.2 X 10 12 J or 0.43 kjA 2 mol. ... 

Figure 2.8 illustrates the SAS concept as well as the method used for its determination. SASs are essentially computed by generating a three-dimensional, graphical representation of the dendrimer and computationally rolling probes (p) of various radii (r) over the surface. Intuitively, as well as physically, the larger the probe radius the less chance for contact the probe has within the internal void region of the dendrimer. For probes with a small radius, and in particular at the limit r = 0 A, the total internal surface area can be determined. Typically, the solvent accessible surface area ( Msas) is plotted versus probe radius or diameter. Thus, a measure of dendritic porosity can be derived. 

To further characterize the structural changes of goat a-lactalbumin during unfolding, we examined the probability distributions of the following four structural parameters in each of the nine clusters of the structural ensemble of MD trajectories (1) the fractional native contact (Q) of the entire molecule, (2) the RMSD of C atoms between a pair of structures that belong to the same cluster, (3) the solvent-accessible surface area (SASA) of hydrophobic side chains, and (4) the SASA of hydrophilic side chains [25]. 

A set of thirty different descriptors [Stanton and Jurs, 1990] which combine shape and electronic information to characterize molecules and therefore encode features responsible for polar interactions between molecules. The molecule representation used for deriving CPSA descriptors views molecule atoms as hard spheres defined by the - van der Waals radius. The - solvent-accessible surface area SASA is used as the molecular surface area it is calculated using a sphere with a radius of 1.5 A to approximate the contact surface formed when a water molecule interacts with the considered molecule. Moreover, the contact surface where polar interactions can take place is characterized by a specific electronic distribution obtained by mapping atomic partial charges on the solvent-accessible surface. 

Connolly surface The Connolly surface is the molecular surface related to the solvent accessible surface area but traced by the inward-facing part of a solvent probe model, represented by a sphere with a given radius, free to touch but not to penetrate the solute when the probe is rolled over its van der Waals surface. The surface combines the contact surface of a solute atom and the probe and the reentrant surface when the probe is in contact with more than one atom. 

As a second contribution to the final form of the PP term, we added a part for the solvent-accessible surface area (SASA). Beyond the molecular recognition in terms of preferred distances, the complementarity of shape constitutes an important descriptor for docking. This concept is well defined on considering the surface that is buried between two molecules, after their complexation. For this purpose, we previously developed an efficient way to calculate the SASA of our reduced models [67], and, consequently, of the interface of dimerization. Many articles are concerned with P-P dimers [68] to form stable complexes, the contact surface between two proteins is generally considered to exceed 1200 [69], but additional... 

Mobile phase parameters that have to be optimized include the salt type, concentration, gradient shape, pH, temperature, and possibly the addition of a surfactant or organic solvent [368-372]. The change in free energy on protein binding to the stationary phase is determined mainly by the contact surface area between the protein and stationary phase and by the salt type determined by its ability to increase the surface tension of aqueous solutions. Solvophobic theory predicts that in the absence of specific salt-protein interactions and at sufficient ionic strength the logarithm of the retention factor is linearly dependent on the surface tension of the mobile phase, which in turn, is a linear function of the salt concentration Eq. (4.13)... 

The interface area is a geometric quantity related to the solvent accessible surface area (Lee and Richards, 1971 Chothia and Janin, 1975). It can be easily derived from atomic coordinates of a complex between two macromolecules and provides a natural way to estimate the extent of their contact. It requires evaluating first the solvent accessible surface areadi2 of the complex, thenTi andd2, the surface areas of dissociated components ... 

The rolling sphere algorithm of Lee and Richards (1971) and a number of related algorithms yield the solvent accessible surface areas (Fig. 1). The radius of the solvent probe is near 1.5 A for water. The interface area B is the area of the protein surface that becomes buried at the interface when the two molecules associate, but, as the calculation uses only coordinates of the complex, it ignores conformation changes which may affect the accessible surface area of the components. The contribution of each molecule to B can be evaluated separately and is approximately equal to fr/2. Thus, other authors may prefer to quote values of fr/2 (Jones and Thornton, 1995, 1996). However, when the surfaces in contact have a strong curvature, the convex side tends to contribute more interface area than the concave side because accessible surface areas are measured one probe radius away from... 

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