Accessible surface areas

SASA Solvent-Accessible Surface Area Q . Average of absolule alomic charges... 

Richmond T J 1984. Solvent Accessible Surface Area and Excluded Volume in Proteins. Journal oj Molecular Biology 178 63-88. 

We conclude that the beneficial effects of water are not necessarily limited to reactions that are characterised by a negative volume of activation. We infer that, apart from the retro Diels-Alder reaction also other reactions, in which no significant reduction or perhaps even an increase of solvent accessible surface area takes place, can be accelerated by water. A reduction of the nonpolar nature during the activation process is a prerequisite in these cases. 

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... 

SAMI (semi-nh initio method one) a semiempirical method SASA (solvent-accessible surface area) algorithm for computing solvation elfects... 

Amino acid Three- letter code One- letter code Mass of residue in. b proteins Accessible surface area, 2 nm Hydrophobicity index ionizable side chain Occurrence in n/ proteins, /o Relative mutabihty... 

In service, supported catalysts frequentiy undergo loss of activity over a period of time. In many cases, such catalyst deactivation is accompanied by the loss of accessible surface area of the active phase by sintering, by the accumulation of poisons, or by conversion of active sites to inactive species. 

In the following sections, we describe an implicit solvent model based on this free energy decomposition that is widely used in biophysics. It consists in representing the nonpolar free energy contributions on the basis of the solvent-accessible surface area... 

In Section III we described an approximation to the nonpolar free energy contribution based on the concept of the solvent-accessible surface area (SASA) [see Eq. (15)]. In the SASA/PB implicit solvent model, the nonpolar free energy contribution is complemented by a macroscopic continuum electrostatic calculation based on the PB equation, thus yielding an approximation to the total free energy, AVP = A different implicit... 

Chuman, H., Mori, A., Tanaka, H., Yamagami, C., Fujita, T. Analyses of the partition coefficient, log P, using ah initio MO parameter and accessible surface area of solute molecules. J. Pharm. Sci. 2004, 93, 2681-2697. 

AGg (X) can be removed by assuming that it is equivalent to the polar contribution to the free energy of solution of solute X in a nonpolar hydrocarbon solvent, such as squalane. A second reason for using a reference hydrocarbon solvent is to correct, at least partially, for the fact that the hardcore van der Haals volume is a poor estimate of the size of the cavity and its accessible surface for solvent interactions for aromatic and cyclic solutes. The solvent accessible surface area would logically be the preferred parameter for the cavity term but is very difficult to calculate while the van der Haals volume is readily accessible. With the above approximations the solvent interaction term for... 

If this hypothesis is true, one could expect the solvent-accessible surface area (ASA) of the polypeptide backbone in the PPII conformation to be correlated with measured PPII helix-forming propensities. In order to test this, Monte Carlo computer simulations of short peptides Ac-Ala-Xaa-Ala-NMe (Xaa = Ala, Asn, Gin, Gly, lie, Leu, Met, Pro, Ser, Thr, and Val) were run. These particular residues were examined because their... 

PPII helix-forming propensities have been measured by Kelly et al. (2001) and A. L. Rucker, M. N. Campbell, and T. P. Creamer (unpublished results). In the simulations the peptide backbone was constrained to be in the PPII conformation, defined as (0,VO = ( — 75 25°, +145 25°), using constraint potentials described previously (Yun and Hermans, 1991 Creamer and Rose, 1994). The AMBER/ OPLS potential (Jorgensen and Tirado-Rives, 1988 Jorgensen and Severance, 1990) was employed at a temperature of 298° K, with solvent treated as a dielectric continuum of s = 78. After an initial equilibration period of 1 x 104 cycles, simulations were run for 2 x 106 cycles. Each cycle consisted of a number of attempted rotations about dihedrals equal to the total number of rotatable bonds in the peptide. Conformations were saved for analysis every 100 cycles. Solvent-accessible surface areas were calculated using the method of Richmond (1984) and a probe of 1.40 A radius. 

The sum of the estimated average solvent-accessible surface areas, (ASA), for the peptide units (—CO—NH—) on either side of residue Xaa, plus the Ca of Xaa, in each peptide simulated are given in Table II. Also shown are the estimated PPII helix-forming propensities for each residue measured by Kelly et al. (2001) and A. L. Rucker, M. N. Campbell, and... 

In (2.105), the assumption of the proportionality of solvent-accessible surface and cavity energy is explicitly shown, and therefore ak depends on the type of the k-atom interacting with the solvent. Ak(p ) is the complex function describing the solvent accessible surface area, and depends on p, which is defined by the following expression ... 

Fig. 12.4. Vapor-to-water transfer data for saturated hydrocarbons as a function of accessible surface area, from [131]. Standard states are 1M ideal gas and solution phases. Linear alkanes (small dots) are labeled by the number of carbons. Cyclic compounds (large dots) are a = cyclooctane, b = cycloheptane, c = cyclopentane, d = cyclohexane, e = methylcyclopentane, f = methylcyclohexane, g = cA-l,2-dimethylcyclohexane. Branched compounds (circles) are h = isobutane, i = neopentane, j = isopentane, k = neohexane, 1 = isohexane, m = 3-methylpentane, n = 2,4-dimethylpentane, o = isooctane, p = 2,2,5-tri-metbylhexane. Adapted with permission from [74], Copyright 1994, American Chemical Society...

However, just considering the individual properties of each amino acid type is not enough to determine its accessibility to the surrounding aqueous environment. There have been many attempts at developing analytical models with predictive value for determining buried or surface accessible amino acids in a folded polypeptide chain. These studies have concluded fractional assignments for each residue that relate to its accessible surface area (ASA) or its solvent exposed area (SEA). 

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