Solvent Accessible Surface Area ASas

In 1990, it had been proposed1851 that the repetitive, generational, branching topology inherent in dendritic structures could be characterized as being fractal. Support for this conjecture was provided by a computational1861 examination of the solvent accessible surface area (ASas) of dendrimers at different generations. 

These curves thus suggest an open and vacuous structure characterized by dynamic channels and pockets. The solvent accessible surface area, as measured for the first generation 12-acid, indicates a non-porous structure possessing little or no void regions as evidenced by experimental values falling below the ideal surface area. Data for the second generation 36-acid reveal a structure intermediate between dendritic and simply branched . 

GEPOU87 Sovent Accessible Surface (Area) as a Function of Probe Radius 

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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... 

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... 

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). 

The strategy used in this review to dissect specific fundamental interactions is to isolate first the hydrophobic effects and subsequently other interactions. Within this context the hydrophobic effect is defined as that contribution to the overall thermodynamics of a process that is proportional to the amount of apolar surface that becomes exposed to the solvent (Hermann, 1972 Gill and Wadso, 1976 Livingstone etal, 1991). The apolar surface area exposed to solvent can be computed using various algorithms (Lee and Richards, 1971 Hermann, 1972 Shrake and Rupley, 1973 Connolly, 1983) that yield the accessible surface area (ASA) in units of square angstroms (A2). 

Vadja and Camacho [69] concluded that in rigid-body docking the best docking results were obtained for complexes with a standard interface area of 1400 A2 < I asA < 2000 A2 (where ASAA indicates changes in solvent accessible surface after separation of the complex). 

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