Accessible surface area

The accessible surface area (ASA) is the surface area of a biomolecule (protein, DNA, etc.) that is accessible to a solvent. The ASA is usually quoted in square ångstrom (a standard unit of measurement in molecular biology). ASA was first described by Lee & Richards in 1971 is sometimes called the Lee-Richards molecular surface.^[1] ASA is typically calculated using the 'rolling ball' algorithm developed by Shrake & Rupley in 1973.^[2] This algorithm uses a sphere (of solvent) of a particular radius to 'probe' the surface of the molecule. The choice of the 'probe radius' does have an effect on the observed surface area, as using a smaller probe radius detects more surface details and therefore reports a larger surface. A typical value is 1.4Å, which approximates the radius of a water molecule. Another factor that affects the results is the definition of the VDW radii of the atoms in the molecule under study. For example, the molecule may often lack hydrogen atoms which are implicit in the structure. The hydrogen atoms may be implicitly included in the atomic radii of the 'heavy' atoms, with a measure called the 'group radii'.

The ASA is closely related to the concept of the solvent-excluded surface (also known as the molecular surface or Connolly surface), which is imagined as a cavity in bulk solvent (effectively the inverse of the solvent-accessible surface). It is also calculated in practice via a rolling-ball algorithm developed by Frederic Richards^[3] and independently implemented three-dimensionally by Michael Connolly in 1983^[4] and Tim Richmond in 1984.^[5] Connolly spent several more years perfecting the method^[6] and it is thus sometimes called the Connolly surface.

See also

• Implicit solvation
• Van der Waals surface

References

1. ^ Lee B, Richards FM. (1971). The interpretation of protein structures: estimation of static accessibility. J Mol Biol 55(3):379-400. doi:10.1016/0022-2836(71)90324-X
2. ^ Shrake A, Rupley JA. (1973). Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J Mol Biol 79(2):351-71. doi:10.1016/0022-2836(73)90011-9
3. ^ Richards FM. (1977). "Areas, volumes, packing and protein structure." Annu Rev Biophys Bioeng, 6:151–176. doi:10.1146/annurev.bb.06.060177.001055
4. ^ M. L. Connolly. "Analytical molecular surface calculation." J Appl Cryst, 16(5):548–558, Oct 1983. doi:10.1107/S0021889883010985
5. ^ T. J. Richmond. "Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect." J Mol Biol, 178(1):63–89, Sep 1984. doi:10.1016/0022-2836(84)90231-6
6. ^ M. L. Connolly. "The molecular surface package." J Mol Graphics, 11(2):139-141, Oct 1992. doi:10.1016/0263-7855(93)87010-3

Further reading

• Connolly,M.L. "solvent-accessible surfaces of proteins and nucleic-acids" (1983) Science, 221, 709–713
• Connolly, M.L. et al. "Molecular interstitial skeleton," 1991.
• Sanner, M.F. et al. "Modelling and Applications of Molecular Surfaces," PhD, 1992.
• Connolly, M.L. et al. "Shape distributions of protein topography," 1992.
• Blaney, J. M. et al. "Distance Geometry in Molecular Modeling," 1994.
• Boissonnat, J.-D. et al. "Computing Connolly Surfaces," 1994
• Connolly, M.L. et al. "Molecular Surfaces: A Review," 1996.
• Lin, S. L. et al. "Molecular surface representations by sparse critical points," 1994.
• Connolly, M.L. et al. "Molecular Surfaces: Calculations, Uses and Representations," 2001.
• Gerstein, M & Richards, F.S. "Protein Geometry: Distances, Areas, and Volumes," 2001
• Voss, N.R. et al. "The Geometry. of the Polypeptide Exit Tunnel," 2006

External links

• NetSurfP - Secondary Structure and Surface Accessibility predictor – Free for academic use
• Network Science, Part 5: Solvent-Accessible Surfaces
• Michel Sanner's Molecular Surface – the fastest program to calculate the excluded surface.
• Molecular Surface Package — Michael Connolly's program.
• Volume Voxelator — A web-based tool to generate excluded surfaces.
• AREAIMOL is a command line tool in the CCP4 Program Suite for calculating ASA.
• pov4grasp render molecular surfaces.
• NACCESS solvent accessible area calculations.
• Surface RacerOleg Tsodikov's Surface Racer program. Fast, exact and easy-to-use solvent accessible and molecular surface area and average curvature calculation. Free for academic use.