Molecular Surfaces
11. Surface Biology, Chemistry and Physics

Michael L. Connolly

1259 El Camino Real, #184
Menlo Park, CA 94025
U.S.A.

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As would be expected from the origin of solvent-accessibility work, molecular and accessible surfaces have been applied to the study of solvation and hydrophobicity (Ooi, Oobatake, Nemethy and Scheraga, 1987). Martha Teeter (1991) has reviewed theoretrical and experimental work on protein-solvent interactions. Roe and Teeter (1993) have developed a method to predict the positions of water molecules near polar amino acid side chains. Colonna-Cesari and Sander (1990) have studied contacts between protein and solvent atoms. Solvent molecules in protein grooves are more fixed and so show up better in the electron density (Kuhn, Siani, Pique, Fisher, Getzoff and Tainer, 1992). Solvent-accessible area has been related to hydrophobicity (Tu–—n, Silla and Pascual-Ahuir, 1992) and hydrophilicity (Heiden, Moeckel and Brickmann, 1993). Jackson and Sternberg (1993) have studied the interaction between protein and solvent in the defining of protein surface area. Neutron diffraction has been applied to the study of the first hydration layer of the insulin protein (Badger, Kapulsky, Caspar and Korszun, 1995). Also see recent work by Michael Levitt's group at Stanford (Levitt and Park, 1993; Gerstein and Levitt, 1996). There is an interesting web page on HINT (Hydropathic INTeractions).

Solvent-accessibility calculations have been applied to the protein folding problem (Wang, Zhang and Scott, 1995), energy calculations and structure refinement. Delarue and Koehl (1995) have studied atomic accessible areas in relation to distinguishing correctly and incorrectly folded protein structures. Hydrophobic surface area has been incorporated into energy minimization calculations (von Freyberg and Braun 1993; von Freyberg, Richmond and Braun, 1993).

Tainer, Getzoff, Alexander, Houghten, Olson and Lerner (1984) have graphically displayed atomic mobility and related it to to the reactivity of anti-peptide antibodies. Geysen, Tainer, Rodda, Mason, Alexander, Getzoff and Lerner (1987) showed that antigenic regions tend to be mobile and convex. Novotny, Handschumacher, Haber, Bruccoleri, Carlson, Fanning, Smith and Rose (1986) have shown that antigenic regions are accessible to large probes.

Protein motions are related to surface areas and volumes, and can be visualized with molecular graphics. Sheriff, Hendrickson, Stenkamp, Sieker and Jensen (1985) have studied the relationship between solvent accessibility and atomic mobilities. Fisher, Tainer, Pique and Getzoff (1990) have visualized protein surface flexibility. Zheng, Wong and McCammon (1990) have studied fluctuation of solvent-accessible surface area during a molecular dynamics simulation. Islam and Weaver (1990) have studied the relationship between solvent accessible surface area and protein crystal stability. Gerstein, Sonnhammer and Chothia (1994) have studied protein volume changes not with motion, actually, but with evolution. Zachmann, Kast and Brickmann (1995) have visualized molecular surface flexibility.

Lastly, we consider molecular surfaces and electrostatics calculations. Lavery and Pullman, (1981) studied electrostatic potential on the solvent-accessible surface of DNA. Weiner, Langridge, Blaney, Schaeffer and Kollman (1982) mapped electrostatic potential onto the molecular dot surface. The solvent-accessibility of atoms has been used to the local dielectric constant of charged atoms on the protein surface (Matthew, 1985; Matthew and Ohlendorf, 1985). Various groups have colored the solvent-accessible or molecular surface by electrostatic potential: (Nakamura, Kusunoki and Yasuoka, 1984; Sjoberg, Murray, Brinck, Evans and Politzer, 1990). Visualizations of the electrostatic potential and electrostatic field have been produced by Getzoff, Tainer, Weiner, Kollman, Richardson and Richardson (1983), Lavery, Pullman and Pullman (1983), Purvis and Culberson (1986), and Hermsmeier and Gund (1989). The role of electrostatic recognition in the interaction of cytochrome c and cytochrome b5 has been studied (Salemme, 1977; Mauk, Mauk, Weber and Matthew, 1986; Northrup, Wensel, Meares, Wendoloski and Matthew, 1990). A protein docking method using electrostatics has been developed by Warwicker (1989). Naray-Szabo (1989) studied electrostatic complementarity in molecular associations. Namasivayam and Dean (1986) have studied matching molecules by their electrostatic surfaces. Klapper, Hagstrom, Fine, Sharp and Honig (1986) performed electrostatic calcultions on superoxide dismutase using different dielectrics for points inside or outside the molecular surface. The use of the Poisson-Boltzmann equation has been described (Gilson and Honig, 1988; Gilson, Davis, Luty and McCammon, 1993). Polyhedral electrostatic potential molecular surfaces have been computed by Zauhar and Morgan (1990) and by the Columbia group (Nicholls and Honig, 1991; Nicholls, Sharp and Honig, 1991; Nicholls, Bharadwaj and Honig, 1993).

[ 1. Introduction ] [ 2. Physical Molecular Models ] [ 3. Electron Density Fitting ] [ 4. Molecular Graphics ] [ 5. Solvent-Accessible Surfaces ] [ 6. Molecular Surface Graphics ] [ 7. Molecular Volume and Protein Packing ] [ 8. Shapes of Small Molecules and Proteins ] [ 9. Structure-based Drug Design ] [ 10. Protein-Protein Interactions ] [ *** 11. Surface Biology, Chemistry and Physics *** ] [ 12. Bibliography ]

All material in ths article Copyright © 1996 by Michael L. Connolly



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