Chapter 22.1. Protein surfaces and volumes: measurement and use

References

Acharya, R., Fry, E., Logan, D., Stuart, D., Brown, F., Fox, G. & Rowlands, D. (1990). The three-dimensional structure of foot-and-mouth disease virus. New aspects of positive-strand RNA viruses, edited by M. A. Brinton & S. X. Heinz, pp. 319–327. Washington DC: American Society for Microbiology.Google Scholar
Arnold, E. & Rossmann, M. G. (1990). Analysis of the structure of a common cold virus, human rhinovirus 14, refined at a resolution of 3.0 Å. J. Mol. Biol. 211, 763–801.Google Scholar
Baker, E. N. & Hubbard, R. E. (1984). Hydrogen bonding in globular proteins. Prog. Biophys. Mol. Biol. 44, 97–179.Google Scholar
Bernal, J. D. & Finney, J. L. (1967). Random close-packed hard-sphere model II. Geometry of random packing of hard spheres. Discuss. Faraday Soc. 43, 62–69.Google Scholar
Blake, C. C. F., Koenig, D. F., Mair, G. A., North, A. C. T., Phillips, D. C. & Sarma, V. R. (1965). Structure of hen egg-white lysozyme, a three-dimensional Fourier synthesis at 2 Å resolution. Nature (London), 206, 757–761.Google Scholar
Bondi, A. (1964). van der Waals volumes and radii. J. Phys. Chem. 68, 441–451.Google Scholar
Bondi, A. (1968). Molecular crystals, liquids and glasses. New York: Wiley.Google Scholar
Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983). CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4, 187–217.Google Scholar
Chandler, D., Weeks, J. D. & Andersen, H. C. (1983). van der Waals picture of liquids, solids, and phase transformations. Science, 220, 787–794.Google Scholar
Chapman, M. S. (1993). Mapping the surface properties of macromolecules. Protein Sci. 2, 459–469.Google Scholar
Chapman, M. S. (1994). Sequence similarity scores and the inference of structure/function relationships. Comput. Appl. Biosci. (CABIOS), 10, 111–119.Google Scholar
Chothia, C. (1975). Structural invariants in protein folding. Nature (London), 254, 304–308.Google Scholar
Chothia, C. (1976). The nature of the accessible and buried surfaces in proteins. J. Mol. Biol. 105, 1–12.Google Scholar
Chothia, C. & Janin, J. (1975). Principles of protein–protein recognition. Nature (London), 256, 705–708.Google Scholar
Connolly, M. (1986). Measurement of protein surface shape by solid angles. J. Mol. Graphics, 4, 3–6.Google Scholar
Connolly, M. L. (1983). Analytical molecular surface calculation. J. Appl. Cryst. 16, 548–558.Google Scholar
Connolly, M. L. (1991). Molecular interstitial skeleton. Comput. Chem. 15, 37–45.Google Scholar
Diamond, R. (1974). Real-space refinement of the structure of hen egg-white lysozyme. J. Mol. Biol. 82, 371–391.Google Scholar
Dunfield, L. G., Burgess, A. W. & Scheraga, H. A. (1979). J. Phys. Chem. 82, 2609.Google Scholar
Edelsbrunner, H., Facello, M. & Liang, J. (1996). On the definition and construction of pockets in macromolecules, pp. 272–287. Singapore: World Scientific.Google Scholar
Edelsbrunner, H., Facello, M., Ping, F. & Jie, L. (1995). Measuring proteins and voids in proteins. Proc. 28th Hawaii Intl Conf. Sys. Sci. pp. 256–264.Google Scholar
Edelsbrunner, H. & Mucke, E. (1994). Three-dimensional alpha shapes. ACM Trans. Graphics, 13, 43–72.Google Scholar
Eisenberg, D. & McLachlan, A. D. (1986). Solvation energy in protein folding and binding. Nature (London), 319, 199–203.Google Scholar
Fauchere, J.-L. & Pliska, V. (1983). Hydrophobic parameters π of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides. Eur. J. Med. Chem. Chim. Ther. 18, 369–375.Google Scholar
Finkelstein, A. (1994). Implications of the random characteristics of protein sequences for their three-dimensional structure. Curr. Opin. Struct. Biol. 4, 422–428.Google Scholar
Finney, J. L. (1975). Volume occupation, environment and accessibility in proteins. The problem of the protein surface. J. Mol. Biol. 96, 721–732.Google Scholar
Finney, J. L., Gellatly, B. J., Golton, I. C. & Goodfellow, J. (1980). Solvent effects and polar interactions in the structural stability and dynamics of globular proteins. Biophys. J. 32, 17–33.Google Scholar
Fritz-Wolf, K., Schnyder, T., Wallimann, T. & Kabsch, W. (1996). Structure of mitochondrial creatine kinase. Nature (London), 381, 341–345.Google Scholar
Gelin, B. R. & Karplus, M. (1979). Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment. Biochemistry, 18, 1256–1268.Google Scholar
Gellatly, B. J. & Finney, J. L. (1982). Calculation of protein volumes: an alternative to the Voronoi procedure. J. Mol. Biol. 161, 305–322.Google Scholar
Gerstein, M. (1992). A resolution-sensitive procedure for comparing surfaces and its application to the comparison of antigen-combining sites. Acta Cryst. A48, 271–276.Google Scholar
Gerstein, M. & Chothia, C. (1996). Packing at the protein–water interface. Proc. Natl Acad. Sci. USA, 93, 10167–10172.Google Scholar
Gerstein, M., Lesk, A. M., Baker, E. N., Anderson, B., Norris, G. & Chothia, C. (1993). Domain closure in lactoferrin: two hinges produce a see-saw motion between alternative close-packed interfaces. J. Mol. Biol. 234, 357–372.Google Scholar
Gerstein, M., Lesk, A. M. & Chothia, C. (1994). Structural mechanisms for domain movements. Biochemistry, 33, 6739–6749.Google Scholar
Gerstein, M. & Lynden-Bell, R. M. (1993a). Simulation of water around a model protein helix. 1. Two-dimensional projections of solvent structure. J. Phys. Chem. 97, 2982–2991.Google Scholar
Gerstein, M. & Lynden-Bell, R. M. (1993b). Simulation of water around a model protein helix. 2. The relative contributions of packing, hydrophobicity, and hydrogen bonding. J. Phys. Chem. 97, 2991–2999.Google Scholar
Gerstein, M. & Lynden-Bell, R. M. (1993c). What is the natural boundary for a protein in solution? J. Mol. Biol. 230, 641–650.Google Scholar
Gerstein, M., Sonnhammer, E. & Chothia, C. (1994). Volume changes on protein evolution. J. Mol. Biol. 236, 1067–1078.Google Scholar
Gerstein, M., Tsai, J. & Levitt, M. (1995). The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. J. Mol. Biol. 249, 955–966.Google Scholar
Grant, J. A. & Pickup, B. T. (1995). A Gaussian description of molecular shape. J. Phys. Chem. 99, 3503–3510.Google Scholar
Greer, J. & Bush, B. L. (1978). Macromolecular shape and surface maps by solvent exclusion. Proc. Natl Acad. Sci. USA, 75, 303–307.Google Scholar
Harber, J., Bernhardt, G., Lu, H.-H., Sgro, J.-Y. & Wimmer, E. (1995). Canyon rim residues, including antigenic determinants, modulate serotype-specific binding of polioviruses to mutants of the poliovirus receptor. Virology, 214, 559–570.Google Scholar
Harpaz, Y., Gerstein, M. & Chothia, C. (1994). Volume changes on protein folding. Structure, 2, 641–649.Google Scholar
Hermann, R. B. (1977). Use of solvent cavity area and number of packed solvent molecules around a solute in regard to hydrocarbon solubilities and hydrophobic interactions. Proc. Natl Acad. Sci. USA, 74, 4144–4195.Google Scholar
Hubbard, S. J. & Argos, P. (1994). Cavities and packing at protein interfaces. Protein Sci. 3, 2194–2206.Google Scholar
Hubbard, S. J. & Argos, P. (1995). Evidence on close packing and cavities in proteins. Curr. Opin. Biotechnol. 6, 375–381.Google Scholar
Kapp, O. H., Moens, L., Vanfleteren, J., Trotman, C. N. A., Suzuki, T. & Vinogradov, S. N. (1995). Alignment of 700 globin sequences: extent of amino acid substitution and its correlation with variation in volume. Protein Sci. 4, 2179–2190.Google Scholar
Kauzmann, W. (1959). Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14, 1–63.Google Scholar
Kelly, J. A., Sielecki, A. R., Sykes, B. D., James, M. N. & Phillips, D. C. (1979). X-ray crystallography of the binding of the bacterial cell wall trisaccharaide NAM-NAG-NAM to lysozymes. Nature (London), 282, 875–878.Google Scholar
Kim, K. H., Willingmann, P., Gong, Z. X., Kremer, M. J., Chapman, M. S., Minor, I., Oliveira, M. A., Rossmann, M. G., Andries, K., Diana, G. D., Dutko, F. J., McKinlay, M. A. & Pevear, D. C. (1993). A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A. J. Mol. Biol. 230, 206–227.Google Scholar
Kleywegt, G. J. & Jones, T. A. (1994). Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Cryst. D50, 178–185.Google Scholar
Kocher, J. P., Prevost, M., Wodak, S. J. & Lee, B. (1996). Properties of the protein matrix revealed by the free energy of cavity formation. Structure, 4, 1517–1529.Google Scholar
Kraulis, P. J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946–950.Google Scholar
Kuhn, L. A., Siani, M. A., Pique, M. E., Fisher, C. L., Getzoff, E. D. & Tainer, J. A. (1992). The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures. J. Mol. Biol. 228, 13–22.Google Scholar
Lee, B. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379–400.Google Scholar
Leicester, S. E., Finney, J. L. & Bywater, R. P. (1988). Description of molecular surface shape using Fourier descriptors. J. Mol. Graphics, 6, 104–108.Google Scholar
Levitt, M., Hirshberg, M., Sharon, R. & Daggett, V. (1995). Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comput. Phys. Comm. 91, 215–231.Google Scholar
Lewis, M. & Rees, D. C. (1985). Fractal surfaces of proteins. Science, 230, 1163–1165.Google Scholar
Lim, V. I. & Ptitsyn, O. B. (1970). On the constancy of the hydrophobic nucleus volume in molecules of myoglobins and hemoglobins. Mol. Biol. (USSR), 4, 372–382.Google Scholar
Madan, B. & Lee, B. (1994). Role of hydrogen bonds in hydrophobicity: the free energy of cavity formation in water models with and without the hydrogen bonds. Biophys. Chem. 51, 279–289.Google Scholar
Matthews, B. W., Morton, A. G. & Dahlquist, F. W. (1995). Use of NMR to detect water within nonpolar protein cavities. (Letter.) Science, 270, 1847–1849.Google Scholar
Merritt, E. A. & Bacon, D. J. (1997). Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505–525.Google Scholar
Molecular Structure Corporation (1995). Insight II user guide. Biosym/MSI, San Diego.Google Scholar
Nemethy, G., Pottle, M. S. & Scheraga, H. A. (1983). Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions and hydrogen bond interactions for the naturally occurring amino acids. J. Phys. Chem. 87, 1883–1887.Google Scholar
Nicholls, A. (1992). GRASP: graphical representation and analysis of surface properties. New York: Columbia University.Google Scholar
Nicholls, A. & Honig, B. (1991). A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson–Boltzmann equation. J. Comput. Chem. 12, 435–445.Google Scholar
Nicholls, A., Sharp, K. & Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins, 11, 281–296.Google Scholar
Olson, N., Kolatkar, P., Oliveira, M. A., Cheng, R. H., Greve, J. M., McClelland, A., Baker, T. S. & Rossmann, M. G. (1993). Structure of a human rhinovirus complexed with its receptor molecule. Proc. Natl Acad. Sci. USA, 90, 507–511.Google Scholar
O'Rourke, J. (1994). Computational geometry in C. Cambridge University Press.Google Scholar
Palmenberg, A. C. (1989). Sequence alignments of picornaviral capsid proteins. In Molecular aspects of picornavirus infection and detection, edited by B. L. Semler & E. Ehrenfeld, pp. 211–241. Washington DC: American Society for Microbiology.Google Scholar
Pattabiraman, N., Ward, K. B. & Fleming, P. J. (1995). Occluded molecular surface: analysis of protein packing. J. Mol. Recognit. 8, 334–344.Google Scholar
Pauling, L. (1960). The nature of the chemical bond, 3rd ed. Ithaca: Cornell University Press. Google Scholar
Peters, K. P., Fauck, J. & Frommel, C. (1996). The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. J. Mol. Biol. 256, 201–213.Google Scholar
Petitjean, M. (1994). On the analytical calculation of van der Waals surfaces and volumes: some numerical aspects. J. Comput. Chem. 15, 1–10.Google Scholar
Pontius, J., Richelle, J. & Wodak, S. J. (1996). Deviations from standard atomic volumes as a quality measure for protein crystal structures. J. Mol. Biol. 264, 121–136.Google Scholar
Procacci, P. & Scateni, R. (1992). A general algorithm for computing Voronoi volumes: application to the hydrated crystal of myoglobin. Int. J. Quant. Chem. 42, 151–152.Google Scholar
Rashin, A. A., Iofin, M. & Honig, B. (1986). Internal cavities and buried waters in globular proteins. Biochemistry, 25, 3619–3625.Google Scholar
Reynolds, J. A., Gilbert, D. B. & Tanford, C. (1974). Empirical correlation between hydrophobic free energy and aqueous cavity surface area. Proc. Natl Acad. Sci. USA, 71, 2925–2927.Google Scholar
Richards, F. M. (1974). The interpretation of protein structures: total volume, group volume distributions and packing density. J. Mol. Biol. 82, 1–14.Google Scholar
Richards, F. M. (1977). Areas, volumes, packing, and protein structure. Annu. Rev. Biophys. Bioeng. 6, 151–176.Google Scholar
Richards, F. M. (1979). Packing defects, cavities, volume fluctuations, and access to the interior of proteins. Including some general comments on surface area and protein structure. Carlsberg Res. Commun. 44, 47–63.Google Scholar
Richards, F. M. (1985). Calculation of molecular volumes and areas for structures of known geometry. Methods Enzymol. 115, 440–464.Google Scholar
Richards, F. M. & Lim, W. A. (1994). An analysis of packing in the protein folding problem. Q. Rev. Biophys. 26, 423–498.Google Scholar
Richmond, T. J. (1984). Solvent accessible surface area and excluded volume in proteins: analytical equations for overlapping spheres and implications for the hydrophobic effect. J. Mol. Biol. 178, 63–89.Google Scholar
Richmond, T. J. & Richards, F. M. (1978). Packing of alpha-helices: geometrical constraints and contact areas. J. Mol. Biol. 119, 537–555.Google Scholar
Rossmann, M. G. (1989). The canyon hypothesis. J. Biol. Chem. 264, 14587–14590.Google Scholar
Rossmann, M. G. & Palmenberg, A. C. (1988). Conservation of the putative receptor attachment site in picornaviruses. Virology, 164, 373–382.Google Scholar
Rowland, R. S. & Taylor, R. (1996). Intermolecular nonbonded contact distances in organic crystal structures: comparison with distances expected from van der Waals radii. J. Phys. Chem. 100, 7384–7391.Google Scholar
Sgro, J.-Y. (1996). Virus visualization. In Encyclopedia of virology plus (CD-ROM version), edited by R. G. Webster & A. Granoff. San Diego: Academic Press.Google Scholar
Sharp, K. A., Nicholls, A., Fine, R. F. & Honig, B. (1991). Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science, 252, 107–109.Google Scholar
Sherry, B., Mosser, A. G., Colonno, R. J. & Rueckert, R. R. (1986). Use of monoclonal antibodies to identify four neutralization immunogens on a common cold picornavirus, human rhinovirus 14. J. Virol. 57, 246–257.Google Scholar
Sherry, B. & Rueckert, R. (1985). Evidence for at least two dominant neutralization antigens on human rhinovirus 14. J. Virol. 53, 137–143.Google Scholar
Shrake, A. & Rupley, J. A. (1973). Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J. Mol. Biol. 79, 351–371.Google Scholar
Sibbald, P. R. & Argos, P. (1990). Weighting aligned protein or nucleic acid sequences to correct for unequal representation. J. Mol. Biol. 216, 813–818.Google Scholar
Singh, R. K., Tropsha, A. & Vaisman, I. I. (1996). Delaunay tessellation of proteins: four body nearest-neighbor propensities of amino acid residues. J. Comput. Biol. 3, 213–222.Google Scholar
Sreenivasan, U. & Axelsen, P. H. (1992). Buried water in homologous serine proteases. Biochemistry, 31, 12785–12791.Google Scholar
Tanford, C. (1997). How protein chemists learned about the hydrophobicity factor. Protein Sci. 6, 1358–1366.Google Scholar
Tanford, C. H. (1979). Interfacial free energy and the hydrophobic effect. Proc. Natl Acad. Sci. USA, 76, 4175–4176.Google Scholar
Ten Eyck, L. F. (1977). Efficient structure-factor calculation for large molecules by the fast Fourier transform. Acta Cryst. A33, 486–492.Google Scholar
Tsai, J., Gerstein, M. & Levitt, M. (1996). Keeping the shape but changing the charges: a simulation study of urea and its isosteric analogues. J. Chem. Phys. 104, 9417–9430.Google Scholar
Tsai, J., Gerstein, M. & Levitt, M. (1997). Estimating the size of the minimal hydrophobic core. Protein Sci. 6, 2606–2616.Google Scholar
Tsai, J., Taylor, R., Chothia, C. & Gerstein, M. (1999). The packing density in proteins: standard radii and volumes. J. Mol. Biol. 290, 253–266.Google Scholar
Tsai, J., Voss, N. & Gerstein, M. (2001). Voronoi calculations of protein volumes: sensitivity analysis and parameter database. Bioinformatics. In the press.Google Scholar
Voronoi, G. F. (1908). Nouvelles applications des paramétres continus à la théorie des formes quadratiques. J. Reine Angew. Math. 134, 198–287.Google Scholar
Williams, M. A., Goodfellow, J. M. & Thornton, J. M. (1994). Buried waters and internal cavities in monomeric proteins. Protein Sci. 3, 1224–1235.Google Scholar
Wodak, S. J. & Janin, J. (1980). Analytical approximation to the accessible surface areas of proteins. Proc. Natl Acad. Sci. USA, 77, 1736–1740.Google Scholar
Xie, Q. & Chapman, M. S. (1996). Canine parvovirus capsid structure, analyzed at 2.9 Å resolution. J. Mol. Biol. 264, 497–520.Google Scholar
Zhou, G., Somasundaram, T., Blanc, E., Parthasarathy, G., Ellington, W. R. & Chapman, M. S. (1998). Transition state structure of arginine kinase: implications for catalysis of bimolecular reactions. Proc. Natl Acad. Sci. USA, 95, 8449–8454.Google Scholar