Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins

Proteins: Structure, Function and Genetics

Volumn 33, Issue 1, 1998, Pages 18-29

  Liang, Jie ^a,b,d   Edelsbrunner, Herbert ^b   Fu, Ping ^a   Sudhakar, Pamidighantam V ^a   Subramaniam, Shankar ^a,c  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b Digital Computer Laboratory   (United States)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^d GLAXOSMITHKLINE   (United Kingdom)

Author keywords

Alpha shape; Delaunay complex; Molecular cavities; Packing defects; Structural solvent in proteins

Indexed keywords

ALGORITHM; ARTICLE; CONFORMATIONAL TRANSITION; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ALGORITHMS; BACTERIORHODOPSINS; MACROMOLECULAR SUBSTANCES; MATHEMATICAL COMPUTING; MODELS, MOLECULAR; MYOGLOBIN; PROTEIN CONFORMATION; RIBONUCLEASES;

EID: 0032189626     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H     Document Type: Article

References (50)

1. Kellis, J.T.J., Nyberg, K., and Fersht, A.R. Energetics of complementary side-chain packing in a protein hydrophobiccore. Biochemistry 28:4914-4922, 1989.
2. Eriksson, A.E., Baase, W.A., Wozniak, J.A., Mathews, B.M. A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene. Nature 355:371-373, 1992.
3. Erikson, A.E., Baase, W.A., Zhang, X.-J., Heinz, D.W., Baldwin, E.P., Mathews, B.M. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science 255:178-183, 1992.
4. Lambright, D.G., Balasubramanian, S., Decatur, S.M. Anatomy and dynamics of a ligand-binding pathway in myoglobin: The roles of residues 45, 60, 64, and 68. Biochemistry 33:5518-5525, 1994.
5. Lee, B., Richards, F.M. The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol. 55:379-400, 1971.
6. Rashin, A., Iofin, M., Honig, B. Internal cavities and buried waters in globular proteins. Biochemistry 25:3619-3625, 1986.
7. Hubbard, S.J., Gross, K.-H., Argos, P. Intramolecular cavities in globular proteins. Protein Eng. 7:613-626, 1994.
8. Hubbard, S.J., Argos, P. Cavities and packing at protein interfaces. Protein Sci. 3:2194-2206, 1994.
9. Ernst, J.A., Clubb, R.T., Zhou, H.X., Gronenborn, A.M., Clore, G.M. Demonstration of positionally disordered water within a protein hydrophobic cavity by nmr. Science 267:1813-1817, 1995.
10. Zhang, L., Hermans, J. Hydrophilicity of cavities in proteins. Proteins 24:433-438, 1996
11. Richards, F.M. Areas, volumes, packing, and protein structures. Annu. Rev. Biophys. Bioeng. 6:151-176, 1977.
12. Connolly, T. Analytical molecular surface calculation. J. Appl. Cryst. 16:548-558, 1983.
13. Edelsbrunner, H., Mücke, E. Three-dimensional alpha shapes. ACM Trans. Graphics 13:43-72, 1994.
14. Voronoi, G. Nouvelles applications des paramètres continus à la théorie des formes quadratiques. Premier mémoire: Sur quelques propriétés de formes quadratiques positives parfaites. Journal für die Reine und Angewandte Mathematik 133:97-178, 1907 (in French).
15. Edelsbrunner, H. The union of balls and its dual shape. Discrete Comput. Geom. 13:415-440, 1995.
16. Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P., Subramaniam, S. Analytic shape computation of macromolecules. I. Molecular area and volume through alpha shape. Proteins 32: 1998.
17. Perrot, G., Cheng, B., Gilson, K., Palmer, K., Nayeem, A., Maigret, B., Scheraga, H. MSEED: A program for the rapid analytical determination of accessible surface areas and their derivatives. J. Comp. Chem. 13:1-11, 1992.
18. Akkiraju, N., Edelsbrunner, H. Triangulating the surface of a molecule. Discrete Appl. Math. 71:5-54, 1996.
19. Bernatein, F.C., Koetzle, T.F.W., B., G.J., Meyer, E.J., Brice, M.D., Rogers, J.R., Kennerd, O., Shimanouchi, T. The protein data bank: A computer based archival file for macromolecular structures. J. Mol. Biol. 112:532-542, 1977.
20. Ansari, A., Jones, C.M., Henry, E.R. Conformational relaxation and ligand binding in myoglobin. Biochemistry 33: 5128-5145, 1994.
21. Nienhaus, G.U., Mourant, J.R., Chu, K. Ligand binding to heme proteins: The effect of light on ligand binding in myoglobin. Biochemistry 33:13413-13430, 1994.
22. Elber, R., Karplus, M. Enhanced sampling in molecular dynamics - Use of the time dependent hartree approximation for a simulation of carbon monoxide diffusion through myoglobin. J. Amer. Chem. Soc. 112:9161-9175, 1990.
23. Tilton, R.F., Kuntz, I.D., Petsko, G.A. Cavities in proteins: Structure of a myoglobin-xenon complex solved to 1.9 Å. Biochemistry 23:2849-2857, 1984.
24. Schoenborn, B.P. Binding of xenon to horse haemoglobin. Nature (London) 208:760-762,1965.
25. Schoenborn, B.P. Structure of alkaline metmyoglobin-xenon complex. J. Mol. Biol. 45:297-303, 1969.
26. Tilton, Jr., R.F., Kuntz, I.D. Jr. Nuclear magnetic resonance stidues of xenon-129 with myoglobin and hemoglobin. Biochemistry 21:6850-6857, 1982.
27. Hermans, J., Shankar, S. The free energy of xenon binding to myoglobin from molecular dynamics. Israel J. Chem. 27:225-227, 1986.
28. Varadarajan, R., Richards, F. Crystallographic structures of ribonuclease s variants with nonpolar substitution at position 13: Packing and cavities. Biochemistry 31:12315-12327, 1992.
29. Henderson, R., Baldwin, J.M., Ceska, T.A., Zemlin, F., Beckmann, E., Downing, K.H. Model for the structure of bacteriorhodopsin based on high-resolution electron cryomicroscopy. J. Mol. Biol 213:899-929, 1990.
30. Grigorieff, N., Ceska, T., Downing, K., Baldwin, J., Henderson, R. Electron-crystallographic refinement of the structure of bacteriorhodopsin. J. Mol. Biol. 259:393-421, 1996.
31. Mogi, T., Stern, L.J., Hackett, N.R., Khorana, H.G. Bacteriorhodopsin mutants containing single tyrosine to phenylalanine substitution are all active in proton translocation. Proc. Natl. Acad. Sci. USA 85:5595-5599, 1987.
32. Mogi, T., Stern, L.J., Marti, T., Chao, B.H., Khorana, H.G. Aspartic acid substitutions affect proton translocation by bacteriorhodopsin. Proc. Natl. Acad. Sci. USA 85:4148-4152, 1988.
33. Stern, L.J., Khorana, H.G. Structure-function studies on bacteriorhodopsin. Individual substitutions of Arg residues by Gln affect chromophore formation, photocylce and proton translocation. J. Biol. Chem. 264:14202-14208, 1989.
34. Greenlagh, D.A.C., Altenbach, C., Hubbel, W.L., Khorana, H.G. Location of Arg-82, Asp-85, and Asp-96 in helix C of bacteriorhodopsin relative to the aquesous boundaries. Proc. Natl. Acad. Sci. USA 88:8626-8630, 1991.
35. Marti, T., Otto, H., Mogi, T., Rosselet, S.J., Heyn, M.P., Khorana, H.G. Bacteriorhodopsin mutants containing single substitution of seine or threonine residues are all active in proton translocation. J. Biol. Chem. 266:6919-6927, 1991.
36. Rath, P., Marti, T., Sonar, S., Khorana, H.G., Rothschild, K.J. Hydrogen bonding interactions with the Schiff base of bacteriorhodopsin. Resonance Raman spectroscopy of the mutants D85N and D85A. J. Biol. Chem. 268:17742-17749, 1993.
37. leCoutre, J., Tittor, J., Oesterhelt, D. Experimental evidence for hydrogen-bonded network proton transfer in bacteriorhodopsin shown by Fourier-transform infrared spectroscopy using azide as catalyst. Proc. Natl. Acad. Sci. USA 92:4962-4966, 1995.
38. Hildebrandt, P., Stockburger, M. Role of water in bacteriorhodopsin's chromophore: Resonance Raman study. Biochemistry 23:5539-5548, 1984.
39. Harbison, G.S., Roberts, J.E., Herzfeld, J., Griffin, R.G. Solid state NMR detection of proton exchange between the bacteriorhodopsin Schiff base and bulk water. J. Am. Chem. Soc. 110:7221-7227, 1988.
40. Cao, Y., Varo, G., Chang, M., Ni. B., Needleman, R., Lanyi, J. Water is required for proton transfer from Asp96 to the bacteriorhodopsin Schiff base. Biochemistry 30:10972-10979, 1991.
41. Rothschild, K.J., He, Y.-W., Sonar, S., Marti, T., Khorana, H.G. Vibrational spectroscopy of bacteriorhodopsin mutants. Evidence that Thr-89 and Thr-89 form part of a transient network of hydrogen bonds. J. Biol. Chem. 267: 1615-1622, 1992.
42. Deng, H., Callender, R., Ebrey, T. Evidence for a bound water molecule next to the retinal Schiff base in bacteriorhodopsin and rhodopsin: A resonance Raman study of the Schiff base hydrogen/deuterium exchange. Biophys. J. 66: 1129-1136, 1994.
43. Humphrey, W., Loguno, I., Schulten, K., Sheves, M. Molecular dynamics study of bacteriorhodopsin and artificial pigments. Biochemistry 33:3668-3678, 1994.
44. Balashov, S.P., Imasheva, E.S., Govindjee, R., Ebrey, T.G. Titration of aspartate-85 in bacteriorhodopsin: What it says about chromophore isomerization and proton release. Biophys. J. 70:473-481, 1996.
45. a of the bacteriorhodopsin Schiff base by use of artificial retinal analogue. Proc. Natl. Acad. Sci. USA 86:3262-3266, 1986.
46. Subramaniam, S., Gerstein, M., Oesterhelt, D., Henderson, R. Electron diffraction analysis of structural changes in photocyle of bacteriorhodopsin. EMBO J. 12:1-8, 1993.
47. Varo, G., Lanyi, J.K. Effect of hydrostatic pressure on the kinetics reveal a volume increase in the bacteriorhodopsin photocyle. Biochem. 34:12161-12169, 1995.
48. Varo, G., Needleman, R., Lanyi, J.K. Protein structural change at the cytoplasmic surface as the cause of cooperativity in the bacteriorhodopsin photocycle. Biophys. J. 70: 461-467, 1996.
49. Cormen, T., Leiserson, C., Rivest, R. "Introduction to Algorithms." Cambridge, MA: MIT Press, 1990.
50. Edelsbrunner, H., Fu, P. Measuring space filling diagrams and voids. Rept. UIUC-BI-MB-94-01, Molecular Biophysics Group, Beckman Inst. Univ. Illinois, Urbana, IL, 1994.