Accessibility to internal cavities and ligand binding sites monitored by protein crystallographic thermal factors

Proteins: Structure, Function and Genetics

Volumn 31, Issue 2, 1998, Pages 201-213

  Carugo, Oliviero ^a,b   Argos, Patrick ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b UNIVERSITY OF PAVIA   (Italy)

Author keywords

Accessibility to internal cavities; Crystallographic thermal factors; Ligand binding; Protein dynamic; Protein structure

Indexed keywords

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; HYDROPHOBICITY; LIGAND BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SITE DIRECTED MUTAGENESIS; STRUCTURE ANALYSIS; THERMODYNAMICS;

ANIMALS; BACTERIOPHAGE T4; BINDING SITES; CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; LIGANDS; MODELS, MOLECULAR; MOTION; MURAMIDASE; MUTAGENESIS, SITE-DIRECTED; MYOGLOBIN; OXYGEN; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT FUSION PROTEINS; SOLUTIONS; TEMPERATURE; VIRAL PROTEINS; WHALES;

CETACEA; PHYSETER CATODON;

EID: 0032080521     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980501)31:2<201::AID-PROT9>3.0.CO;2-O     Document Type: Article

References (64)

1. Ogata, K., Kanei-Ishii, C., Sasaki, M., et al. The cavity in the hydrophobic core of Myb DNA-binding domain is reserved for DMA recognition and trans-activation. Nature Struct. Biol. 3:178-187, 1996.
2. Denisov, V.P., Peters, J., Horlein, H.D., Halle, B. Using buried water molecules to explore the energy landscape of proteins. Nature Struct. Biol. 3:505-509, 1996.
3. Feher, V.A., Baldwin, E.P., Dahlquist, W. Access of ligand to cavities within the core of a protein is rapid. Nature Struct. Biol. 3:516-521, 1996
4. Frauenfelder, H., Sligar, S.G., Wolynes, P.G. The energy landscapes and motions of proteins. Science 254:1598-1603, 1991.
5. Ringe, D., Petsko, G.A. Study of protein dynamics by X-ray diffraction. Methods Enzymol. 131:389-433, 1986.
6. Karplus, M. Internal dynamics of proteins. Methods Enzymol. 131:283-307, 1986.
7. Chothia, C., Lesk, A., Dodson, G.G., Hodgkin, D.C. Transmission of conformational change in insulin. Nature 302: 500-505, 1983.
8. Lesk, A., Chothia, C. Mechanisms of domain closure in proteins. J. Mol. Biol. 174:175-191, 1984.
9. Gerstein, M., Lesk, A., Chothia, C. Structural mechanism for domain movements in proteins. Biochemistry 22:6739-6749, 1991.
10. Bryant, R.G. The dynamics of water-protein interactions. Annu. Rev. Biophys. Biomol. Struct. 25:29-53, 1996.
11. Mozzarelli, A., Rossi, G.L. Protein function in the crystal. Annu Rev. Biophys. Biomol. Struct. 25:343-365, 1996.
12. Trueblood, K.N., Bürgi, H.B., Burzlaff, H., et al. Atomic displacement parameter nomenclature: Report of a subcommittee on atomic displacement parameter nomenclature. Acta Crystallogr. A52:770-781, 1996.
13. Bürgi, H.B., Dunitz, J.D. "Structure Correlation." Weinheim, Germany: VCH Verlagsgesellschaft, 1994.
14. Domenicano, A., Hargittai, I. "Accurate Molecular Structures." Oxford, UK: Oxford University Press, 1992.
15. Giacovazzo, C. "Fundamentals of Crystallography." Oxford, UK: Oxford University Press, 1992.
16. Glusker, J.P., Lewis, M., Rossi, M. "Crystal Structure Analysis for Chemists and Biologists." New York: VCH Publishers, 1994.
17. Lionetti, C., Guanziroli, M.G., Frigerio, F., Ascenzi, P., Bolognesi, M. X-ray crystal structure of the ferric sperm whale myoglobin: Imidazole complex at 2.0 Å resolution. J. Mol. Biol. 217:409-412, 1991.
18. Lim, M., Jacksin, T.A., Anfinrud, P.A. Ultrafast rotation and trapping of carbon monoxide dissociated from myoglobin. Nature Struct. Biol. 4:209-214, 1997.
19. Srajer, V., Teng, T., Ursby, T., et al. Photolysis of the carbon monoxide complex of myoglobin: Nanosecond time-resolved crystallography. Science 274:1726-1729, 1996.
20. Vitkup, D., Petsko, G.A., Karplus, M. A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin. Nature Struct. Biol. 4:202-208, 1997.
21. Case, D.A., Karplus, M. Dynamics of ligand binding to heme proteins. J. Mol. Biol. 132:343-368, 1979.
22. Bolognesi, M., Cannillo, E., Ascenzi, P., Giacometti, G.M., Merli, A., Brunori, M. Reactivity of ferric Aplysia and sperm whale myoglobins towards imidazole: X-ray and binding study. J. Mol. Biol. 65:305-315, 1982.
23. Ringe, D., Petsko, G.A., Kerr, D.E., Ortiz de Montellano, P.R. Reaction of myoglobin with phenylhydrazine: A molecular doorstop. Biochemistry 23:2-4, 1984.
24. Johnson, K.A. "High-Resolution X-Ray Structures of Myoglobin and Hemoglobin-Alkyl Isocyanide Complexes." Doctoral thesis, Rice University, Houston, TX, USA, 1993.
25. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., et al. The protein databank: Computer-based archival file for macro-molecular structure. J. Mol. Biol. 112:535-542, 1977.
26. Eisenhaber, F., Lijnzaad, P., Argos, P., Sander, C., Scharf, M. The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J. Comput. Chem. 16:273-284, 1995.
27. Hubbard, S.J., Argos, P. Detection of internal cavities in globular proteins. Protein Eng. 10:1011-1015, 1996.
28. Frishman, D., Argos, P. Knowledge-based secondary structure assignment. Proteins 23:566-579, 1995.
29. Laskowski, R.A. SURFNET: A program for visualizing molecular surfaces, cavities and intermolecular interactions. J. Mol. Graph. 13:323-330, 1995.
30. Kabsch, W. A discussion of the best solution of the best rotation to relate two sets of vectors. Acta Crystallogr. A34:828-828, 1978.
31. McLachan, A.D. Gene duplication in the structural evolution of chymotrypsin. J. Mol. Biol. 128:48-67, 1979.
32. McDonald, I.K., Thornton, J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238:777-793, 1994.
33. Gandini, D., Gogioso, L., Bolognesi, M., Bordo, D. Patterns in ionizable side chain interactions in protein structures. Proteins 24:439-449, 1996.
34. Tronrud, D.E. Knowledge-based B-factor restraints for the refinement of proteins. J. Appl. Crystallogr. 29:100-104, 1996.
35. Schlichtig, I., Berendzen, J., Phillips, G.N. Jr, Sweet, R.M. Crystal structure of photolysed carbomonoxy myoglobin. Nature 371:808-810, 1994.
36. Sato, T., Tanaka, N., Moryiama, H., et al. Authors of the PDB file. 1993.
37. Eriksson, A.E., Baase, W.A., Wozniak, J.A., Matthews, B.W. The cavity-containing mutant of T4 lysozyme is stabilized by buried benzene. Nature 355:371-373, 1992.
38. Morton, A., Baase, W.A., Matthews, B.W. Energetic origins of specificity of ligand binding in an internal nonpolar cavity of T4 lysozyme. Biochemistry 34:8564-8575, 1995.
39. Morton, A., Matthews, B.W. Specificity of ligand binding in a burial nonpolar cavity of T4 lysozyme: Linkage of dynamics and structural plasticity. Biochemistry 34:8576-8588, 1995.
40. Antonini, E., Brunori, M. "Hemoglobin and Myoglobin in Their Reactions With Ligands." Amsterdam: Elsevier/North-Holland, 1971.
41. Kuriyan, J., Wilz, S., Karplus, M., Petsko, G.A. X-ray structure and refinement of carbo-monoxy (Fe(II))-myoglobin at 1.5 angstroms resolution. J. Mol. Biol. 192:133-154, 1986.
42. Austin, R.H., Beeson, K.W., Eisenstein, L., Frauenfelder, H., Gonsalus, I.C. Dynamics of ligand binding to myoglobins. Biochemistry 14:5355-5373, 1975.
43. Trueblood, K.N. Diffraction studies of molecular motion in crystals. In: "Accurate Molecular Structures." Domenicano, A., Hargittai, I. (eds.). Oxford, U.K.: Oxford University Press, 1992:199-219.
44. Cruickshank, D.W.J. The analysis of the anisotropic thermal motion of molecules in crystals. Acta Crystallogr. 9:754-756, 1959.
45. Schomaker, V., Trueblood, K.N. On the rigid-body motion of molecules in crystals. Acta Crystallogr. 624:63-76, 1968.
46. Janin, J., Rodier, F. Protein-protein interaction at crystal contacts. Proteins 23:580-587, 1995.
47. Carugo, O., Argos, P. Protein crystal packing contacts. Protein Sci. 6:2261-2263, 1997.
48. Walshaw, J., Goodfellow, J.M. Distribution of solvent molecules around apolar side-chains in protein crystals. J. Mol. Biol. 231:392-414, 1993.
49. Levitt, M., Park, B.H. Water: Now you see it, now you don't. Structure 1:223-226, 1993.
50. Wilmanns, M., Nilges, M. Molecular replacement with NMR models using distance-derived pseudo B factors. Acta Crystallogr. D52:973-982, 1996.
51. Iwata, S., Ostermeier, C., Ludwig, B., Michel, H. Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature 376:660-669, 1995.
52. Tsukihara, T., Aoyama, H., Yamashita, E., et al. The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å. Science 272:1136-1144, 1996.
53. Clarke, J., Fersht, A.R. An evaluation of the use of hydrogen exchange at equilibrium to probe intermediates on the protein folding pathway. Folding Design 1:243-254, 1996.
54. Eriksson, A.E., Baase, W.A., Matthews, B.W. Similar hydrophobic replacements of leu 99 and phe 153 within the core of T4 lysozyme have different structural and thermodynamic consequences. J. Mol. Biol. 229:747-769, 1993
55. Rose, D.R., Phipps, J., Michmiewicz, J., et al. Crystal structure of T4-lysozyme generated from synthetic coding DNA expressed in Escherichia coli. Protein Eng. 2:277-282, 1988.
56. Weaver, L.H., Matthews, B.W. Structure of bacteriophage T4 lysozyme refined at 1.7 angstroms resolution. J. Mol. Biol. 193:189-199, 1987.
57. Wilson, K., Fabe, R., Dao-Pin, S., Matthews, B.W. Authors of the PDB file, 1989.
58. Bell, J.A., Wilson, K., Zhang, X.J., Faber, H.R., Nicholson, H., Matthews, B.W. Comparison of the crystal structure of bacteriophage T4 lysozyme at low, medium, and high ionic strengths. Proteins 10:10-21, 1991.
59. Phillips, S.E.V., Schoenborn, B.P. Neutron diffraction reveals oxygen-histidine hydrogen bond in oxymyoglobin. Nature 292:81-82, 1981.
60. Yang, F., Phillips, G.N. Jr. Crystal structure of CO-, deoxy-and Met-myoglobins at various pH values. J. Mol. Biol. 256:762-774, 1996.
61. Takano. T. Refinement of myoglobin and cytochrome C. In: "Methods and Applications in Crystallographic Computing." Hall S.R., Ashida T. (eds.). Oxford, U.K.: Oxford University Press, 1984:262-289.
62. Phillips, S.E.V. Structure and refinement of oxymyoglobin at 1.6 angstroms resolution. J. Mol. Biol. 142:531-554, 1980.
63. Rizzi, M., Ascenzi, P., Coda, A., Brunori, M., Bolognesi, M. Molecular bases for heme:ligand recognition in sperm whale (Physeter catodon) and Aplysia limacina myoglobin. Rend. Fis. Ac. Lincei 89:65-73, 1993.
64. Johnson, K.A, Olson, J.S., Phillips, G.N. Jr. Structure of myoglobin-ethyl isocyanide: Histidine as a swinging door for ligand entry. J. Mol. Biol. 207:459-463, 1989.