Structural symmetry and protein function

Annual Review of Biophysics and Biomolecular Structure

Volumn 29, Issue , 2000, Pages 105-153

  Goodsell, David S ^a   Olson, Arthur J ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Oligomeric proteins; Protein structure function relationships; Protein symmetry

Indexed keywords

COMPLEX FORMATION; OLIGOMERIZATION; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN STRUCTURE; REVIEW; STRUCTURE ACTIVITY RELATION;

ALLOSTERIC SITE; ANIMALS; DIMERIZATION; DNA; MODELS, BIOLOGICAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0033886522     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.29.1.105     Document Type: Review

References (101)

1. 1. Abrahams JP, Leslie AGW, Lutter R, Walker JE. 1994. Structure at 2.8 angstroms resolution of F1-ATPase from bovine heart mitochondria. Nature 370:621-28
2. 2. Adams MJ, Blundell TL, Dodson EJ, Dodson GG, Vijayan M, et al. 1969. Structure of rhombohedral 2 zinc insulin crystals. Nature 224:491-95
3. 3. Barford D, Johnson LN. 1989. The allosteric transition of glycogen phosphorylase. Nature 340:609-16
4. 4. Bennett MJ, Schlunegger MP, Eisenberg D. 1995. 3D domain swapping: a mechanism for oligomer assembly. Protein Sci. 4:2455-68
5. 5. Berger B, Shor PW. 1998. On the structure of the scaffolding core of bacteriophage T4 and its role in head length determination. J. Struct. Biol. 121:285-94
6. 6. Beuron F, Maurizi MR, Belnap DM, Kocsis E, Booy FP, et al. 1998. At sixes and sevens: characterization of the symmetry mismatch of the ClpAP chaperone-assisted protease. J. Struct. Biol. 123:248-59
7. 7. Blundell T, Dodson G, Hodgkin D, Mercola D. 1972. Insulin: the structure in the crystal and its reflection in chemistry and biology. Adv. Protein Chem. 26:279-402
8. 8. Blundell TL, Srinivasan N. 1996. Symmetry, stability, and dynamics of multidomain and multicomponent protein systems. Proc. Natl. Acad. Sci. USA 93:14243-48
9. 9. Boyer PD. 1993. The binding site change mechanism for ATP synthase - some probabilities and possibilities. Biochim. Biophys. Acta 1140:215-50
10. 10. Calladine CR. 1978. Change of waveform in bacterial flagella: the role of mechanics at the molecular level. J. Mol. Biol. 118:457-79
11. 11. Caspar DLD. 1966. Design and assembly of organized biological structure. Molecular Architecture in Cell Physiology, Symp. Soc. Gen. Physiol., pp. 191-207. New York: Prentice Hall
12. 12. Caspar DLD, Klug A. 1962. Physical principles in the construction of regular viruses. Cold Spring Harbor Symp. Quant. Biol. 27: 1-24
13. 13. Chothia C. 1991. Asymmetry in protein structures. CIBA Found. Symp. 162:36-57
14. 14. Chothia C, Janin J. 1975. Principles of protein-protein recognition. Nature 256: 705-8
15. 15. Clegg JS. 1984. Properties and metabolism of the aqueous cytoplasm and its boundaries. Am. J. Physiol. 246:R133-51
16. 16. Cornish-Bowden AJ, Koshland DE Jr. 1971. The quaternary structure of proteins composed of identical subunits. J. Biol. Chem. 246:3092-102
17. 17. Crane HR. 1950. Principles and problems of biological growth. Sci. Monthly June:376-89
18. 18. Crick FHC, Watson JD. 1956. Structure of small viruses. Nature 177:473-75
19. 19. Crick FHC, Watson JD. 1957. Virus structure: general principles. CIBA Found. Symp. "The Nature of Viruses", pp. 5-13. Boston: Little, Brown
20. 20. Crothers DM, Metzger H. 1972. The influence of polyvalency on the binding properties of antibodies. Immunochemistry 9:341-57
21. 21. Degani Y, Degani C. 1980. Enzymes with asymmetrically arranged subunits. Trends Biochem. Sci. 5:337-41
22. 22. DeVos AM, Ultsch M, Kossiakoff AA. 1992. Human growth hormone and extracellular domain of its receptor: crystal structure of the complex. Science 255:306-12
23. 23. Evans PR. 1991. Structural aspects of allostery. Curr. Opin. Struct. Biol. 1:773-79
24. 24. Fulton AB. 1982. How crowded is the cytoplasm? Cell 30:345-47
25. 25. Ganser BK, Li S, Klishko VY, Finch JT, Sundquist WI. 1999. Assembly and analysis of conical models for the HIV-1 core. Science 283:80-83
26. 26. Garcia-Bellido A. 1996. Symmetries throughout organic evolution. Proc. Natl. Acad. Sci. USA 93:14229-32
27. 27. Goodsell DS. 1991. Inside a living cell. Trends Biochem. Sci. 16:203-6
28. 28. Goodsell DS, Olson AJ. 1993. Soluble proteins: size, shape and function. Trends Biochem. Sci. 18:65-68
29. 29. Gouax JE, Lipscomb WN. 1990. Crystal structures of phosphoacetamide ligated T and phosphoacetamide and malonate ligated R states of aspartate carbamoyltransferase at 2.8-Å resolution and neutral pH. Biochemistry 29:389-402
30. 30. Greenbury CL, Moore DH, Nunn LAC. 1965. The reaction with red cells of 7S rabbit antibody, its sub-units and their recombinants. Immunology 8:420-31
31. 31. Grimes JM, Burroughs JN, Gouet P, Diprose JM, Malby R, et al. 1998. The atomic structure of the bluetongue virus core. Nature 395:470-78
32. 32. Groll M, Ditzel L, Lowe J, Stock D, Bochtler M, et al. 1997. Structure of the 20S proteasome from yeast at 2.4 Å resolution. Nature 386:463-71
33. 33. Hanson KR. 1966. Symmetry of protein oligomers formed by isologous association. J. Mol. Biol. 22:405-9
34. 34. Hargittai I, Hargittai M. 1995. Symmetry through the Eyes of a Chemist. New York: Plenum
35. 35. Harrison SC, Olson AJ, Schutt CE, Winkler FK, Bricogne G. 1978. Tomato bushy stunt virus at 2.9 Angstroms resolution. Nature 276:368-73
36. 36. Hendrix RW. 1978. Symmetry mismatch and DNA packaging in large bacteriophages. Proc. Natl. Acad. Sci. USA 75:4779-83
37. 37. Herendeen DR, Kelly TJ. 1996. DNA polymerase III: running rings around the fork. Cell 84:5-8
38. 38. Heuser J, Kirchhausen T. 1985. Deep-etch views of clathrin assemblies. J. Ultrastruct. Res. 92:1-27
39. 39. Hewitt JA. 1977. On the influence of polyvalent ligands on membrane curvature. J. Theor. Biol. 64:455-72
40. 40. Hoare MR, Pal P. 1975. Physical cluster mechanics: statistical thermodynamics and nucleation theory for monatomic systems. Adv. Phys. 24:645-78
41. 41. Iwata S, Kamata K, Yoshida S, Minowa T, Ohta T. 1994. T and R states in the crystals of bacterial L-lactate dehydrogenase reveal the mechanism for allosteric control. Nature Struct. Biol. 1:176-85
42. 42. Johnson JE, Speir JA. 1997. Quasiequivalent viruses: a paradigm for protein assemblies. J. Mol. Biol. 269:665-75
43. 43. Jones S, Thornton JM. 1996. Principles of protein-protein interactions. Proc. Natl. Acad. Sci. USA 93:13-20
44. 44. Juo ZS, Chiu TK, Leiberman PM, Baikalov I, Berk AJ, Dickerson RE. 1996. How proteins recognize the TATA box. J. Mol. Biol. 261:239-54
45. 45. Kamiya R, Asakura S, Wakabayashi K, Namba K. 1979. Transition of bacterial flagella from helical to straight forms with different subunit arrangements. J. Mol. Biol. 131:725-42
46. 46. Kellenberger E. 1990. Form determination of the heads of bacteriophages. Eur. J. Biochem. 190:233-48
47. 47. Kelman Z, Finkelstein J, O'Donnell M. 1995. Why have six-fold symmetry? Curr. Biol. 5:1239-42
48. 48. Klotz IM. 1967. Protein subunits: a table. Science 155:697-98
49. 49. Klotz IM, Darnall DW, Langerman NR, eds. 1975. Quaternary Structure of Proteins, pp. 293-411. New York: Academic
50. 50. Klotz IM, Langerman NR, Darnall DW. 1970. Quaternary structure of proteins. Annu. Rev. Biochem. 39:25-62
51. 51. Klug A. 1968. Point groups and the design of aggregates. Nobel Symp. "Symmetry and Function of Biological Systems at the Macromolecular Level" 11th, Stockholm, pp. 425-36. Wiley & Sons, New York
52. 52. Kohlstaedt LA, Wang J, Friedman JM, Rice PA, Steitz TA. 1992. Crystal structure at 3.5 Å resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 256:1783-89
53. 53. Kong X-P, Onrust R, O-Donnell M, Kuriyan J. 1992. Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp. Cell 69:425-37
54. 54. Koshland DE. 1976. The evolution of function in enzymes. Fed. Proc. 35:2104-11
55. 55. Koshland DE, Nemethy G, Filmer D. 1966. Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5:365-85
56. 56. Krishna TSR, Kong X-P, Gary S, Burgers PM, Kuriyan J. 1994. Crystal structure of the eukaryotic DNA processivity factor PCNA. Cell 79:1233-43
57. 57. Kurland CG. 1992. Translational accuracy and the fitness of bacteria. Annu. Rev. Genet. 26:29-50
58. 58. Labeit S, Kolmerer B. 1995. Titins: giant proteins in charge of muscle ultrastructure and elasticity. Science 270:293-96
59. 59. Ladenstein R, Schneider M, Huber R, Bartunik H-D, Wilson K, et al. 1988. Heavy riboflavin synthase from Bacillus subtilis: crystal structure analysis of the icosahedral beta-60 capsid at 3.3 A resolution. J. Mol. Biol. 203:1045-70
60. 60. Larsen TA, Olson AJ, Goodsell DS. 1998. Morphology of protein-protein interfaces. Structure 6:421-27
61. 61. Lewis MS, Youle RJ. 1986. Ricin subunit association: thermodynamics and the role of the disulfide bond in toxicity. J. Biol. Chem. 261:11571-77
62. 62. Liddington RC, Yan Y, Moulai J, Sahli R, Benjamin TL, Harrison SC. 1991. Structure of simian virus 40 at 3.8-Angstrom resolution. Nature 354:278-84
63. 63. Lipscomb WN. 1991. Structure and function of allosteric enzymes. CHEMTRACTS-Biochem. Mol. Biol. [Data Trace Chem. Publ] 2:1-15
64. 64. Lowe J, Stock D, Jap B, Zwickl P, Baumeister W, Huber R. 1995. Crystal structure of the 20S proteosome from the archaeon T. acidophilum at 3.4 Å resolution. Science 268:533-39
65. 65. Lumry R, Rajender S. 1970. Enthalpyentropy compensation phenomena in water solutions of proteins and small molecules: a ubiquitous property of water. Biopolymers 9:1125-227
66. 66. Matsudaira P. 1991. Modular organization of actin crosslinking proteins. Trends Biochem. Sci. 16:87-92
67. 67. Mattevi A, Rizzi M, Bolognesi M. 1996. New structures of allosteric proteins revealing remarkable conformational changes. Curr. Opin. Struct. Biol. 6:824-29
68. 68. Mattevi A, Valentini G, Rizzi M, Speranza ML, Bolognesi M, Coda A. 1995. Crystal structure of Escherichia coli pyruvate kinase type I: molecular basis of the allosteric transition. Structure 3:729-41
69. 69. Mitchison T, Kirschner M. 1984. Dynamic instability of microtubule growth. Nature 312:237-42
70. 70. Mitchison TJ. 1988. Microtubule dynamics and kinetochore function in mitosis. Annu. Rev. Cell Biol. 4:527-49
71. 71. Monod J. 1968. On symmetry and function in biological systems. Nobel Symp. Symmetry Funct. Biol. Syst. Macromol. Lev., 11th, Stockholm, pp. 15-27. New York: Wiley
72. 72. Monod J, Wyman J, Changeux J-P. 1965. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12:88-118
73. 73. Moras D, Olsen KW, Sabesan MN, Buehner M, Ford GC, Rossmann MG. 1975. Studies of asymmetry in the three-dimensional structure of lobster D-glyceraldehyde-3-phosphate dehydrogenase. J. Biol. Chem. 250:9137-62
74. 74. Olson AJ, Bricogne G, Harrison SC. 1983. Structure of tomato bushy stunt virus IV. The virus particle at 2.9 Å resolution. J. Mol. Biol. 171:61-93
75. 75. Parker J. 1989. Errors and alternatives in reading the universal genetic code. Microbiol. Rev. 53:273-98
76. 76. Pauling L. 1953. Protein interactions: aggregation of globular proteins. Discov. Faraday Soc. 13:170-76
77. 77. Paulson JR, Laemmli UK. 1977. Morphogenetic core of the bacteriophage T4 head. Structure of the core in polyheads. J. Mol. Biol. 111:459-85
78. 78. Pereira PJB, Bergner A, Macedo-Ribeiro S, Huber R, Matxchiner G, et al. 1998. Human beta-trypsin is a ring-like tetramer with active sites facing a central pore. Nature 392:306-11
79. 79. Perutz MF. 1989. Mechanisms of cooperativity and allosteric regulation in proteins. Q. Rev. Biophys. 22:139-236
80. 80. Reed LJ, Hackert ML. 1990. Structure-function relationships in dihydrolipoamide acyltransferases. J. Biol. Chem. 265:8971-74
81. 81. Ricard J, Noat G. 1985. Kinetic cooperativity of monomeric mnemonical enzymes. Eur. J. Biochem. 152:557-64
82. 82. Rossmann MG. 1984. Constraints on the assembly of spherical virus particles. Virology 134:1-11
83. 83. Seydoux F, Malhotra OP, Bernhard SA. 1974. Half-site reactivity. CRC Crit. Rev. Biochem. 2:227-57
84. 84. Sharp K, Fine R, Honig B. 1987. Computer simulations of the diffusion of a substrate to an active site of an enzyme. Science 236:1460-64
85. 85. Sixma TK, Pronk SE, Kalk KH, Wartna ES, Zanten BAM, et al. 1991. Crystal structure of a cholera toxin-related heat-labile enterotoxin from E. coli. Nature 351:371-77
86. 86. Srere PA. 1981. Protein crystals as a model for mitochondrial proteins. Trends Biochem. Sci. 6:4-7
87. 87. Srere PA. 1984. Why are enzymes so big? Trends Biochem. Sci. 9:387-90
88. 88. Stossel TP. 1989. From signal to pseudopod: How cells control cytoplasmic actin assembly. J. Biol. Chem. 264:18261-64
89. 89. Strater N, Hakansson K, Schnappauf G, Braus G, Lipscomb WN. 1996. Crystal structure of the T state of allosteric yeast chorismate mutase and comparison with the R state. Proc. Natl. Acad. Sci. USA 93:3330-34
90. 90. Svedberg T. 1929. Mass and size of protein molecules. Nature 123:871
91. 91. Theil EC. 1987. Ferritin: structure, gene regulation, and cellular function in animals, plants and microorganisms. Annu. Rev. Biochem. 56:289-315
92. 92. vanHeel M, Orlova EV, Dube P, Tavares P. 1996. Intrinsic versus imposed curvature in cyclical oligomers: the portal protein of bacteriophage SPP1. EMBO J. 15:4785-88
93. 93. Wilson DR. 1993. Bacterial flagellar filaments and their component flagellins. Can. J. Microbiol. 39:451-72
94. 94. Wlodawer A, Erickson JW. 1993. Structure-based inhibitors of HIV-1 protease. Annu. Rev. Biochem. 62:543-85
95. 95. Wolynes PG. 1996. Symmetry and the energy landscapes of biomolecules. Proc. Natl. Acad. Sci. USA 93:14249-55
96. 96. Xu D, Tsai C-J, Nussinov R. 1998. Mechanism and evolution of protein dimerization. Protein Sci. 7:533-44
97. 97. Xu Z, Horwich AL, Sigler PB. 1997. The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex. Nature 388:741-50
98. 98. Yang M, Chen X-p, Militello K, Hoffman R, Fernandez B, et al. 1997. Alanine-scanning mutagenesis of Bacillus subtilis trp RNA-binding attenuation protein (TRAP) reveals residues involved in tryptophan binding and RNA binding. J. Mol. Biol. 270:696-710
99. 99. Yeager M, Berriman JA, Baker TS, Bellamy AR. 1994. Three-dimensional structure of the rotavirus haemagglutinin VP4 by cryo-electron microscopy and difference map analysis. EMBO J. 13:1011-18
100. 100. Zhang R-G, Scott DL, Westbrook ML, Nance S, Spangler BD, et al. 1995. The three-dimensional crystal structure of cholera toxin. J. Mol. Biol. 251:563-73
101. 101. Protein Data Bank accession codes for structures used in the figures. The PDB may be reached at http://www.rcsb. org/pdb. Figure 1: pepsin, 5pep; alcohol dehydrogenase, 2ohx; porin, 2por; neuraminidase, 1ivb; phosphofructokinase, 1pfk; aspartate carbamoyltransferase, 1atl; glycolate oxidase, 1gox; glutamine synthetase, 2gls; protocatechuate-3,4-dioxygenase, 3pcg; ferritin, 1hrs; satellite tobacco necrosis virus, 2stv. Figure 2 superoxide dismutase, 1xso; interleukin 10, 1ilk. Figure 4: fructose-1,6-bisphosphatase, 4fbp (T) and 5fbp (R); aspartate carbamoyltransferase, 4atl (T) and 1atl (R). Figure 5: β subunit of RNA pol III, 2pol; PCNA, 1axc. Figure 6: GroEL, 1der; proteasome, 1ryp. Figure 7: satellite tobacco necrosis virus, 2stv; tomato bushy stunt virus, 2tbv. Figure 8: bluetongue virus, 2btv; simian virus 40, 1sva. Figure 11: hemoglobin, 4hhb. Figure 13: HIV-1 protease, 7hvp. Figure 14: GroEL:GroES, 1aon. Figure 16: reverse transcriptase, 3hvt.