Protein folds in the all-β and all-α classes

Annual Review of Biophysics and Biomolecular Structure

Volumn 26, Issue , 1997, Pages 597-627

  Chothia, Cyrus ^a   Hubbard, Tim ^a   Brenner, Steven ^a   Barns, Hugh ^a   Murzin, Alexey ^a  

^a MRC CENTRE FOR PROTEIN ENGINEERING   (United Kingdom)

Author keywords

Helix bundles; Helix layer structures; Helix polyhedra; Barrels; Helices; Prisms; Propellers; Sandwiches

Indexed keywords

PROTEIN SUBUNIT;

ALPHA CHAIN; BETA CHAIN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN QUATERNARY STRUCTURE; PROTEIN SECONDARY STRUCTURE; REVIEW;

DATABASES, FACTUAL; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 0030920501     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.26.1.597     Document Type: Review

References (103)

1. Adams MJ, Ellis GH, Gover S, Naylor, CE, Phillips, C. 1994. Crystallographic study of coenzyme, coenzyme analog and substrate binding in 6-phosphogluconate dehydrogenase implications for NADP specificity and the enzyme mechanism. Structure 2:651-68
2. Aleshin AE, Golubev A, Firsov LM, Honzatko RB. 1992. Crystal structure of glucoamylase from Aspergillus awamori var. X100. J. Biol. Chem. 267:9291-98
3. Baumann U, Wu S, Flaherty KM, Mckay DB. 1993. Three dimensional structure of the alkaline protease from Ps. aeruginosa: a two domain protein with a calcium binding parallel β-roll motif. EMBO J. 12:3357-64
4. Bentley GA, Boulot G, Karjalainen K, Mariuzza RA. 1995. Crystal structure of the β-chain of a T cell antigen receptor. Science 267:1984-87
5. Bernstein FC, Koetzle TF, Williams GJ, Meyer EJ, Brice MD, et al. 1977. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-42
6. Bowie JU, Pakula AA, Simon MI. 1995. The 3-dimensional structure of the aspartate receptor from Escherichia coli. Acta Cryst. D 51:145-54
7. Brannigan JA, Dodson G, Duggleby HJ, Moody P, Smith JL, et al. 1995. A protein catalytic framework with an N-terminal nucleophile is capable of self-activation. Nature 378:416-19
8. Breiter DR, Kanost MR, Benning MM, Wesenberg G, Law JH, et al. 1991. Molecular structure of an apolipoprotein determined at 2.5 Å resolution. Biochemistry 30:603-8
9. Cedergren-Zeppezauer ES, Larsson G, Nyman PO, Dauter Z, Wilson KS. 1992. Crystal structure of a DUTPase. Nature 335:740-43
10. Chirgadze YN. 1987. Deduction and systematic classification of spatial motifs of the antiparallel β-structure in globular proteins. Acta Cryst. A 43:405-17
11. Chothia C. 1984. Principles that determine the structure of proteins. Annu. Rev. Biochem. 53:537-72
12. Chothia C, Finkelstein AV. 1990. The classification and origins of protein folding patterns. Annu. Rev. Biochem. 59:1007-39
13. Chothia C, Janin J. 1981. Relative orientation of close-packed β-pleated sheets in proteins. Proc. Natl. Acad. Sci. USA 78:4146-50
14. Chothia C, Janin J. 1982. Orthogonal packing of β-pleated sheets in proteins. Biochemistry. 21:3955-65
15. Chothia C, Levitt M, Richardson D. 1977. Structure of proteins: packing of α-helices and β-sheets. Proc. Natl. Acad. Sci. USA 74:4130-34
16. Chothia C, Levitt M, Richardson D. 1981. Helix to helix packing in proteins. J. Mol. Biol. 145:215-50
17. Chothia C, Murzin AG. 1993. New folds for all-β proteins. Structure 1:217-22
18. Cohen FE, Sternberg M, Taylor WR. 1981. Analysis of the tertiary structure of protein β-sheet sandwiches. J. Mol. Biol. 148:253-72
19. Cowan SW, Newcomer ME, Jones TA. 1990. Crystallographic refinement of human serum retinol binding protein at 2 Å resolution. Proteins 8:44-61
20. Crennell SJ, Garman EF, Philippon C, Vasella A, Laver WG, et al. 1996. The structures of Salmonella typhimurium LT2 neuraminidase and its complexes with three inhibitors at high resolution. J. Mol. Biol. 259:264-80
21. Crick F. 1953. The packing of α-helices: simple coiled coils. Acta Crystallogr. 6:689-97
22. Dardel F, Davis AL, Laue ED, Perham RN. 1993. Three-dimensional structure of the lipoyl domain from Bacillus-stearothermophilus pyruvate dehydrogenase multienzyme complex. J. Mol. Biol. 229:1037-48
23. Efimov AV. 1993. Supersecondary involving triple-strand β-sheets. FEBS Lett. 334:253-56
24. Efimov AV. 1994. Favored structural motifs in globular proteins. Structure 2:999-1002
25. Emsley P, Charles IG, Fairweather NF, Isaacs NW. 1996. Structure of Bordetella pertussis virulence factor P.69 pertactin. Nature 381:90-92
26. Finkelstein AV, Ptitsyn OB. 1987. Why do globular proteins fit the limited set of folding patterns. Prog. Biophys. Mol. Biol. 50:171-90
27. Finzel BC, Clancy LL, Holland DR, Muchmore SW, Watenpaugh KD, Einspahr HM. 1989. Crystal structure of recombinant human interleukin-1 β at 2.0 Å resolution. J. Mol. Biol. 209:779-91
28. Fujinaga M, Berthetcolominas C, Yaremchuk AD, Tukalo MA, Cusack S. 1993. Refined crystal structure of the seryl-tRNA-synthetase from Thermus thermophilus at 2.5 Å resolution. J. Mol. Biol. 234:222-33
29. Fujinaga M, Delbaere L, Brayer GD, James M. 1985. Refined structure of α-lytic protease at 1.7 Å resolution-analysis of hydrogen-bonding and solvent structure. J. Mol. Biol. 184:479-502
30. Hardman KD, Ainsworth CF. 1972. Structure of concanavalin at 2.4 Å resolution. Biochemistry 11:4910-19
31. Harris NL, Presnell SR, Cohen FE. 1994. Four helix bundle diversity in globular proteins. J. Mol. Biol. 236:1356-68
32. Hester G, Kaku H, Goldstein IJ, Wright CS. 1995. Structure of mannose-specific snowdrop (Galanthus nivalis) lectin is representative of a new plant lectin family. Nature Struct. Biol. 2:472-79
33. Holm L, Sander C. 1993. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:123-38
34. Holm L, Sander C. 1994. Searching protein structure databases has come of age. Proteins 19:65-73
35. Holm L, Sander C. 1996. The FSSP database of structurally aligned protein fold families. Nucleic Acids Res 24:206-10
36. Holmes MA, Matthews BW. 1982. Structure of thermolysin refined at 1.6 Å resolution. J. Mol. Biol. 160:623-39
37. Huber R, Roemisch J, Paques EP. 1990. The crystal and molecular structure of human annexin V, an anticoagulant protein that binds to calcium and membranes. EMBO J. 9:3867-74
38. Ito N, Phillips S, Stevens C, Ogel ZB, McPherson MJ, et al. 1991. Novel thioether bond revealed by a 1.7 Å crystal structure of galactose oxidase. Nature 350:87-90
39. Jabri E, Carr MB, Hausinger RP, Karplus PA. 1995. The crystal structure of urease from Klebsiella aerogenes. Science 268:998-1004
40. Ke H. 1992. Similarities and differences between human cyclophilin A and other β-barrel structures. J. Mol. Biol. 228:539-50
41. Kendrew JC, Dickerson RE, Strandberg BE, Hart RG, Davies DR, et al. 1960. Structure of myoglobin. Nature 185:422-30
42. Kjeldgaard M, Nissen P, Thirup S, Nyborg J. 1993. The crystal-structure of elongation factor EF-TU from Thermus aquaticus in the GTP conformation. Structure 1:35-50
43. Klemm JD, Rould MA, Aurora R, Herr W, Pabo CO. 1994. Crystal structure of the oct-1 POU domain bound to an octamer site DNA recognition with tethered DNA-binding modules. Cell 77:21-32
44. Ko TP, Day J, Greenwood A, McPherson A. 1994. Structures of three crystal forms of the sweet protein thaumatin. Acta Cryst. D 50:813-25
45. Kuhn P, Tarentin, AL, Plummer TH, Van Roey P. 1994. Crystal structure of peptide-N-4-(N-acetyl-β-D-glucosaminyl)asparagine amidase F at 2.2 Å resolution. Biochemistry 33:11699-706
46. Kumar V, Kannan KK. 1994. Enzyme-substrate interactions structure of human carbonic-anhydrase-I complexed with bicarbonate. J. Mol. Biol. 241:226-32
47. +, and pyruvate. Biochemistry 33:6301-9
48. Lasters I, Wodak SJ, Alard P, Van Cutsem E. 1988. Structural principles of parallel β-barrels in proteins. Proc. Natl. Acad. Sci. USA 85:3338-42
49. Lasters I, Wodak SJ, Pio F. 1990. The design of idealized α/β-barrels: analysis of β-sheet closure requirements. Proteins 7:249-56
50. Lawrence MC, Suzuki E, Varghese JN, Davis PC, van Donkelaar A, et al. 1990. The three dimensional structure of the seed storage protein phaseolin at 3 Å resolution. EMBO J 9:9-15
51. Lesk AM, Bränden CI, Chothia C. 1989. Structural principles of a/β-barrel proteins: the packing of the interior of the sheet. Proteins 5:139-48
52. Levitt M, Chothia C. 1976. Structural patterns in globular proteins. Nature 261:552-58
53. Li J, Brick P, Ohare MC, Skarzynski T, Lloyd LF, et al. 1995. Structure of full-length porcine synovial collagenase reveals a C-terminal domain containing a calcium-linked, four-bladed β-propeller. Structure 3:541-49
54. Li JD, Carroll J, Ellar DJ. 1991. Crystal-structure of insecticidal δ-endotoxin from Bacillus thuringiensis at 2.5 Å resolution. Nature 353:815-21
55. Liao DI, Kapadia G, Reddy P, Saier MH, Reizer J, Herzberg O. 1991. Structure of the IIA domain of the glucose permease of Bacillus subtilis at 2.2 Å resolution. Biochemistry 30:9583-94
56. Massiah MA, Starich MR, Paschall C, Summers MF, Christensen AM, Sundquist WI. 1994. 3-Dimensional structure of the human immunodeficiency virus type-1 matrix protein. J. Mol. Biol. 244:198-223
57. Matthews DA, Appelt K, Oatley SJ. 1989. Stacked β-bulges in thymidylate synthase account for a novel right-handed rotation between opposing β-sheets. J. Mol. Biol. 205:449-54
58. McLachlan AD. 1979. Gene duplications in the structural evolution of chymotrypsin. J. Mol. Biol. 128:49-79
59. Murzin AG. 1992. Structural principles for the propeller assembly of β-sheets: the preference for 7-fold symmetry. Proteins 14:191-201
60. Murzin AG. 1994. New-protein folds. Curr. Opin. Struct. Biol. 4:441-49
61. Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:536-40
62. Murzin AG, Finkelstein AV. 1983. Polyhedrons describing packing of helices in a protein globule. Biofizika 28:905-911
63. Murzin AG, Finkelstein AV. 1988. General architecture of the α-helical globule. J. Mol. Biol. 204:749-69
64. Murzin AG, Lesk AM, Chothia C. 1992. β-trefoil fold: patterns of structure and sequence in the kunitz inhibitors interleukins-1β and 1α and fibroblast growth factors. J. Mol. Biol. 223:531-43
65. Murzin AG, Lesk AM, Chothia C. 1994. Principles determining the structure of β-sheet barrels in proteins. I. A theoretical-analysis. J. Mol. Biol. 236:1369-81
66. Murzin AG, Lesk AM, Chothia C. 1994. Principles determining the structure of β-sheet barrels in proteins. II. The observed structures. J. Mol. Biol. 236:1382-400
67. Novotny J, Bruccoleri RE, Newell J. 1984. Twisted hyperboloid (strophoid) as a model of β-barrels in proteins. J. Mol. Biol. 177:567-73
68. Nureki O, Vassylyev DG, Katayanagi K, Shimizu T, Sekine S, et al. 1995. Architectures of class-defining and specific domains of glutamyl-tRNA synthetase. Science 267: 1958-65
69. Ohkawa H, Hogue C, Bryant S, Kans J, Epstein J, et al. 1996. MMDB: Entrez's Structure Database. http://www.ncbi.-nlm.nih.gov/Structure//struchelp.html
70. Orengo C. 1994. Classification of protein folds. Curr. Opin. Struct. Biol. 4:429-40
71. Orengo C, Flores TP, Taylor WR, Thorton JM. 1993. Identifying and classifying protein fold families. Protein Eng. 6:485-500
72. Orengo C, Michie AD, Thornton JM, Taylor WR. 1995. Class, architecture, topology and homology (CATH) classification of proteins. http://www.biochem.ucl.ac.uk/bsm/cath
73. Orengo CA, Jones DT, Thorton JM. 1994. Protein superfamilies and domain superfolds. Nature 372:631-34
74. Otwinowski Z, Schevitz RW, Zhang RG, Lawson CL, Joachimiak A, et al. 1988. Crystal structure of Trp repressor operator complex at atomic resolution. Nature 335:321-29
75. Papamokos E, Weber E, Bode W, Huber R, Empie MW, et al. 1982. Crystallographic refinement of Japanese quail ovomucoid, a kazal-type inhibitor, and model-building studies of complexes with serine proteases. J. Mol. Biol. 158:515-37
76. Pflugrath JW, Wiegand G, Huber R, Vertesy L. 1986. Crystal structure determination, refinement and the molecular model of the α-amylase inhibitor Hoe-467A. J. Mol. Biol. 189:383-86
77. Presnell SR, Cohen FE. 1989. Topological distribution of four α-helix bundles. Proc. Natl. Acad. Sci. USA 86:6592-96
78. Ptitsyn OB, Finkelstein AV. 1981. Similarities in protein topologies: evolutionary divergence, functional convergence or principles of folding. Q. Rev. Biophys. 13:339-86
79. Raetz C, Roderick SL. 1996. A left-handed parallel β-helix in the structure of UDP-N-acetylglucosamine acetyltransferase. Science 270:997-1000
80. Remington S, Wiegand G, Huber R. 1982. Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 Å and 1.7 Å resolution. J. Mol. Biol. 158:111-52
81. Richardson JS. 1976. Handedness of crossover connections in β-sheets. Proc. Natl. Acad. Sci. USA 73:2619-23
82. Richardson JS. 1981. The anatomy and taxonomy of protein structure. Adv. Protein Chem. 34:167-339
83. Salemme FR. 1981. Conformational and geometrical properties of β-sheets in proteins: III isotropically stressed configurations. J. Mol. Biol. 146:143-56
84. Salemme FR, Weatherford DW. 1981. Conformational and geometrical properties of β-sheets in proteins. I. Parallel β-sheets. J. Mol. Biol. 146:101-17
85. Salemme FR, Weatherford DW. 1981. Conformational and geometrical properties of β-sheets in proteins. II. Antiparallel and mixed β-sheets. J. Mol. Biol. 146:119-41
86. Schindelin H, Marahiel MA, Heinemann U. 1993. Universal nucleic acid-binding domain revealed by crystal structure of the Bacillus subtilis major cold shock protein. Nature 364:164-68
87. Schirmer T, Keller TA, Wang YF, Rosenbusch JP. 1995. Structural basis for sugar translocation through maltoporin channels at 3.1 Å resolution. Science 267:512-14
88. Shimizu T, Vassylyev DG, Kido S, Doi Y, Morikawa K. 1994. Crystal structure of vitelline membrane outer layer protein-I (VMO-I) - a folding motif with homologous Greek key structures related by an internal 3-fold symmetry. EMBO J. 13:1003-10
89. Sternberg MJE, Thornton JM. 1976. On the conformation of proteins: the handedness of the β-strand-α-helix-β-strand unit. J. Mol. Biol. 105:367-82
90. Suzuki M, Sugimoto H, Nakagawa A, Tanaka I, Nishihira J, Sakai M. 1996. Crystal structure of the macrophage migration inhibitory factor from rat liver. Nature Struct. Biol. 3:259-66
91. Svensson LA, Thulin E, Forsen S. 1992. Proline cis-trans isomers in calbindin D9k observed by X-ray crystallography. J. Mol. Biol. 223:601-6
92. Tarshis LC, Yan MJ, Poulter CD, Sacchettini JC. 1994. Crystal structure of recombinant famesyl diphosphate synthase at 2.6 Å resolution. Biochemistry 33:10871-77
93. Thayer MM, Ahern H, Xing DX, Cunningham RP, Tainer JA. 1995. Novel DNA-binding motifs in the DNA repair enzyme endonuclease III crystal structure. EMBO J. 14:4108-20
94. Tronrud DE, Schmid MF, Matthews BW. 1986. Structure and x-ray amino-acid sequence of a bacteriochlorophyll-A protein from Prosthecochloris aestuarii refined at 1.9 Å resolution. J. Mol. Biol. 188:443-54
95. Varghese JN, Laver WG, Colman PM. 1983. Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9 Å resolution. Nature 303:35-40
96. Weaver LH, Grutter MG, Matthews BW. 1995. The refined structures of goose lysozyme and its complex with a bound trisaccharide show that the goose-type lysozymes lack a catalytic aspartate residue. J. Mol. Biol. 245:54-68
97. Weber PC, Salemme, FR. 1980. Structural and functional diversity in 4-α-helical proteins. Nature 287:82-84
98. Weiss MS, Anderson DH, Raffioni S, Bradshaw RA, Ortenzi C, et al. 1995. A cooperative model for receptor recognition and cell adhesion: evidence from the molecular packing in the 1.6 Å crystal-structure of the pheromone ER-1 from the ciliated protozoan Euplotes raikovi. Proc. Natl. Acad. Sci. USA 92:10172-76
99. White S, Boyd G, Mathews FS, Xia ZX, Dai WW, et al. 1993. The active site structure of the calcium-containing quinoprotein methanol dehydrogenase. Biochemistry 32:12955-58
100. Woolfson DN, Evans PA, Hutchinison EG, Thornton J. 1993. Topological and stereochemical restrictions in β-sandwich protein structures. Protein Eng. 6:461-70
101. Xu WG, Rould MA, Jun S, Desplan C, Pabo CO. 1995. Crystal structure of a paired domain-DNA complex at 2.5 Å resolution reveals structural basis for pax developmental mutations. Cell 80:639-50
102. Yee DP, Dill KA. 1993. Families and the structural relatedness among globular proteins. Protein Sci. 2:884-99
103. Yoder MD, Lietzke SE, Jurnak F. 1993. Unusual structural features in the parallel β-helix in pectate lyases. Structure 1:241-25