Structural and sequence characteristics of long α helices in globular proteins

Biophysical Journal

Volumn 71, Issue 3, 1996, Pages 1574-1586

  Kumar, Sandeep ^a   Bansal, Manju ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

GLOBULAR PROTEIN;

ALGORITHM; ALPHA HELIX; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARTICLE; GEOMETRY; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE;

EID: 0029738679     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(96)79360-8     Document Type: Article

References (41)

1. Banner, D. W., M. Kokkinidis, and D. Tsernoglou. 1987. Structure of the ColE1 Rop protein at 1.7 Å resolution. J. Mol. Biol. 196:657-675.
2. Barlow, D. J., and J. M. Thornton. 1988. Helix geometry in proteins. J. Mol. Biol. 201:601-619.
3. Bernstein, F. C., T. F. Koetzle, G. J. B. Williams, E. F. Meyer. Jr., M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi. 1977. The Protein Data Bank: a computer based archival file for macromolecular structures. J. Mol Biol. 112:535-542.
4. Blundell, T., D. Barlow, N. Borkakoti, and J. M. Thornton. 1983. Solvent induced distortions and the curvature of α helices. Nature. 306:281-283.
5. Chakarabarti, P., M. Bernard, and D. C. Rees. 1986. Peptide bond distortions and curvature of a helices. Biopolymers. 25:1087-1093.
6. Chou, P. Y., and G. D. Fasman. 1978. Prediction of the secondary structure of proteins from their amino acid sequence. Adv. Enzymol. 47:45-148.
7. Creighton, T. E. 1993. Proteins: Structure and Molecular Properties, 2nd Ed. W. H. Freeman and Company, New York.
8. DeGrado, W. F., Z. R. Wasserman, and J. D. Lear. 1989. Protein design, a minimalist approach. Science. 243:622-628.
9. Eisenberg, D., W. Wilcox, S. M. Eshita, P. M. Prycak, S. P. Ho, and W. F. DeGrado. 1986. The design, synthesis and crystallization of an α-helical peptide. Proteins Struct. Funct. Genet. 1:16-22.
10. Eisenhaber, F., B. Persson, and P. Argos. 1995. Protein structure prediction: recognition of primary, secondary and tertiary structural features from amino acid sequence. Crit. Rev. Biochem. Mol. Biol. 30:1-94.
11. Finzel, B. C., P. C. Weber, K. D. Hardman, and F. R. Salemme. 1985. Structure of ferricytochrome c′ from Rhodospirillum molischianum at 1.67 Å resolution. J. Mol. Biol. 186:627-643.
12. Hecht, M. M., J. S. Richardson, D. C. Richardson, and R. C. Ogden. 1990. De novo design, expression and characterization of felix: a four-helix bundle protein of native-like sequence. Science. 249:884-891.
13. Hill, C. P., T. D. Oslund, and D. Eisenberg. 1993. The structure of granulocyte-colony-stimulating factor and its relationship to other growth factors. Proc. Natl. Acad. Sci. USA. 90:5167-5171.
14. Hobohm, U., M. Scharf, R. Schneider, and C. Sander. 1992. Selection of representative protein data sets. Protein Sci. 1:409-417.
15. Hodges, R. S., P. D. Semchuk, A. K. Taneja, C. M. Kay, J. M. R. Parker, and C. T. Mant. 1988. Protein design using model synthetic peptides. Pept. Res. 1:19-30.
16. Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers. 22:2577-2637.
17. Karplus, P. A., and G. E. Schulz. 1987. Refined structure of glutathione reductase at 1.54 Å resolution. J. Mol Biol. 195:701-729.
18. Kim, E. E., and H. W. Wyckoff. 1991. Reaction mechanism of alkaline phosphatase base on crystal structures: two metal ion catalysis. J. Mol. Biol. 218:449-464.
19. Lawson, D. M., P. J. Artymuik, S. J. Yewdall, J. M. A. Smith, J. C. Livingstone, A. Treffery, A. Luzzago, S. Levi, P. Arosio, G. Cesareni, C. D. Thomas, W. V. Shaw, and P. M. Harrison. 1991. Solving the structure of human H ferritin by genetically engineering intermolecular crystal contacts. Nature. 349:541-544.
20. Lederer, F., A. Glatigny, P. H. Bethge, H. D. Bellamy, and F. S. Mathews. 1981. Improvement of 2.5 Å resolution model of cytochrome b562 by redetermining the primary structure and using molecular graphics. J. Mol. Biol. 148:427-448.
21. Lovejoy, B., S. Choe, D. Cascio, D. K. McRorie, W. F. DeGrado, and D. Eisenberg. 1993. Crystal structure of a synthetic triple stranded α-helical bundle. Science. 259:1288-1292.
22. Ludwig, M. L., A. L. Metzer, K. A. Pattridge, and W. C. Stallings. 1991. Manganese Superoxide dismutase from Thermus thermophilus. A structural model refined at 1.8 Å resolution. J. Mol. Biol. 219:335-358.
23. McCaldon, P., and P. Argos. 1988. Oligopeptide biases in protein sequences and their use in predicting protein coding regions in nucleotide sequences. Proteins Struct. Funct. Genet. 4:99-122.
24. Myszka, D. G., and I. M. Chaiken. 1994. Design and characterization of an intramolecular antiparallel coiled coil peptide. Biochemistry. 33: 2363-2372.
25. α geometry in protein structures. Proteins Struct. Fund. Genet. 18:324-337.
26. O'Shea, E. K., J. D. Klemm, P. S. Kim, and T. Alber, 1991. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science. 254:539-544.
27. Parry, D. A. D., and E. Suzuki. 1969. Intrachain potential energy of the α-helix and a coiled coil strand. Biopolymers. 7:189-197.
28. Pauling, L., and R. B. Corey. 1953. Compound configurations of polypeptide chains: structure of proteins of the α-keratin type. Nature. 171: 59-61.
29. Poulos, T. L., B. C. Finzel, I. C. Gunsalus, G. C. Wagner, and J. Kraut. 1985. The 2.6 Å crystal structure of Pseudomonas putida cytochrome P-450. J. Biol. Chem. 260:16122-16130.
30. Richardson, J. S., and D. C. Richardson. 1988. Amino acid preferences for specific locations at the ends of a helices. Science. 240:1648-1652.
31. Rost, B., and C. Sander. 1994. Structure prediction of proteins - where are we now? Curr. Opin. Struct. Biol. 5:372-380.
32. Rost, B., C. Sander, and R. Schneider. 1994. Redefining the goals of protein secondary structure prediction. J. Mol. Biol. 235:13-26.
33. Satyshur, K. A., T. R. Sambhorao, D. Pyzalska, W. Drendel, M. Greaser, and M. Sundaralingam. 1988. Refined structure of chicken skeletal muscle troponin C in the two-calcium state at 2-Å resolution. J. Biol. Chem. 263:1628-1647.
34. Shaw, A., D. E. McRee, V. D. Vacquir, and C. D. Stout. 1993. The crystal structure of lysin, a fertilization protein. Science. 262:1864-1867.
35. Srinivasan, R., R. Balasubramanian, and S. S. Rajan. 1975. Some new methods and general results of analysis of protein crystallographic data. J. Mol. Biol. 98:739-747.
36. Sugeta, H., and T. Miyazawa. 1967. General method for calculating helical parameters of polymer chains from bond lengths, bond angles and internal-rotation angles. Biopolymers. 5:673-679.
37. Sundaralingam, M., W. Drendel, and M. Greaser. 1985. Stabilization of the long central helix of troponin C by intra helical salt bridges between charged amino side chains. Proc. Natl. Acad. Sci. USA. 82:7944-7947.
38. Ultsch, M. H., W. Somers, A. A. Kossiakoff, and A. M. de Vos. 1994. Crystal structure of affinity-matured human growth hormone at 2 Å resolution. J. Mol. Biol. 236:286-299.
39. Wiegand, G., S. Remington, J. Deisenhofer, and R. Huber. 1984. Crystal structure analysis and molecular model of a complex of citrate synthase with oxaloacetate and S-acetonyl-coenzyme A. J. Mol. Biol. 174: 205-219.
40. Williams, R. W., A. Chang, D. Juretic, and S. Loughran. 1987. Secondary structure predictions and medium range interactions. Biochim. Biophys. Acta. 916:200-204.
41. Wilson, C., M. R. Wardell, K. H. Weisgraber, R. W. Mahley, and D. A. Agard. 1991. Three-dimensional structure of the LDL receptor-binding domain of human apolipoprotein E. Science. 252:1817-1822.