Structural and Functional Characterization of π Bulges and Other Short Intrahelical Deformations

Structure

Volumn 12, Issue 1, 2004, Pages 133-144

  Cartailler, Jean Philippe ^a   Luecke, Hartmut ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBONYL DERIVATIVE; HYDROGEN; PROTEIN; WATER;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; HYDROGEN BOND; LIGAND BINDING; MOLECULAR STABILITY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DATA BANK; PROTEIN DETERMINATION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STABILITY; QUALITY CONTROL; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

EID: 1642534352     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2003.12.001     Document Type: Article

References (47)

1. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28:2000;235-242.
2. Bousset L., Belrhali H., Melki R., Morera S. Crystal structures of the yeast prion Ure2p functional region in complex with glutathione and related compounds. Biochemistry. 40:2001;13564-13573.
3. Creighton T. Proteins. Structures and Molecular Properties 2nd Edition:1993;W.H. Freeman & Co, New York.
4. Deacon A.M., Ni Y.S., Coleman W.G. Jr., Ealick S.E. The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase. catalysis with a twist Struct. Fold. Des. 8:2000;453-462.
5. Duneau J.P., Genest D., Genest M. Detailed description of an alpha helix→pi bulge transition detected by molecular dynamics simulations of the p185c-erbB2 V659G transmembrane domain. J. Biomol. Struct. Dyn. 13:1996;753-769.
6. Fodje M.N., Al-Karadaghi S. Occurrence, conformational features and amino acid propensities for the pi-helix. Protein Eng. 15:2002;353-358.
7. Gadola S.D., Zaccai N.R., Harlos K., Shepherd D., Castro-Palomino J.C., Ritter G., Schmidt R.R., Jones E.Y., Cerundolo V. Structure of human CD1b with bound ligands at 2.3 A, a maze for alkyl chains. Nat. Immunol. 3:2002;721-726.
8. Gibbs N., Sessions R.B., Williams P.B., Dempsey C.E. Helix bending in alamethicin. molecular dynamics simulations and amide hydrogen exchange in methanol Biophys. J. 72:1997;2490-2495.
9. Goetz M., Carlotti C., Bontems F., Dufourc E.J. Evidence for an alpha-helix → pi-bulge helicity modulation for the neu/erbB-2 membrane-spanning segment. A 1H NMR and circular dichroism study. Biochemistry. 40:2001;6534-6540.
10. Gu P., Ishii Y., Spencer T.A., Shechter I. Function-structure studies and identification of three enzyme domains involved in the catalytic activity in rat hepatic squalene synthase. J. Biol. Chem. 273:1998;12515-12525.
11. Hutchinson E.G., Thornton J.M. Promotif. a program to identify and analyze structural motifs in proteins Protein Sci. 5:1996;212-220.
12. Kabsch W., Sander C. Dictionary of protein secondary structure. pattern recognition of hydrogen-bonded and geometrical features Biopolymers. 22:1983;2577-2637.
13. Keefe L.J., Sondek J., Shortle D., Lattman E.E. The alpha aneurism. a structural motif revealed in an insertion mutant of staphylococcal nuclease Proc. Natl. Acad. Sci. USA. 90:1993;3275-3279.
14. Kirichenko A., Vygodina T., Mkrtchyan H.M., Konstantinov A. Specific cation binding site in mammalian cytochrome oxidase. FEBS Lett. 423:1998;329-333.
15. Kleiger G., Beamer L.J., Grothe R., Mallick P., Eisenberg D. The 1.7 A crystal structure of BPI. a study of how two dissimilar amino acid sequences can adopt the same fold J. Mol. Biol. 299:2000;1019-1034.
16. Kleywegt G.J. Recognition of spatial motifs in protein structures. J. Mol. Biol. 285:1999;1887-1897.
17. Kleywegt G.J., Jones T.A. Databases in protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 54:1998;1119-1131.
18. Kolbe M., Besir H., Essen L.O., Oesterhelt D. Structure of the light-driven chloride pump halorhodopsin at 1.8 A resolution. Science. 288:2000;1390-1396.
19. Kumar S., Bansal M. Dissecting alpha-helices. position-specific analysis of alpha-helices in globular proteins Proteins. 31:1998;460-476. a.
20. Kumar S., Bansal M. Geometrical and sequence characteristics of alpha-helices in globular proteins. Biophys. J. 75:1998;1935-1944. b.
21. Lee K.H., Benson D.R., Kuczera K. Transitions from alpha to pi helix observed in molecular dynamics simulations of synthetic peptides. Biochemistry. 39:2000;13737-13747.
22. Lesburg C.A., Zhai G., Cane D.E., Christianson D.W. Crystal structure of pentalenene synthase. mechanistic insights on terpenoid cyclization reactions in biology Science. 277:1997;1820-1824.
23. Low B.W., Baybutt R.B. The pi-helix - a hydrogen bonded configuration of the polypeptide chain. J. Am. Chem. Soc. 74:1952;5806.
24. Low B.W., Greenville-Wells H.J. Generalized mathematical relationships for polypeptide chain helices. The coordinates of the pi-helix. Proc. Natl. Acad. Sci. USA. 39:1953;785-801.
25. Luecke H., Schobert B., Richter H.T., Cartailler J.P., Lanyi J.K. Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution. Science. 286:1999;255-261. a.
26. Luecke H., Schobert B., Richter H.T., Cartailler J.P., Lanyi J.K. Structure of bacteriorhodopsin at 1.55 A resolution. J. Mol. Biol. 291:1999;899-911. b.
27. Luecke H., Schobert B., Lanyi J.K., Spudich E.N., Spudich J.L. Crystal structure of sensory rhodopsin II at 2.4 angstroms. insights into color tuning and transducer interaction Science. 293:2001;1499-1503.
28. Magasanik B. The Molecular and Cellular Biology of the Yeast Saccharomyces, Volume 2. 1992;Cold Spring Harbor Laboratory Press, Plainview, NY.
29. McDonald I.K., Thornton J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238:1994;777-793.
30. Morgan D.M., Lynn D.G., Miller-Auer H., Meredith S.C. A designed Zn2+-binding amphiphilic polypeptide. energetic consequences of pi-helicity Biochemistry. 40:2001;14020-14029.
31. Palczewski K., Kumasaka T., Hori T., Behnke C.A., Motoshima H., Fox B.A., Le Trong I., Teller D.C., Okada T., Stenkamp R.E.et al. Crystal structure of rhodopsin. a G protein-coupled receptor Science. 289:2000;739-745.
32. Pandit J., Danley D.E., Schulte G.K., Mazzalupo S., Pauly T.A., Hayward C.M., Hamanaka E.S., Thompson J.F., Harwood H.J. Jr. Crystal structure of human squalene synthase. A key enzyme in cholesterol biosynthesis. J. Biol. Chem. 275:2000;30610-30617.
33. Pauling L., Corey R.B. Atomic coordinates and structure factors for two helical configurations of polypeptide chains. Proc. Natl. Acad. Sci. USA. 37:1951;235-240.
34. Rajashankar K.R., Ramakumar S. Pi-turns in proteins and peptides. classification, conformation, occurrence, hydration and sequence Protein Sci. 5:1996;932-946.
35. Ramachandran G.N., Sasisekharan V. Conformation of polypeptides and proteins. Adv. Protein Chem. 23:1968;283-438.
36. Rohl C.A., Doig A.J. Models for the 3(10)-helix/coil, pi-helix/coil, and alpha-helix/3(10)-helix/coil transitions in isolated peptides. Protein Sci. 5:1996;1687-1696.
37. Royant A., Nollert P., Edman K., Neutze R., Landau E.M., Pebay-Peyroula E., Navarro J. X-ray structure of sensory rhodopsin II at 2.1-A resolution. Proc. Natl. Acad. Sci. USA. 98:2001;10131-10136.
38. Sajot N., Genest M. Structure prediction of the dimeric neu/ErbB-2 transmembrane domain from multi-nanosecond molecular dynamics simulations. Eur. Biophys. J. 28:2000;648-662.
39. Schneider T.D., Stephens R.M. Sequence logos. a new way to display consensus sequences Nucleic Acids Res. 18:1990;6097-6100.
40. Shirley W.A., Brooks C.L. 3rd. Curious structure in "canonical" alanine-based peptides. Proteins. 28:1997;59-71.
41. Starks C.M., Back K., Chappell J., Noel J.P. Structural basis for cyclic terpene biosynthesis by tobacco 5-epi-aristolochene synthase. Science. 277:1997;1815-1820.
42. Tarshis L.C., Proteau P.J., Kellogg B.A., Sacchettini J.C., Poulter C.D. Regulation of product chain length by isoprenyl diphosphate synthases. Proc. Natl. Acad. Sci. USA. 93:1996;15018-15023.
43. Thoden J.B., Frey P.A., Holden H.M. Crystal structures of the oxidized and reduced forms of UDP-galactose 4-epimerase isolated from Escherichia coli. Biochemistry. 35:1996;2557-2566.
44. Wang G., Dunbrack R.L. Jr. Pisces. a protein sequence culling server Bioinformatics. 19:2002;1589-1591.
45. Weaver T.M. The pi-helix translates structure into function. Protein Sci. 9:2000;201-206.
46. Wickner R.B. as an altered URE2 protein. evidence for a prion analog in Saccharomyces cerevisiae Science. 264:1994;566-569. [URE3].
47. Yoshikawa S., Shinzawa-Itoh K., Nakashima R., Yaono R., Yamashita E., Inoue N., Yao M., Fei M.J., Libeu C.P., Mizushima T.et al. Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase. Science. 280:1998;1723-1729.