Analysis of the sequence and structural features of the left-handed β-helical fold

Proteins: Structure, Function and Genetics

Volumn 73, Issue 1, 2008, Pages 150-160

  Choi, Jay H ^a   Govaerts, Cedric ^b   May, Barnaby C H ^a,c   Cohen, Fred E ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Amyloid; Antifreeze protein; Fibrils; Hexapeptide motif; Left handed parallel helix; Nanostructure design; Parallel helix

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; LEFT HANDED BETA HELIX; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; SIMULATION;

ALGORITHMS; ANIMALS; GLYCINE; HUMANS; PROLINE; PROTEIN FOLDING; PROTEIN ISOFORMS; PROTEIN STRUCTURE, SECONDARY; SEQUENCE ANALYSIS, PROTEIN;

EUKARYOTA; PROKARYOTA;

EID: 50849106747     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22051     Document Type: Article

References (41)

1. Jenkins J, Pickersgill R. The architecture of parallel beta-helices and related folds. Prog Biophys Mol Biol 2001;77:111-175.
2. Iengar P, Joshi NV, Balaram P. Conformational and sequence signatures in beta helix proteins. Structure 2006;14:529-542.
3. Kajava AV, Steven AC. Beta-rolls, beta-helices, and other beta-solenoid proteins. Adv Protein Chem 2006;73:55-96.
4. Simkovsky R, King J. An elongated spine of buried core residues necessary for invivo folding of the parallel beta-helix of P22 tail-spike adhesin. Proc Natl Acad Sci USA 2006;103:3575-3580.
5. Govaerts C, Wille H, Prusiner SB, Cohen FE. Evidence for assembly of prions with left-handed beta-helices into trimers. Proc Natl Acad Sci USA 2004;101:8342-8347.
6. Raetz CR, Roderick SL. A left-handed parallel beta helix in the structure of UDP-N-acetylglucosamine acyltransferase. Science 1995;270:997-1000.
7. Graether SP, Kuiper MJ, Gagne SM, Walker VK, Jia Z, Sykes BD, Davies PL. Beta-helix structure and ice-binding properties of a hyperactive antifreeze protein from an insect. Nature 2000;406:325-328.
8. Leinala EK, Davies PL, Jia Z. Crystal structure of beta-helical antifreeze protein points to a general ice binding model. Structure 2002;10:619-627.
9. Leinala EK, Davies PL, Doucet D, Tyshenko MG, Walker VK, Jia Z. A beta-helical antifreeze protein isoform with increased activity. Structural and functional insights. J Biol Chem 2002;277:33349-33352.
10. Parisi G, Echave J. The structurally constrained protein evolution model accounts for sequence patterns of the LbetaH superfamily. BMC Evol Biol 2004;4:41.
11. Olsen LR, Roderick SL. Structure of the Escherichia coli GlmU pyrophosphorylase and acetyltransferase active sites. Biochemistry 2001;40:1913-1921.
12. Brown K, Pompeo F, Dixon S, Mengin-Lecreulx D, Cambillau C, Bourne Y. Crystal structure of the bifunctional N-acetylglucosamine 1-phosphate uridyltransferase from Escherichia coli: a paradigm for the related pyrophosphorylase superfamily. EMBO J 1999;18:4096-4107.
13. Sulzenbacher G, Gal L, Peneff C, Fassy F, Bourne Y. Crystal structure of Streptococcus pneumoniae N-acetylglucosamine-1-phosphate uridyltransferase bound to acetyl-coenzyme A reveals a novel active site architecture. J Biol Chem 2001;276:11844-11851.
14. Parisi G, Echave J. Structural constraints and emergence of sequence patterns in protein evolution. Mol Biol Evol 2001;18:750-756.
15. Yang S, Levine H, Onuchic JN, Cox DL. Structure of infectious prions: stabilization by domain swapping. Faseb J 2005;19:1778-1782.
16. Langedijk JP, Fuentes G, Boshuizen R, Bonvin AM. Two-rung model of a left-handed beta-helix for prions explains species barrier and strain variation in transmissible spongiform encephalopathies. J Mol Biol 2006;360:907-920.
17. Merlino A, Esposito L, Vitagliano L. Polyglutamine repeats and beta-helix structure: molecular dynamics study. Proteins 2006;63:918-927.
18. Stork M, Giese A, Kretzschmar HA, Tavan P. Molecular dynamics simulations indicate a possible role of parallel beta-helices in seeded aggregation of poly-Gln. Biophys J 2005;88:2442-2451.
19. Zheng J, Zanuy D, Haspel N, Tsai CJ, Aleman C, Nussinov R. Nanostructure design using protein building blocks enhanced by conformationally constrained synthetic residues. Biochemistry 2007;46:1205-1218.
20. Haspel N, Zanuy D, Zheng J, Aleman C, Wolfson H, Nussinov R. Changing the charge distribution of beta-helical-based nanostructures can provide the conditions for charge transfer. Biophys J 2007;93:245-253.
21. Haspel N, Zanuy D, Aleman C, Wolfson H, Nussinov R. De novo tubular nanostructure design based on self-assembly of beta-helical protein motifs. Structure 2006;14:1137-1148.
22. InsightII software. San Diego, CA: Accelrys, Inc. 2000.
23. Canutescu AA, Shelenkov AA, Dunbrack RL, Jr. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 2003;12:2001-2014.
24. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: fast, flexible, and free. J Comput Chem 2005;26:1701-1718.
25. Daura X, Mark AE, van Gunsteren WF. Parametrization of aliphatic CHn united atoms of GROMOS96 force field. J Comput Chem 1998;19:535-547.
26. Eisenberg D, McLachlan AD. Solvation energy in protein folding and binding. Nature 1986;319:199-203.
27. Berendsen HJ, Postma JP, van Gunsteren WF, Hermans J. Interaction models for water in relation to protein hydration. In: Pullman B, editor. Intermolecular Forces. Dordrecht: Reidel Publishing Company; 1981. pp 331-342.
28. Berendsen HJ, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
29. Hess B, Bekker H, Hermans J, Berendsen HJ, Fraaije JGEM. LINCS: a linear constraint solver for molecular simulations. J Comput Chem 1997;18:1463-1472.
30. The Uniprot Consortium. The Universal Protein Resource (Uni-Prot). Nucleic Acids Res 2007;35 (database issue):D193-D197.
31. Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000;28:10-14.
32. Pearson WR. Using the FASTA program to search protein and DNA sequence databases. Meth Mol Biol 1994;24:307-331.
33. Pearson WR. Using the FASTA program to search protein and DNA sequence databases. Methods Mol Biol 1994;25:365-389.
34. Eddy SR. Profile hidden Markov models. Bioinformatics 1998;14:755-763.
35. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
36. Binkowski TA, Naghibzadeh S, Liang J. CASTp: computed atlas of surface topography of proteins. Nucleic Acids Res 2003;31:3352-3355
37. Creighton TE. Proteins: structures and molecular properties. New York: Freeman; 1993.
38. Parisi G, Fornasari MS, Echave J. Dynactins p25 and p27 are predicted to adopt the LbetaH fold. FEBS Lett 2004;562:1-4.
39. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A. Pfam: clans, web tools and services. Nucleic Acids Res 2006;34 (database issue):D247-D251.
40. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
41. Schuler B, Rachel R, Seckler R. Formation of fibrous aggregates from a non-native intermediate: the isolated P22 tailspike beta-helix domain. J Biol Chem 1999;274:18589-18596.