49
Views
0
CrossRef citations to date
0
Altmetric
Original

De novo design of β-helical polypeptides

, &
Pages 168-190 | Published online: 11 Jul 2009

References

  • Arnold GE, Ornstein RL. An evaluation of implicit and explicit solvent model systems for the molecular dynamics simulation of bacteriophage T4 lysozyme. Proteins Struct Funct Genet 1994; 18: 19–33
  • Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J. Molecular dynamics with coupling to an external bath. J Chem Phys 1984; 81: 3684–3690
  • Branden C, Tooze J. Introduction to protein structure. Garland Publishing, Inc, New York and London 1991
  • Brünger AT. X-PLOR Version 3.1, A System for X-ray crystallography and NMR. Yale University Press, New Haven 1992
  • Chothia C, Murzin AG. New folds for all-β proteins. Structure 1993; 1: 217–222
  • Chothia C, Hubard T, Brenner S, Barns H, Murzin A. Protein folds in the all-β and all-α classes. Annu Rev Biophys Biomol Struct 1997; 26: 597–627
  • Cohen FE. The parallel b helix of pectate lyase C: Something to sneeze at. Science 1993; 260: 1444–1445
  • Emsley P, Charles IG, Fairweather NF, Isaacs NW. Structure of Bordetella pertussis virulence factore P.69 pertactin. Nature 1996; 381: 90–92
  • Garrett TPJ, McKern NM, Lou M, Frenkel MJ, Bentley JD, Lovrecz GO, Elleman TC, Cosgrove LJ, Ward CW. Crystal structure of the first three domains of the type-1insulin-like growth factor receptor. Nature 1998; 394: 395–399
  • Garrett TPJ, McKern NM, Lou M, Elleman TC, Adams TE, Lovrecz GO, Zhu HJ, Walker F, Frenkel MJ, Hoyne PA, Jorissen RN, Nice EC, Burgess AW, Ward CW. Cell 2002; 110: 763–773
  • Graether SP, Kulper MJ, Gagne SM, Walker VK, Jia Z, Sykes BD, Davies PL. β-Helix structure and ice-binding properties of a hyperactive antifreeze protein from an insect. Nature 2000; 406: 325–328
  • Heffron S, Moe GR, Sieber V, Cossart P, Mengaud J, Vitali J, Jurnak F. Sequence profile of the parallel β-helix in the pectate lyase superfamily. J Struct Biol 1998; 122: 223–235
  • Hegde SS, Vetting MW, Roderick SL, Mitchenall LA, Maxwell A, Takiff HE, Blanchard JS. A fluoroquinolone resistance protein from Mycobacterium tuberculosis that mimics DNA. Science 2005; 308: 1480–1483
  • Iverson TM, Alber BE, Kisker C, Ferry JG, Rees DC. A closer look at the active site of γ-class carbonic anhydrases: High-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila. Biochemistry 2000; 39: 9222–9231
  • Jenkins J, Pickersgill R. The architecture of parallel β-helics and related folds. Prog Biophys Mol Biol 2001; 77: 111–175
  • Jenkins J, Mayans O, Pickersgill R. Structure and evolution of parallel β-helix proteins. J Struct Biol 1998; 122: 236–246
  • Jenkins J, Mayans O, Smith D, Worboys K, Pickersgill RW. Three-dimensional structure of Erwinia chrysanthemi pectin methylesterase reveals a novel esterase active site. J Mol Biol 2001; 305(4)951–960
  • Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983; 79: 926–935
  • Jurnak F, Yoder MD, Pickersgill R, Jenkins J. Parallel β-domains: A new fold in protein structures. Opin Struct Biol 1994; 4: 802–806
  • Kale L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shinozaki A, Varadarajan K, Schulten K. NAMD2: Greater scalability for parallel molecular dynamics. J Comput Phys 1999; 151: 283–312
  • Kishimoto A, Hasegawa K, Suzuki H, Taguchi H, Namba K, Yoshida M. β-Helix is a likely core structure of yeast prion Sup25 amyloid fibers. Biochem Biophys Res Commun 2004; 315: 739–745
  • Kisker C, Schindelin H, Alber BE, Ferry JG, Rees DC. A left-handed β-helix revealed by the crystal structure of carbonic anhydrase from archaeon Methanosarcina thermophila. EMBO J 1996; 15: 2323–2330
  • Kobe B. Leucines on a roll. Nat Struct Biol 1996; 3: 977–980
  • Kobe B, Deisenhofer J. Crystal structure of porcine ribonuclease inhibitor, a protein with leucine-rich repeats. Nature 1993; 366: 751–756
  • Kobe B, Kajava AV. The leucine-rich repeat as a protein recognition motif. Curr Opin Struct Biol 2001; 11: 725–732
  • Kraulis PJ. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991; 24: 946–950
  • Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993; 26: 283–291
  • Lietzke SE, Keen NT, Yoder MD, Jurnak F. The three-dimensional structure of pectate lyase E, a plant virulence factor from Erwinia chrysanthemi. Plant Physiol 1994; 106: 849–862
  • Lietzke SE, Scavetta RD, Yoder MD, Jurnak F. The refined three-dimensional structure of pectate lyase E from Erwinia chrysanthemi. Plant Physiol 1996; 111: 73–92
  • Liou Y, Tocilj A, Davies PL, Jia Z. Mimicry of ice structure by surface hydroxyls and water of a β-helix antifreeze protein. Nature 2000; 406: 322–324
  • MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998; 102: 3586–3616
  • MSI InsightII HELP. 2001. www.accelrys.com/products/insight/index
  • Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP-a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995; 247: 536–540
  • Nummelin H, Merckel MC, Leo JC, Lankinen H, Skurnik M, Goldman A. The Yersinia adhesinYada collagen-binding domain structure is a novel left handed parallel beta-roll. EMBO J 2004; 23: 701–711
  • Oomen CJ, Van Ulsen P, Van Gelder P, Feijen M, Tommassen J, Gros P. Structure of the translocator domain of a bacterial autotransporter. EMBO J 2004; 23: 1257–1266
  • Pauling L, Corey RB. Two hydrogen-bonded spiral configurations of the polypeptide chain. J Am Chem Soc 1950; 72: 5349
  • Perutz MF, Finch JT, Berriman J, Lesk A. Amyloid fibres are water-filled nanotubes. PNAS 2002; 99: 5591–5595
  • Petersen HG. Accuracy and efficiency of the particle mesh Ewald method. J Chem Phys 1995; 103: 3668–3679
  • Peterson TN, Kauppinen S, Larsen S. The crystal structure of a rhamnagalacturonase A from Aspergillus aculeatus: A right-handed β-helix. Structure 1997; 5: 533–544
  • Pontius J, Richelle J, Odak SJ. Deviations from standard atomic volumes as a quality measure for protein crystal structures. J Mol Biol 1996; 246(1)121–136
  • Powell MJD. Restart procedures for the conjugate gradient method. Math Program 1977; 12: 241–254
  • Raetz CRH, Roderick SL. A left-handed parallel β helix in the structure of UDP-N-acetylglucosamine acyltransferase. Science 1995; 270: 997–1000
  • Ramachandran GN, Ramakrishnan C, Sasisekharan V. Stereochemistry of polypeptide chain configurations. J Mol Biol 1963; 7: 95–99
  • Richardson JS. Adv Protein Chem 1981; 34: 167–339
  • Richardson JS, Richardson DC. Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc Natl Acad Sci USA 2002; 99: 2754–2759
  • Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J Comp Phys 1977; 23: 327–341
  • Sprang SR. On a (b-) roll. TIBS 1993; 18: 313–314
  • Taylor SI, et al. Mutation in the insulin receptor gene: Update 1994. Endocr Rev 1994; 2: 58–65
  • Tyshenko MG, Doucet D, Davies PL, Walker VK. The antifreeze potential of the spruce budworm thermal hysteresis protein. Nat Biotechnol 1997; 15: 887–890
  • Verlet L. Computer “experiments” on classical fluids. Phys Rev 1967; 159: 98
  • Vetting MW, Hegde SS, Fajardo JE, Fiser A, Roderick SL, Takiff HE, Blanchard JS. Pentapeptide Repeat Proteins. Biochemistry 2006; 45: 1–10
  • Ward CW, Garrett TPJ. The relationship between the L1 and L2 domains of the insulin and epidermal growth factor receptors and leucine-rich repeate modules. BMC Bioinformatics 2001; 2(4)
  • Yoder MD, Jurnak F. The parallel β helix and other coiled folds. FASEB J 1995; 9: 335–342
  • Yoder MD, Jurnak F. The refined three-dimensional structure of pectate lyase C from Erwinia chrysanthemi at 2.2 Å resolution. Plant Physiol 1995; 107: 349–364
  • Yoder MD, Lietzke SE, Jurnak F. New domain motif: The structure of pectate lyase C, a secreted plant virulence factor. Science 1993; 260: 1503–1507
  • Yoder MD, Lietzke SE, Jurnak F. Unusual structural features in the parallel β-helix in pectate lyases. Structure 1993; 1: 24–251

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.