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Original Articles

The Tumbleweed: Towards a synthetic protein motor

, , , , , , , , , , & show all
Pages 204-212 | Received 08 Dec 2008, Accepted 12 Mar 2009, Published online: 07 Sep 2010

References

  • Ambroggio , XI and Kuhlman , B . 2006 . “Computational design of a single amino acid sequence that can switch between two distinct protein folds.” . J. Am. Chem. Soc. , 128 (4) : 1154 – 1161 .
  • Asbury , CL . 2005 . “Kinesin: world's tiniest biped.” . Curr. Opin. Cell Biol. , 17 : 89 – 97 .
  • Astumian , RD . 1997 . “Thermodynamics and kinetics of a Brownian motor.” . Science , 276 (5314) : 917 – 922 .
  • Astumian , RD . 2007 . “Design principles for Brownian molecular machines: how to swim in molasses and walk in a hurricane.” . Phys. Chem. Chem. Phys. , 9 (37) : 5067 – 5083 .
  • Astumian , RD and Hänggi , P . 2002 . “Brownian motors.” . Phys. Today , 55 (11) : 33 – 39 .
  • Balzani , V , Credi , A , Silvi , S and Venturi , M . 2006 . “Artificial nanomachines based on interlocked molecular species: recent advances.” . Chem. Soc. Rev. , 35 (11) : 1135 – 1149 .
  • Bar‐Nahum , G , Epshtein , V , Ruckenstein , AE , Rafikov , R , Mustaev , A and Nudler , E . 2005 . “A ratchet mechanism of transcription elongation and its control.” . Cell , 120 (2) : 183 – 193 .
  • Bath , J , Green , SJ and Turberfield , AJ . 2005 . “A free‐running DNA motor powered by a nicking enzyme.” . Angew. Chem., Int. Ed. , 44 (28) : 4358 – 4361 .
  • Bath , J and Turberfield , AJ . 2007 . “DNA nanomachines.” . Nat. Nanotechnol. , 2 (5) : 275 – 284 .
  • Berman , HM , Westbrook , J , Feng , Z , Gilliland , G , Bhat , TN , Weissig , H , Shindyalov , IN and Bourne , PE . 2000 . “The protein data bank.” . Nucleic Acids Res. , 28 : 235 – 242 .
  • Block , SM . 2007 . “Kinesin motor mechanics: binding, stepping, tracking, gating, and limping.” . Biophys. J. , 92 (9) : 2986 – 2995 .
  • Borden , KLB , Beckmann , P and Lane , AN . 1991 . “Determination of the orientations of tryptophan analogues bound to the TRP repressor and the relationship to activation.” . Eur. J. Biochem. , 202 (2) : 459 – 470 .
  • Bromley , EHC , Channon , K , Moutevelis , E and Woolfson , DN . 2008 . “Peptide and protein building blocks for synthetic biology: from programming biomolecules to self‐organized biomolecular systems.” . Chem. Biol. , 3 (1) : 38 – 50 .
  • Bustamante , C , Chemla , YR , Forde , NR and Izhaky , D . 2004 . “Mechanical processes in biochemistry.” . Annu. Rev. Biochem. , 73 : 705 – 748 .
  • Bustamante , C , Keller , D and Oster , G . 2001 . “The physics of molecular motors.” . Acc. Chem. Res. , 34 (6) : 412 – 420 .
  • Carey , J . 1988 . “Gel retardation at low PH resolves TRP repressor‐DNA complexes for quantitative study.” . Proc. Natl. Acad. Sci. U.S.A. , 85 (4) : 975 – 979 .
  • Cerasoli , E , Sharpe , BK and Woolfson , DN . 2005 . “ZiCo: a peptide designed to switch folded state upon binding zinc.” . J. Am. Chem. Soc. , 127 : 15008 – 15009 .
  • Ciani , B , Hutchinson , EG , Sessions , RB and Woolfson , DN . 2002 . “A designed system for assessing how sequence affects alpha to beta conformational transitions in proteins.” . J. Biol. Chem. , 277 (12) : 10150 – 10155 .
  • Cooper , A , McAlpine , A and Stockley , PG . 1994 . “Calorimetric studies of the energetics of protein‐DNA interaction in the Escherichia‐coli methionine repressor (METJ) system.” . FEBS Lett. , 348 (1) : 41 – 45 .
  • Craig , E and Linke , H . 2009 . “A mechanokinetic model for the myosin V walking mechanism.” . Biophys. J. , 96 (3) : 128a
  • See EPAPS Document No.E‐HJFOA5–3‐007904 for supplemental material. This document can be reached through a direct link in the online article's HTML reference section or via the EPAPS homepage (http://www.aip.org/pubservs/epaps.html).
  • Feringa , BL . 2007 . “The art of building small: from molecular switches to molecular motors.” . J. Org. Chem. , 72 (18) : 6635 – 6652 .
  • Feynman , R . 1989 . “Feynman's office: the last blackboards.” . Phys. Today , 42 : 88
  • Finer , JT , Simmons , RM and Spudich , JA . 1994 . “Single myosin molecule mechanics—piconewton forces and nanometer steps.” . Nature (London) , 368 (6467) : 113 – 119 .
  • Finucane , MD and Jardetzky , O . 2003 . “Surface plasmon resonance studies of wild‐type and AV77 tryptophan repressor resolve ambiguities in super‐repressor activity.” . Protein Sci. , 12 : 1612 – 1620 .
  • Garvie , CW and Phillips , SEV . 2000 . “Direct and indirect readout in mutant Met repressor‐operator complexes.” . Structure (London) , 8 (9) : 905 – 914 .
  • Glasfeld , A , Koehler , AN , Schumacher , MA and Brennan , RG . 1999 . “The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions.” . J. Mol. Biol. , 291 (2) : 347 – 361 .
  • Greenleaf , WJ , Woodside , MT and Block , SM . 2007 . “High‐resolution, single‐molecule measurements of biomolecular motion.” . Annu. Rev. Biophys. Biomol. Struct. , 36 : 171 – 190 .
  • Guajardo , R and Sousa , R . 1997 . “A model for the mechanism of polymerase translocation.” . J. Mol. Biol. , 265 (1) : 8 – 19 .
  • He , YY , Garvie , CW , Elworthy , S , Manfield , IW , McNally , T , Lawrenson , ID , Phillips , SEV and Stockley , PG . 2002 . “Structural and functional studies of an intermediate on the pathway to operator binding by Escherichia coli MetJ.” . J. Mol. Biol. , 320 (1) : 39 – 53 .
  • Howard , J . 1997 . “Molecular motors: structural adaptations to cellular functions.” . Nature (London) , 389 (6651) : 561 – 567 .
  • Howard , J . 2006 . “Protein power strokes.” . Curr. Biol. , 16 (14) : R517 – R519 .
  • Jiang , L . 2008 . “De novo computational design of retro‐aldol enzymes.” . Science , 319 : 1387 – 1391 .
  • Jülicher , F , Adjari , A and Prost , J . 1997 . “Modeling molecular motors.” . Rev. Mod. Phys. , 69 (4) : 1269 – 1281 .
  • Kafri , Y , Lubensky , DK and Nelson , DR . 2005 . “Dynamics of molecular motors with finite processivity on heterogeneous tracks.” . Phys. Rev. E , 71 (4) : 041906
  • Kay , ER , Leigh , DA and Zerbetto , F . 2007 . “Synthetic molecular motors and mechanical machines.” . Angew. Chem., Int. Ed. , 46 (1–2) : 72 – 191 .
  • Kempe , T , Kent , SBH , Chow , F , Peterson , SM , Sundquist , WI , Litalien , JJ , Harbrecht , D , Plunkett , D and Delorbe , WJ . 1985 . “Multiple‐copy genes—production and modification of monomeric peptides from large multimeric fusion proteins.” . Gene , 39 (2–3) : 239 – 245 .
  • Kitamura , K , Tokunaga , M , Iwane , AH and Yanagida , T . 1999 . “A single myosin head moves along an actin filament with regular steps of 5.3 nanometres.” . Nature (London) , 397 (6715) : 129 – 134 .
  • Kojima , H , Muto , E , Higuchi , H and Yanagida , T . 1997 . “Mechanics of single kinesin molecules measured by optical trapping nanometry.” . Biophys. J. , 73 (4) : 2012 – 2022 .
  • Kolomeisky , AB and Fisher , ME . 2007 . “Molecular motors: a theorist's perspective.” . Annu. Rev. Phys. Chem. , 58 : 675 – 695 .
  • Kottas , GS , Clarke , LI , Horinek , D and Michl , J . 2005 . “Artificial molecular rotors.” . Chem. Rev. (Washington, D.C.) , 105 (4) : 1281 – 1376 .
  • Kuhlman , B , Dantas , G , Ireton , GC , Varani , G , Stoddard , BL and Baker , D . 2003 . “Design of a novel globular protein fold with atomic level accuracy.” . Science , 302 (5649) : 1364 – 1368 .
  • Lawson , CL . 1993 . “Tandem binding in crystals of a Trp repressor operator half‐site complex.” . Nature (London) , 366 (6451) : 178 – 182 .
  • Lippow , SM and Tidor , B . 2007 . “Progress in computational protein design.” . Curr. Opin. Biotechnol. , 18 (4) : 305 – 311 .
  • Liu , Y and Kuhlman , B . 2006 . “Rosetta Design server for protein design.” . Nucleic Acids Res. , 34 : W235 – W238 .
  • Lupas , AN . 2005 . “The structure of alpha‐helical coiled coils.” . Adv. Protein Chem. , 70 : 37 – 78 .
  • Mickler , M , Schleiff , E and Hugel , T . 2008 . “From biological towards artificial molecular motors.” . Chem Phys Chem , 9 (11) : 1503 – 1509 .
  • Nagadoi , A . 1995 . “Structural comparison of the free and DNA bound forms of the purine repressor DNA‐binding domain.” . Structure (London) , 3 (11) : 1217 – 1224 .
  • Nishiyama , M , Higuchi , H , Ishii , Y , Taniguchi , Y and Yanagida , T . 2003 . “Single molecule processes on the stepwise movement of ATP‐driven molecular motors.” . BioSystems , 71 (1–2) : 145 – 156 .
  • Noji , H , Yasuda , R , Yoshida , M and Kinosita , K . 1997 . “Direct observation of the rotation of F‐1‐ATPase.” . Nature (London) , 386 (6622) : 299 – 302 .
  • Otwinowski , Z , Schevitz , RW , Zhang , RG , Lawson , CL , Joachimiak , A , Marmorstein , RQ , Luisi , BF and Sigler , PB . 1988 . “Crystalstructure of Trp repressor operator complex at atomic resolution.” . Nature (London) , 335 (6188) : 321 – 329 .
  • Pandya , MJ , Cerasoli , E , Joseph , A , Stoneman , RG , Waite , E and Woolfson , DN . 2004 . “Sequence and structural duality: designing peptides to adopt two stable conformations.” . J. Am. Chem. Soc. , 126 (51) : 17016 – 17024 .
  • Parsons , ID , Persson , B , Mekhalfia , A , Blackburn , GM and Stockley , PG . 1995 . “Probing the molecular mechanism of action of co‐repressor in the E. coli methionine repressor‐operator complex using surface‐plasmon resonance (SPR).” . Nucleic Acids Res. , 23 (2) : 211 – 216 .
  • Pei , R , Taylor , SK , Stefanovic , D , Rudchenko , S , Mitchell , TE and Stojanovic , MN . 2006 . “Behavior of polycatalytic assemblies in a substrate‐displaying matrix.” . J. Am. Chem. Soc. , 128 (39) : 12693 – 12699 .
  • Phillips , K and Phillips , SE V . 1994 . “Electrostatic activation of Escherichia‐coli methionine repressor.” . Structure (London) , 2 (4) : 309 – 316 .
  • Poole , AM and Ranganathan , R . 2006 . “Knowledge‐based potentials in protein design.” . Curr. Opin. Struct. Biol. , 16 (4) : 508 – 513 .
  • Reedstrom , RJ , Brown , MP , Grillo , A , Roen , D and Royer , CA . 1997 . “Affinity and specificity of trp repressor‐DNA interactions studied with fluorescent oligonucleotides.” . J. Mol. Biol. , 273 (3) : 572 – 585 .
  • Reimann , P and Hänggi , P . 2002 . “Introduction to the physics of Brownian motors.” . Appl. Phys. A: Mater. Sci. Process. , 75 (2) : 169 – 178 .
  • Rice , S . 1999 . “A structural change in the kinesin motor protein that drives motility.” . Nature (London) , 402 (6763) : 778 – 784 .
  • Rief , M , Rock , RS , Mehta , AD , Mooseker , MS , Cheney , RE and Spudich , JA . 2000 . “Myosin‐V stepping kinetics: A molecular model for processivity.” . Proc. Natl. Acad. Sci. U.S.A. , 97 (17) : 9482 – 9486 .
  • Rolfes , RJ and Zalkin , H . 1990 . “Purification of the Escherichia‐coli purine regulon repressor and identification of co‐repressors.” . J. Bacteriol. , 172 (10) : 5637 – 5642 .
  • Schevitz , RW , Otwinowski , Z , Joachimiak , A , Lawson , CL and Sigler , PB . 1985 . “The 3‐dimensional structure of TRP repressor.” . Nature (London) , 317 (6040) : 782 – 786 .
  • Schief , WR and Howard , J . 2001 . “Conformational changes during kinesin motility.” . Curr. Opin. Cell Biol. , 13 : 19 – 28 .
  • Schnitzer , MJ , Visscher , K and Block , SM . 2000 . “Force production by single kinesin motors.” . Nat. Cell Biol. , 2 (10) : 718 – 723 .
  • Schumacher , MA , Choi , KY , Lu , F , Zalkin , H and Brennan , RG . 1995 . “Mechanism of corepressor‐mediated specific DNA‐binding by the purine repressor.” . Cell , 83 (1) : 147 – 155 .
  • Schumacher , MA , Choi , KY , Zalkin , H and Brennan , RG . 1994 . “Crystalstructure of LacI member, PurR, bound to DNA‐minor‐groove binding by alpha‐helices.” . Science , 266 (5186) : 763 – 770 .
  • Sellers , JR and Veigel , C . 2006 . “Walking with myosin V.” . Curr. Opin. Cell Biol. , 18 (1) : 68 – 73 .
  • Shin , JS and Pierce , NA . 2004 . “A synthetic DNA walker for molecular transport.” . J. Am. Chem. Soc. , 126 (35) : 10834 – 10835 .
  • Stockley , PG , Baron , AJ , Wild , CM , Parsons , ID , Miller , CM , Holtham , CAM and Baumberg , S . 1998 . “Dissecting the molecular details of prokaryotic transcriptional control by surface plasmon resonance: the methionine and arginine repressor proteins.” . Biosens. Bioelectron. , 13 : 637 – 650 .
  • Svoboda , K , Schmidt , CF , Schnapp , BJ and Block , SM . 1993 . “Direct observation of kinesin stepping by optical trapping interferometry.” . Nature (London) , 365 (6448) : 721 – 727 .
  • Vale , RD and Milligan , RA . 2000 . “The way things move: looking under the hood of molecular motor proteins.” . Science , 288 (5463) : 88 – 95 .
  • Vale , RD and Oosawa , F . 1990 . “Protein motors and Maxwell's demons: does mechanochemical transduction involve a thermal ratchet?” . Adv. Biophys. , 26 : 97 – 134 .
  • Wang , HY , Elston , T , Mogilner , A and Oster , G . 1998 . “Force generation in RNA polymerase.” . Biophys. J. , 74 (3) : 1186 – 1202 .
  • Wang , HY and Oster , G . 1998 . “Energy transduction in the F‐1 motor of ATP synthase.” . Nature (London) , 396 (6708) : 279 – 282 .
  • Wang , Y , Guo , L , Cox , EC and Ong , NP . 2009 . “Quantitative transcription factor binding kinetics at the single‐molecule level.” . Biophys. J. , 96 : 609 – 620 .
  • Wang , YM , Flyvbjerg , H , Cox , EC and Austin , RH . 2007 . “When is a distribution not a distribution, and why would you care: singlemolecule measurements of repressor protein 1‐D diffusion on DNA.” . In Controlled Nanoscale Motion , Vol. 711 , 217 – 240 . Berlin : Springer .
  • Wang , YM , Tegenfeldt , JO , Reisner , W , Riehn , R , Guan , XJ , Guo , L , Golding , I , Cox , EC , Sturm , J and Austin , RH . 2005 . “Singlemolecule studies of repressor‐DNA interactions show long‐range interactions.” . Proc. Natl. Acad. Sci. U.S.A. , 102 (28) : 9796 – 9801 .
  • Wolenski , JS , Cheney , RE , Mooseker , MS and Forscher , P . 1995 . “Invitro motility of immunoadsorbed brain myosin‐V using a limulus acrosomal process and optical tweezer‐based assay.” . J. Cell. Sci. , 108 : 1489 – 1496 .
  • Woolfson , DN . 2005 . “The design of coiled‐coil structures and assemblies.” . Adv. Protein Chem. , 70 : 79 – 112 .
  • Yildiz , A , Forkey , JN , McKinney , SA , Ha , T , Goldman , YE and Selvin , PR . 2003 . “Myosin V walks hand‐over‐hand: single fluorophore imaging with 1.5‐nm localization.” . Science , 300 (5628) : 2061 – 2065 .
  • Yin , P , Yan , H , Daniell , XG , Turberfield , AJ and Reif , JH . 2004 . “A unidirectional DNA walker that moves autonomously along a track.” . Angew. Chem., Int. Ed. , 43 (37) : 4906 – 4911 .
  • Yurke , B . 2007 . “Using DNA to power the nanoworld.” . Lect. Notes Phys. , 711 : 331 – 347 .
  • Zhang , RG , Joachimiak , A , Lawson , CL , Schevitz , RW , Otwinowski , Z and Sigler , PB . 1987 . “The crystal structure of trp aporepressor at 1.8 Å shows how binding tryptophan enhances DNA affinity.” . Nature (London) , 327 (6123) : 591 – 597 .

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