Skip to main content
SpringerLink
Log in

Molecular dynamics simulation of bacterial flagella

  • Review
  • Published:
Biophysical Reviews Aims and scope Submit manuscript

Abstract

The bacterial flagellum is a biological nanomachine for the locomotion of bacteria, and is seen in organisms like Salmonella and Escherichia coli. The flagellum consists of tens of thousands of protein molecules and more than 30 different kinds of proteins. The basal body of the flagellum contains a protein export apparatus and a rotary motor that is powered by ion motive force across the cytoplasmic membrane. The filament functions as a propeller whose helicity is controlled by the direction of the torque. The hook that connects the motor and filament acts as a universal joint, transmitting torque generated by the motor to different directions. This report describes the use of molecular dynamics to study the bacterial flagellum. Molecular dynamics simulation is a powerful method that permits the investigation, at atomic resolution, of the molecular mechanisms of biomolecular systems containing many proteins and solvent. When applied to the flagellum, these studies successfully unveiled the polymorphic supercoiling and transportation mechanism of the filament, the universal joint mechanism of the hook, the ion transfer mechanism of the motor stator, the flexible nature of the transport apparatus proteins, and activation of proteins involved in chemotaxis.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  • Aizawa S (2001) Bacterial flagella and type III secretion systems. FEMS Microbiol Lett 202(2):157–164

  • Arkhipov A, Freddolino PL, Imada K, Namba K, Schulten K (2006) Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum. Biophys J 91(12):4589–4597

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Asai Y, Yakushi T, Kawagishi I, Homma M (2003) Ion-coupling determinants of Na+-driven and H+-driven flagellar motors. J Mol Biol 327(2):453–463

    Article  CAS  PubMed  Google Scholar 

  • Asakura S (1970) Polymerization of flagellin and polymorphism of flagella. Adv Biophys 1:99–155

    CAS  PubMed  Google Scholar 

  • Berg HC (2003) The rotary motor of bacterial flagella. Annu Rev Biochem 72(1):19–54

    Article  CAS  PubMed  Google Scholar 

  • Berg HC, Anderson RA (1973) Bacteria swim by rotating their flagellar filaments. Nature 245(5425):380–382

    Article  CAS  PubMed  Google Scholar 

  • Berry RM (1993) Torque and switching in the bacterial flagellar motor. An electrostatic model. Biophys J 64(4):961–973

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Block SM, Berg HC (1984) Successive incorporation of force-generating units in the bacterial rotary motor. Nature 309(5967):470–472

    Article  CAS  PubMed  Google Scholar 

  • Braun TF, Blair DF (2001) Targeted disulfide cross-linking of the MotB protein of Escherichia coli: evidence for two H(+) channels in the stator complex. Biochemistry 40(43):13051–13059

    Article  CAS  PubMed  Google Scholar 

  • Braun TF, Al-Mawsawi LQ, Kojima S, Blair DF (2004) Arrangement of core membrane segments in the MotA/MotB proton-channel complex of Escherichia coli. Biochemistry 43(1):35–45

    Article  CAS  PubMed  Google Scholar 

  • Calladine CR (1975) Construction of bacterial flagella. Nature 255(5504):121–124

    Article  CAS  PubMed  Google Scholar 

  • Calladine CR (1976) Design requirements for the construction of bacterial flagella. J Theor Biol 57(2):469–489

    Article  CAS  PubMed  Google Scholar 

  • Calladine CR (1978) Change of waveform in bacterial flagella: the role of mechanics at the molecular level. J Mol Biol 118(4):457–479

    Article  CAS  Google Scholar 

  • Chng C-P, Kitao A (2008) Thermal unfolding simulations of bacterial flagellin: insight into its refolding before assembly. Biophys J 94(10):3858–3871

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chng C-P, Kitao A (2010) Mechanical unfolding of bacterial flagellar filament protein by molecular dynamics simulation. J Mol Graph Model 28(6):548–554

    Article  CAS  PubMed  Google Scholar 

  • Chun SY, Parkinson JS (1988) Bacterial motility: membrane topology of the Escherichia coli MotB protein. Science 239(4837):276–278

    Article  CAS  PubMed  Google Scholar 

  • Cornelis GR (2006) The type III secretion injectisome. Nat Rev Microbiol 4(11):811–825

    Article  CAS  PubMed  Google Scholar 

  • Dasgupta J, Dattagupta JK (2008) Structural determinants of V. cholerae CheYs that discriminate them in FliM binding: comparative modeling and MD simulation studies. J Biomol Struct Dyn 25(5):495–503

    Article  CAS  PubMed  Google Scholar 

  • De Mot R, Vanderleyden J (1994) The C-terminal sequence conservation between Ompa-related outer membrane proteins and Motb suggests a common function in both Gram-positive and Gram-negative bacteria, possibly in the interaction of these domains with peptidoglycan. Mol Microbiol 12(2):333–336

    Article  PubMed  Google Scholar 

  • Dean GE, Macnab RM, Stader J, Matsumura P, Burks C (1984) Gene sequence and predicted amino acid sequence of the motA protein, a membrane-associated protein required for flagellar rotation in Escherichia coli. J Bacteriol 159(3):991–999

    CAS  PubMed  PubMed Central  Google Scholar 

  • Elston TC, Oster G (1997) Protein turbines. I: the bacterial flagellar motor. Biophys J 73(2):703–721

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Enomoto M (1966) Genetic studies of paralyzed mutants in Salmonella. II. Mapping of three mot loci by linkage analysis. Genetics 54(5):1069–1076

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fraiberg M, Afanzar O, Cassidy CK, Gabashvili A, Schulten K, Levin Y, Eisenbach M (2015) CheY’s acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli. Mol Microbiol 95(2):231–244

    Article  CAS  PubMed  Google Scholar 

  • Fraser GM, Hirano T, Ferris HU, Devgan LL, Kihara M, Macnab RM (2003) Substrate specificity of type III flagellar protein export in Salmonella is controlled by subdomain interactions in FlhB. Mol Microbiol 48(4):1043–1057

    Article  CAS  PubMed  Google Scholar 

  • Fujii T, Kato T, Namba K (2009) Specific arrangement of alpha-helical coiled coils in the core domain of the bacterial flagellar hook for the universal joint function. Structure 17(11):1485–1493

    Article  CAS  PubMed  Google Scholar 

  • Furuta T, Samatey FA, Matsunami H, Imada K, Namba K, Kitao A (2007) Gap compression/extension mechanism of bacterial flagellar hook as the molecular universal joint. J Struct Biol 157(3):481–490

    Article  CAS  PubMed  Google Scholar 

  • Ghosh A, Albers SV (2011) Assembly and function of the archaeal flagellum. Biochem Soc Trans 39(1):64–69

    Article  CAS  PubMed  Google Scholar 

  • Hasegawa K, Yamashita I, Namba K (1998) Quasi- and nonequivalence in the structure of bacterial flagellar filament. Biophys J 74(1):569–575

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hayward S (1999) Structural principles governing domain motions in proteins. Proteins 36(4):425–435

    Article  CAS  PubMed  Google Scholar 

  • Hayward S, Berendsen HJ (1998) Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins 30(2):144–154

    Article  CAS  PubMed  Google Scholar 

  • Hirano T, Yamaguchi S, Oosawa K, Aizawa S (1994) Roles of FliK and FlhB in determination of flagellar hook length in Salmonella typhimurium. J Bacteriol 176(17):5439–5449

  • Hirota N, Kitada M, Imae Y (1981) Flagellar motors of alkalophilic Bacillus are powered by an electrochemical potential gradient of Na+. FEBS Lett 132(2):278–280

    Article  CAS  Google Scholar 

  • Honda S, Uedaira H, Vonderviszt F, Kidokoro S, Namba K (1999) Folding energetics of a multidomain protein, flagellin. J Mol Biol 293(3):719–732

    Article  CAS  PubMed  Google Scholar 

  • Hotani H (1980) Micro-video study of moving bacterial flagellar filaments II. Polymorphic transition in alcohol. Biosystems 12(3–4):325–330

    Article  CAS  PubMed  Google Scholar 

  • Hotani H (1982) Micro-video study of moving bacterial flagellar filaments: III. Cyclic transformation induced by mechanical force. J Mol Biol 156(4):791–806

    Article  CAS  PubMed  Google Scholar 

  • Hyakutake A, Homma M, Austin MJ, Boin MA, Häse CC, Kawagishi I (2005) Only one of the five CheY homologs in Vibrio cholerae directly switches flagellar rotation. J Bacteriol 187(24):8403–8410

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ikeda T, Yamaguchi S, Hotani H (1993) Flagellar growth in a filament-less Salmonella fliD mutant supplemented with purified hook-associated protein 2. J Biochem 114(1):39–44

    Article  CAS  PubMed  Google Scholar 

  • Isralewitz B, Baudry J, Gullingsrud J, Kosztin D, Schulten K (2001a) Steered molecular dynamics investigations of protein function. J Mol Graph Model 19(1):13–25

    Article  CAS  PubMed  Google Scholar 

  • Isralewitz B, Gao M, Schulten K (2001b) Steered molecular dynamics and mechanical functions of proteins. Curr Opin Struct Biol 11(2):224–230

    Article  CAS  PubMed  Google Scholar 

  • Jensen MØ, Park S, Tajkhorshid E, Schulten K (2002) Energetics of glycerol conduction through aquaglyceroporin GlpF. Proc Natl Acad Sci U S A 99(10):6731–6736

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kamiya R, Asakura S (1976a) Flagellar transformations at alkaline pH. J Mol Biol 108(2):513–518

    Article  CAS  PubMed  Google Scholar 

  • Kamiya R, Asakura S (1976b) Helical transformations of Salmonella flagella in vitro. J Mol Biol 106(1):167–186

    Article  CAS  PubMed  Google Scholar 

  • Kamiya R, Hotani H, Asakura S (1982) Polymorphic transition in bacterial flagella. Symp Soc Exp Biol 35:53–76

    CAS  PubMed  Google Scholar 

  • Kanto S, Okino H, Aizawa S, Yamaguchi S (1991) Amino acids responsible for flagellar shape are distributed in terminal regions of flagellin. J Mol Biol 219(3):471–480

    Article  CAS  PubMed  Google Scholar 

  • Kato S, Okamoto M, Asakura S (1984) Polymorphic transition of the flagellar polyhook from Escherichia coli and Salmonella typhimurium. J Mol Biol 173(4):463–476

    Article  CAS  PubMed  Google Scholar 

  • Kawamoto A, Morimoto YV, Miyata T, Minamino T, Hughes KT, Kato T, Namba K (2013) Common and distinct structural features of Salmonella injectisome and flagellar basal body. Sci Rep 3:3369

    Article  PubMed  PubMed Central  Google Scholar 

  • Khan S, Dapice M, Reese TS (1988) Effects of mot gene expression on the structure of the flagellar motor. J Mol Biol 202(3):575–584

    Article  CAS  PubMed  Google Scholar 

  • Kim EA, Price-Carter M, Carlquist WC, Blair DF (2008) Membrane segment organization in the stator complex of the flagellar motor: implications for proton flow and proton-induced conformational change. Biochemistry 47(43):11332–11339

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kitao A, Takemura K (2017) High anisotropy and frustration: the keys to regulating protein function efficiently in crowded environments. Curr Opin Struct Biol 42:50–58

    Article  CAS  PubMed  Google Scholar 

  • Kitao A, Yonekura K, Maki-Yonekura S, Samatey FA, Imada K, Namba K, Go N (2006) Switch interactions control energy frustration and multiple flagellar filament structures. Proc Natl Acad Sci U S A 103(13):4894–4899

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kojima S, Blair DF (2001) Conformational change in the stator of the bacterial flagellar motor. Biochemistry 40(43):13041–13050

    Article  CAS  PubMed  Google Scholar 

  • Kojima S, Imada K, Sakuma M, Sudo Y, Kojima C, Minamino T, Homma M, Namba K (2009) Stator assembly and activation mechanism of the flagellar motor by the periplasmic region of MotB. Mol Microbiol 73(4):710–718

    Article  CAS  PubMed  Google Scholar 

  • Kutsukake K, Minamino T, Yokoseki T (1994) Isolation and characterization of FliK-independent flagellation mutants from Salmonella typhimurium. J Bacteriol 176(24):7625–7629

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Larsen SH, Adler J, Gargus JJ, Hogg RW (1974a) Chemomechanical coupling without ATP: the source of energy for motility and chemotaxis in bacteria. Proc Natl Acad Sci U S A 71(4):1239–1243

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Larsen SH, Reader RW, Kort EN, Tso WW, Adler J (1974b) Change in direction of flagellar rotation is the basis of the chemotactic response in Escherichia coli. Nature 249(5452):74–77

    Article  CAS  PubMed  Google Scholar 

  • Lountos GT, Austin BP, Nallamsetty S, Waugh DS (2009) Atomic resolution structure of the cytoplasmic domain of Yersinia pestis YscU, a regulatory switch involved in type III secretion. Protein Sci 18(2):467–474

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Macnab RM (2003) How bacteria assemble flagella. Annu Rev Microbiol 57:77–100

    Article  CAS  PubMed  Google Scholar 

  • Macnab RM, Ornston MK (1977) Normal-to-curly flagellar transitions and their role in bacterial tumbling. Stabilization of an alternative quaternary structure by mechanical force. J Mol Biol 112(1):1–30

    Article  CAS  PubMed  Google Scholar 

  • Maki-Yonekura S, Yonekura K, Namba K (2010) Conformational change of flagellin for polymorphic supercoiling of the flagellar filament. Nat Struct Mol Biol 17(4):417–422

    Article  CAS  PubMed  Google Scholar 

  • Matsunami H, Barker CS, Yoon YH, Wolf M, Samatey FA (2016) Complete structure of the bacterial flagellar hook reveals extensive set of stabilizing interactions. Nat Commun 7:13425

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meister M, Lowe G, Berg HC (1987) The proton flux through the bacterial flagellar motor. Cell 49(5):643–650

    Article  CAS  PubMed  Google Scholar 

  • Meshcheryakov VA, Kitao A, Matsunami H, Samatey FA (2013) Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins. Acta Crystallogr D Biol Crystallogr 69(Pt 5):812–820

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Minamino T, Macnab RM (1999) Components of the Salmonella flagellar export apparatus and classification of export substrates. J Bacteriol 181(5):1388–1394

    CAS  PubMed  PubMed Central  Google Scholar 

  • Morgan DG, Macnab RM, Francis NR, DeRosier DJ (1993) Domain organization of the subunit of the Salmonella typhimurium flagellar hook. J Mol Biol 229(1):79–84

    Article  CAS  PubMed  Google Scholar 

  • Muskotál A, Király R, Sebestyén A, Gugolya Z, Végh BM, Vonderviszt F (2006) Interaction of FliS flagellar chaperone with flagellin. FEBS Lett 580(16):3916–3920

    Article  PubMed  Google Scholar 

  • Namba K, Vonderviszt F (1997) Molecular architecture of bacterial flagellum. Q Rev Biophys 30(1):1–65

    Article  CAS  PubMed  Google Scholar 

  • Nishihara Y, Kitao A (2015) Gate-controlled proton diffusion and protonation-induced ratchet motion in the stator of the bacterial flagellar motor. Proc Natl Acad Sci U S A 112(25):7737–7742

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nishima W, Qi G, Hayward S, Kitao A (2009) DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins. Bioinformatics 25(5):628–635

    Article  CAS  PubMed  Google Scholar 

  • O’Brien EJ, Bennett PM (1972) Structure of straight flagella from a mutant Salmonella. J Mol Biol 70(1):133–152

    Article  PubMed  Google Scholar 

  • O’Neill J, Xie M, Hijnen M, Roujeinikova A (2011) Role of the MotB linker in the assembly and activation of the bacterial flagellar motor. Acta Crystallogr D Biol Crystallogr 67(Pt 12):1009–1016

    Article  PubMed  Google Scholar 

  • Ozin AJ, Claret L, Auvray F, Hughes C (2003) The FliS chaperone selectively binds the disordered flagellin C-terminal D0 domain central to polymerisation. FEMS Microbiol Lett 219(2):219–224

    Article  CAS  PubMed  Google Scholar 

  • Patterson-Delafield J, Martinez RJ, Stocker BA, Yamaguchi S (1973) A new fla gene in Salmonella typhimurium—flaR—and its mutant phenotype-superhooks. Arch Microbiol 90(2):107–120

    CAS  Google Scholar 

  • Qi G, Lee R, Hayward S (2005) A comprehensive and non-redundant database of protein domain movements. Bioinformatics 21(12):2832–2838

    Article  CAS  PubMed  Google Scholar 

  • Reboul CF, Andrews DA, Nahar MF, Buckle AM, Roujeinikova A (2011) Crystallographic and molecular dynamics analysis of loop motions unmasking the peptidoglycan-binding site in stator protein MotB of flagellar motor. PLoS One 6(4):e18981

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roujeinikova A (2008) Crystal structure of the cell wall anchor domain of MotB, a stator component of the bacterial flagellar motor: implications for peptidoglycan recognition. Proc Natl Acad Sci U S A 105(30):10348–10353

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saijo-Hamano Y, Imada K, Minamino T, Kihara M, Shimada M, Kitao A, Namba K (2010) Structure of the cytoplasmic domain of FlhA and implication for flagellar type III protein export. Mol Microbiol 76(1):260–268

    Article  CAS  PubMed  Google Scholar 

  • Samatey FA, Imada K, Nagashima S, Vonderviszt F, Kumasaka T, Yamamoto M, Namba K (2001) Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling. Nature 410(6826):331–337

    Article  CAS  PubMed  Google Scholar 

  • Samatey FA, Matsunami H, Imada K, Nagashima S, Shaikh TR, Thomas DR, Chen JZ, Derosier DJ, Kitao A, Namba K (2004) Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism. Nature 431(7012):1062–1068

    Article  CAS  PubMed  Google Scholar 

  • Samuel AD, Berg HC (1996) Torque-generating units of the bacterial flagellar motor step independently. Biophys J 71(2):918–923

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shaikh TR, Thomas DR, Chen JZ, Samatey FA, Matsunami H, Imada K, Namba K, Derosier DJ (2005) A partial atomic structure for the flagellar hook of Salmonella typhimurium. Proc Natl Acad Sci U S A 102(4):1023–1028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sharp LL, Zhou J, Blair DF (1995a) Tryptophan-scanning mutagenesis of MotB, an integral membrane protein essential for flagellar rotation in Escherichia coli. Biochemistry 34(28):9166–9171

    Article  CAS  PubMed  Google Scholar 

  • Sharp LL, Zhou J, Blair DF (1995b) Features of MotA proton channel structure revealed by tryptophan-scanning mutagenesis. Proc Natl Acad Sci U S A 92(17):7946–7950

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Silverman M, Simon M (1974) Characterization of Escherichia coli flagellar mutants that are insensitive to catabolite repression. J Bacteriol 120(3):1196–1203

    CAS  PubMed  PubMed Central  Google Scholar 

  • Stader J, Matsumura P, Vacante D, Dean GE, Macnab RM (1986) Nucleotide sequence of the Escherichia coli motB gene and site-limited incorporation of its product into the cytoplasmic membrane. J Bacteriol 166(1):244–252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tanner DE, Ma W, Chen Z, Schulten K (2011) Theoretical and computational investigation of flagellin translocation and bacterial flagellum growth. Biophys J 100(11):2548–2556

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Terahara N, Sano M, Ito M (2012) A Bacillus flagellar motor that can use both Na+ and K+ as a coupling ion is converted by a single mutation to use only Na+. PLoS One 7(9):e46248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thomas NA, Bardy SL, Jarrell KF (2001) The archaeal flagellum: a different kind of prokaryotic motility structure. FEMS Microbiol Rev 25(2):147–174

    Article  CAS  PubMed  Google Scholar 

  • Turner L, Ryu WS, Berg HC (2000) Real-time imaging of fluorescent flagellar filaments. J Bacteriol 182(10):2793–2801

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vonderviszt F, Aizawa SI, Namba K (1991) Role of the disordered terminal regions of flagellin in filament formation and stability. J Mol Biol 221(4):1461–1474

    Article  CAS  PubMed  Google Scholar 

  • Wagenknecht T, DeRosier DJ, Aizawa S, Macnab RM (1982) Flagellar hook structures of Caulobacter and Salmonella and their relationship to filament structure. J Mol Biol 162(1):69–87

    Article  CAS  PubMed  Google Scholar 

  • Walz D, Caplan SR (2000) An electrostatic mechanism closely reproducing observed behavior in the bacterial flagellar motor. Biophys J 78(2):626–651

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Welch M, Oosawa K, Aizawa S, Eisenbach M (1993) Phosphorylation-dependent binding of a signal molecule to the flagellar switch of bacteria. Proc Natl Acad Sci U S A 90(19):8787–8791

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Welch M, Oosawa K, Aizawa S, Eisenbach M (1994) Effects of phosphorylation, Mg2+, and conformation of the chemotaxis protein CheY on its binding to the flagellar switch protein FliM. Biochemistry 33(34):10470–10476

  • Williams AW, Yamaguchi S, Togashi F, Aizawa S, Kawagishi I, Macnab RM (1996) Mutations in fliK and flhB affecting flagellar hook and filament assembly in Salmonella typhimurium. J Bacteriol 178(10):2960–2970

  • Yamaguchi S, Fujita H, Ishihara A, Aizawa S, Macnab RM (1986) Subdivision of flagellar genes of Salmonella typhimurium into regions responsible for assembly, rotation, and switching. J Bacteriol 166(1):187–193

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yamashita I, Hasegawa K, Suzuki H, Vonderviszt F, Mimori-Kiyosue Y, Namba K (1998) Structure and switching of bacterial flagellar filaments studied by X-ray fiber diffraction. Nat Struct Mol Biol 5(2):125–132

    Article  CAS  Google Scholar 

  • Yonekura K, Maki S, Morgan DG, DeRosier DJ, Vonderviszt F, Imada K, Namba K (2000) The bacterial flagellar cap as the rotary promoter of flagellin self-assembly. Science 290(5499):2148–2152

    Article  CAS  PubMed  Google Scholar 

  • Yonekura K, Maki-Yonekura S, Namba K (2003) Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy. Nature 424(6949):643–650

    Article  CAS  PubMed  Google Scholar 

  • Zarivach R, Deng W, Vuckovic M, Felise HB, Nguyen HV, Miller SI, Finlay BB, Strynadka NC (2008) Structural analysis of the essential self-cleaving type III secretion proteins EscU and SpaS. Nature 453(7191):124–127

    Article  CAS  PubMed  Google Scholar 

  • Zhou J, Fazzio RT, Blair DF (1995) Membrane topology of the MotA protein of Escherichia coli. J Mol Biol 251(2):237–242

    Article  CAS  PubMed  Google Scholar 

  • Zhu S, Takao M, Li N, Sakuma M, Nishino Y, Homma M, Kojima S, Imada K (2014) Conformational change in the periplamic region of the flagellar stator coupled with the assembly around the rotor. Proc Natl Acad Sci U S A 111(37):13523–13528

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This research was supported by MEXT/JSPS KAKENHI (nos. 25104002 and 15H04357) to A.K. and by MEXT as “Priority Issue on Post-K Computer” (Building Innovative Drug Discovery Infrastructure Through Functional Control of Biomolecular Systems) to A.K. The computations were partly performed using the supercomputers at the RCCS, The National Institute of Natural Science, and ISSP, The University of Tokyo. This research also used computational resources of the K computer provided by the RIKEN Advanced Institute for Computational Science through the HPCI System Research project (project IDs: hp120223, hp140030, hp140031, hp150049, hp150270, hp160207, and hp170254).

Author information

Authors and Affiliations

  1. School of Life Science and Technology, Tokyo Institute of Technology, M6-13, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan

    Akio Kitao

  2. Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan

    Hiroaki Hata

Authors
  1. Akio Kitao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hiroaki Hata
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Akio Kitao.

Ethics declarations

Conflict of interest

Akio Kitao declares that he has no conflict of interest. Hiroaki Hata declares that he has no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

This article is part of a Special Issue on ‘Biomolecules to Bio-nanomachines - Fumio Arisaka 70th Birthday’ edited by Damien Hall.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kitao, A., Hata, H. Molecular dynamics simulation of bacterial flagella. Biophys Rev 10, 617–629 (2018). https://doi.org/10.1007/s12551-017-0338-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12551-017-0338-7

Keywords

Search

Navigation