Last updated April 2021

Chronological List of papers from the Lab

86. Steven Johnson, Emily J Furlong, Justin C Deme, Ashley L Nord, Joseph JE Caesar, Fabienne FV Chevance, Richard M Berry, Kelly T Hughes, Susan M Lea. (2021). Molecular structure of the intact bacterial flagellar basal body. Nature Microbiology doi: 10.1038/s41564-021-00895-y. Online ahead of print.

85. Oshri Afanzar, Diana Di Paolo, Miriam Eisenstein, Kohava Levi, Anne Plochowietz, Achillefs N Kapanidis, Richard Michael Berry, Michael Eisenbach. (2021). The switching mechanism of the bacterial rotary motor combines tight regulation with inherent flexibility. The EMBO journal EMBO Press 40:6 e104683

84. Sobti M, Walshe JL, Wu D, Ishmukhametov R, Zeng YC, Robinson CV, Berry RM, Stewart AG. (2020). Cryo-EM structures provide insight into how E. coli F1Fo ATP synthase accommodates symmetry mismatch. Nature Communications. 26;11(1):2615.

83. Yoshiaki Kinosita, Nagisa Mikami, Zhengqun Li, Frank Braun, Tessa EF Quax, Chris van der Does, Robert Ishmukhametov, Sonja-Verena Albers, Richard M Berry. (2020). Motile ghosts of the halophilic archaeon, Haloferax volcanii. Proceedings of the National Academy of Sciences of the United States of America 117:43 26766-26772

82. Yoshiaki Kinosita, Tsubasa Ishida, Myu Yoshida, Rie Ito, Yusuke V Morimoto, Kazuki Goto, Richard M Berry, Takayuki Nishizaka, Yoshiyuki Sowa. (2020). Distinct chemotactic behavior in the original Escherichia coli K-12 depending on forward-and-backward swimming, not on run-tumble movements. Scientific reports 10:1 15887

81. Judith P Armitage, Richard M Berry. (2020). Assembly and Dynamics of the Bacterial Flagellum. Annual review of microbiology 74 181-200

80.   Nirody JA, Nord AL, Berry RM. (2019). Load-dependent adaptation near zero load in the bacterial flagellar motor.    J R Soc Interface   16(159):20190300. 

79.   Hook AL, Flewellen JL, Dubern JF, Carabelli AM, Zaid IM, Berry RM, Wildman RD, Russell N, Williams P, Alexander MR. (2019). Simultaneous Tracking of Pseudomonas aeruginosa Motility in Liquid and at the Solid-Liquid Interface Reveals Differential Roles for the Flagellar Stators.    mSystems.   pii: e00390-19. 

78.   Flewellen JL, Zaid IM, Berry RM. (2019). A multi-mode digital holographic microscope.    Rev Sci Instrum.   90(2):023705.  (Supplementary Information)

77.   Tusk SE, Delalez NJ, Berry RM. (2018). Subunit Exchange in Protein Complexes. J Mol Biol.   430(22):4557-4579.

76.   Galkin MA, Russell AN, Vik SB, Berry RM, Ishmukhametov RR. (2018). Detergent-free Ultrafast Reconstitution of Membrane Proteins into Lipid Bilayers Using Fusogenic Complementary-charged Proteoliposomes.    J Vis Exp.  134 e56909.

75.   Di Paolo D, Berry RM. (2018). Imaging of Single Dye-Labeled Chemotaxis Proteins in Live Bacteria Using Electroporation.    Methods Mol Biol.   1729:233-246.

74.   Nord AL, Gachon E,Perez-Carrasco R, Nirody J, Barducci A, Berry RM, Pedaci F (2017). Catch bond drives stator mechanosensitivity in the bacterial flagellar motor.  Proc Natl Acad Sci U S A.   114:49 12952-12957.

73.   Nord AL, Sowa Y, Steel BC, Lo C-J, Berry RM (2017). Speed of the bacterial flagellar motor near zero load depends on the number of stator units. Proc Natl Acad Sci U S A.   114:11603-11608.

72.   Nord AL, Pedaci F, Berry RM (2016). Transient pauses of the bacterial flagellar motor at low load  New J. Phys.   18:115002

71.   Brenzinger S, Dewenter L, Delalez NJ, Leicht O, Berndt V, Berry RM, Thanbichler M, Armitage JP, Maier B, Thormann KM. (2016). Mutations targeting the plug-domain of the Shewanella oneidensis proton-driven stator allow swimming at increased viscosity and under anaerobic conditions.    Mol. Microbiol. 102:5  925-938. 

70.   Ishmukhametov RR, Aidan N. Russell AN and Berry RM. (2016). A modular platform for one-step assembly of multi-component membrane systems by fusion of charged proteoliposomes.    Nature Communications   7: 13025 (Supplementary Information)

69.   Di Paolo D, Afanzar O, Armitage JP and Berry RM. (2016). Single-molecule imaging of electroporated dye-labelled CheY in live Escherichia coli.    Phil Trans Roy Soc B.   371: 20150492 (Supplementary Information)

68.   Nirody JA, Berry RM and Oster G. (2016). The Limiting Speed of the Bacterial Flagellar Motor.    Biophys J.   111:3 557-564.

67.   Baker MA, Hynson RM, Ganuelas LA, Mohammadi NS, Liew CW, Rey AA, Duff AP, Whitten AE, Jeffries CM, Delalez NJ, Morimoto YV, Stock D, Armitage JP, Turberfield AJ, Namba K, Berry RM, Lee LK. (2016). Domain-swap polymerization drives the self-assembly of the bacterial flagellar motor.    Nat Struct Mol Biol. 2016 Feb 8. doi: 10.1038/nsmb.3172. [Epub ahead of print]   5:8773. (Supplementary Information)

66.   Ishmukhametov RR, Russell AN, Wheeler RJ, Nord AL, Berry RM. (2016) A Simple low-cost device enables four epi-illumination techniques on standard light microscopes.  Sci Rep. Feb 8;6:20729. doi: 10.1038/srep20729.  

65.   Mandadapu KK, Nirody JA, Berry RM, Oster G. (2015). Mechanics of torque generation in the bacterial flagellar motor. Proc Natl Acad Sci U S A. 112(32):E4381-9.  

64.   Steel BC, Nord AL, Wang Y, Pagadala V, Mueller DM, Berry RM. (2015). Comparison between single-molecule and X-ray crystallography data on yeast F1-ATPase.    Sci Rep.   5:8773. (Supplementary Information)

63.   Paulick A, Delalez NJ, Brenzinger S, Steel BC, Berry RM, Armitage JP, Thormann KM. (2015). Dual stator dynamics in the Shewanella oneidensis MR-1 flagellar motor. Mol Microbiol.   96:993-1001.  (Supplementary Information)

62.   Diepold A, Kudryashev M, Delalez NJ, Berry RM, Armitage JP. (2015). Composition, formation, and regulation of the cytosolic c-ring, a dynamic component of the type III secretion injectisome.    PLoS Biol.   13:e1002039.

61.   Delalez NJ, Berry RM, Armitage JP. (2014). Stoichiometry and Turnover of the Bacterial Flagellar Switch Protein FliN.    mBio.   5:e01216-14.

60.   Sowa Y, Homma M, Ishijima A, Berry RM. (2014). Hybrid-fuel bacterial flagellar motors in Escherichia coli.    Proc Natl Acad Sci U S A.   111:3436-41.

59.   Inoue Y, Baker MA, Fukuoka H, Takahashi H, Berry RM, Ishijima A. (2013). Temperature dependences of torque generation and membrane voltage in the bacterial flagellar motor.    Biophys J.   105:2801-10.

58.   Tipping MJ, Delalez NJ, Lim R, Berry RM, Armitage JP. (2013). Load-dependent assembly of the bacterial flagellar motor.    mBio.   4:e00551-13.

57.   Lo CJ, Sowa Y, Pilizota T, Berry RM. (2013). Mechanism and kinetics of a sodium-driven bacterial flagellar motor.    Proc Natl Acad Sci U S A.   110:E2544-51. (Supplementary dataset)

56.   Tipping MJ, Steel BC, Delalez NJ, Berry RM, Armitage JP. (2013). Quantification of flagellar motor stator dynamics through in vivo proton-motive force control.   Mol Microbiol.   87:338-47 (Supplementary Information)

55.   Bilyard T, Nakanishi-Matsui M, Steel BC, Pilizota T, Nord AL, Hosokawa H, Futai M, Berry RM. (2013). High-resolution single-molecule characterization of the enzymatic states in Escherichia coli F1-ATPase.   Philos Trans R Soc Lond B Biol Sci.    368:20120023. (Supplementary Information)

54.   Sowa Y and Berry RM. (2012). The Rotary Bacterial Flagellar Motor.   Chapter 8.4 in: Comprehensive Biophysics, volume 8  , Ed. Edward H. Egelman, Elsevier.

53.   Youle M, RohwerF, Stacy A, Whiteley M, Steel B, Delalez NJ, Nord AL, Berry RM, Armitage JP, Kamoun S, Hogenhout S, Diggle SP, Gurney J, Pollitt EJG, Boetius A and Cary SC. (2012). The Microbial Olympics.   Nature Reviews Microbiology.   10: 583-588. (our section of the article, 100 microns freestyleVideo - 24MB .avi  )

52.   Ma Q, Nicolau DV Jr, Maini PK, Berry RM, Bai F. (2012). Conformational spread in the flagellar motor switch: a model study   PLoS Comput Biol.   8:e1002523.

51.   Brown MT, Steel BC, Silvestrin C, Wilkinson DA, Delalez NJ, Lumb CN, Obara B, Armitage JP, Berry RM. (2012). Flagellar Hook Flexibility Is Essential for Bundle Formation in Swimming Escherichia coli Cells.   J Bacteriol.   194:3495-501. (Supplementary documents : supplementary Movies - 220 MB)

50.   Little MA, Steel BC, Bai F, Sowa Y, Bilyard T, Mueller DM, Berry RM, Jones NS. (2011). Steps and bumps: precision extraction of discrete States   Biophys J.   101:477-85. (Supplementary Information)

49.   Baker MA, Inoue Y, Takeda K, Ishijima A, Berry RM. (2011). Two methods of temperature control for single-molecule measurements.   Eur Biophys J.   40:651-60

48.   Nan B, Chen J, Neu JC, Berry RM, Oster G, Zusman DR. (2011). Myxobacteria gliding motility requires cytoskeleton rotation powered by proton motive force.   Proc Natl Acad Sci U S A.   108:2498-2503.  (Supplementary Information)

47.   Sowa Y, Steel BC, Berry RM (2010). A simple backscattering microscope for fast tracking of biological molecules   Rev. Sci. Instrum.   81: 113704.

46.   Delalez NJ, Wadhams GH, Rosser G, Xue Q, Brown MT, Dobbie IM, Berry RM, Leake MC, Armitage JP (2010). Signal-dependent turnover of the bacterial flagellar switch protein FliM.   Proc Natl Acad Sci U S A.   107:11347-51. (Supplementary Information)

45.   Armitage JP, Berry RM (2010). Time for bacteria to slow down   Cell.   141:24-26.

44.   Bai F, Branch RW, Nicolau DV Jr., Pilizota T, Steel BC, Maini PK, Berry RM (2010). Conformational spread as a mechanism for cooperativity in the bacterial flagellar switch   Science.   327:685-689. (Supplementary Information)

43.   Baker MAB and Berry RM (2009). An introduction to the physics of the bacterial flagellar motor: a nanoscale rotary electric motor.   Contemporary Physics.  50:617 - 32.

42. Pilizota T, Sowa Y and Berry RM (2009). Rotary proteins. in   Handbook of Single-Molecule Biophysics  , Ed. P Hinterdorfer, A van Oijen, Springer, Chapter 7.

41.   Pilizota T, Brown MT, Leake MC, Branch RW, Berry RM, Armitage JP. (2009). A molecular brake, not a clutch, stops the Rhodobacter sphaeroides flagellar motor.   Proc Natl Acad Sci U S A.  106:11582-11587. (Supplementary Information)

40.   Bai F, Lo CJ, Berry RM, Xing J. (2009). Model studies of the dynamics of bacterial flagellar motors.   Biophys. J.  96:3154-67.

39.   Sowa Y and Berry RM (2008). The Bacterial Flagellar Motor. in   Single Molecule Biology  , ed A. E. Knight, Academic Press pp 105-142.

38.   Leake MC, Greene NP, Godun RM, Granjon T, Buchanan G, Chen S, Berry RM, Palmer T, Berks BC. (2008). Variable stoichiometry of the TatA component of the twin-arginine protein transport system observed by in vivo single-molecule imaging.   Proc Natl Acad Sci U S A.  105:15376-15381. (Supplementary Information)

37.   Sowa Y and Berry RM (2008). Bacterial flagellar motor.   Q. Rev. Biophys.  41:103-132.

36.   Piper JD, Li C, Lo C-J, Berry R, Korchev Y, Ying L, Klenerman D. (2008). Characterization and Application of Controllable Local Chemical Changes Produced by Reagent Delivery from a Nanopipet.   J. Am. Chem. Soc.  130:10387-10393. (Supplementary Information)

35.   Berry RM and Armitage JP. (2008). How Bacteria Change Gear  (Perspective).   Science 320:1599-1600.

34.  Inoue Y, Lo C-J, Fukuoka H, Takahashi H, Sowa Y, Pilizota T, Wadhams GH, Homma M, Berry RM, Ishijima A. (2008) Torque-speed relationships of Na+-driven chimeric flagellar motors in Escherichia coli. J. Mol. Biol.  376:1251-1259.

33.  Lo C-J, Leake MC, Pilizota T,  Berry RM. (2007). Non-equivalence of membrane voltage and ion-gradient as driving forces for the bacterial flagellar motor at low load. Biophys. J. 93:294-302. (Supplementary Information)

32.  Pilizota T, Bilyard T, Bai F, Futai M, Hosokawa H, Berry RM. (2007). A programmable optical angle clamp for rotary molecular motors.  Biophys. J. 93:264-275. (Supplementary Information)

31.  Leake MC, Chandler JH, Wadhams GH, Bai F, Berry RM, Armitage JP. (2006). Stoichiometry and turnover in single, functioning membrane protein complexes. Nature. 443:355-358. (Supplementary Information)

30.  Reid S.W., Leake M.C., Chandler J.H., Lo C-J., Armitage J.P., Berry R.M. (2006) The bacterial flagellar motor contains at least 11 torque-generating units.  Proc. Natl. Acad. Sci. USA. 103: 8066-8071. (Supplementary Information)

29.  dePlanque M.R.R., Mendes G.P., Zagoni M., Sandison M.E., Fisher K.H., Berry R.M., Watts A., Morgan H. (2006) Controlled delivery of membrane proteins to artificial bilayers by nystatin-ergosterol modulated vesicle fusion.  IEE Proc. Nanobiotechnology.  153: 21-30.

28.  Xing J., Bai F., Berry R.M., Oster G. (2006) The torque-speed relationship of the bacterial flagellar motor. Proc. Natl. Acad. Sci. USA. 103:1260-1265. (Supplementary Information)

27.  Lo C.-J., Leake M. C., Berry R. M. (2006) Fluorescence measurement of intracellular sodium concentration in single Escherichia coli cells. Biophys. J. 90: 357-365.

26.  Goodman R. P., Schaap I. A. T., Tardin C. F., Erben C. M., Berry R. M., Schmidt C. F., Turberfield A. J.  (2005) Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication.  Science. 310:1661-1665. (Supplementary Information)

25.  Rowe AD, Sowa Y, Leake MC, Yakushi T, Homma M, Ishijima A and Berry RM (2005). Steps in slow flagellar motor rotation. Biophys. J 88: 504A

24. Sowa Y, Rowe AD, Leake MC, Yakushi T, Homma M, Ishijima A, Berry RM. (2005)  Direct observation of steps in rotation of the bacterial flagellar motor. Nature. 437:916-919. (Supplementary Information)

23.  Berry, R.M. (2005) ATP Synthesis: The World's Smallest Wind-up Toy.  Curr. Biol. 15:R385-7.

22.  Berry, R.M. (2005) Book review .E.coli in Motion. Physics Today 58:64-65 .

21.  Sandison M.E., Mendes G., Berry R. Watts A. and Morgan H.  (2004) Microfabricated devices for artificial bilayer lipid membranes.  Proc. MicroMechanics Europe  171-174

20.  Morgan H., Sandison M.E., Mendes G., Berry R. and Watts A.  (2004) Artificial Lipid Bilayers in a Microfabricated System. Proc. uTAS, 330-332  eds. Laurel T., Nilsson J., Jensen K., Harrison D.J. and Kutter J.  Royal Society of Chemistry.

19.  Berry, R.M. (2004) The Bacterial Flagellar Motor in Forces, Growth and Form in Soft Condensed Matter: At the interface between Physics and Biology, eds. Skeltorp, A.T. and Belushkin, A.V., Kluwer, Netherlands.

18.  Goodman, R., Berry, R. and Turberfield, A. (2004) The single-step synthesis of a DNA tetrahedron. Chemical Communications, DOI:10.1039/B402293A.

17.  Rowe, A.D., Leake, M.C., Morgan, H. and Berry, R.M. (2003) Rapid Rotation of Micron and Sub-micron Dielectric Particles Measured Using Optical Tweezers.  J. Mod.Optics 50:1539-1554.

16.  Berry, R.M. (2003) The Bacterial Flagellar Motor in Molecular Motors, ed. Schliwa, M., Wiley-VCH, Weinheim, Berlin.

15.  Ryu, W.S., Berry, R.M. and Berg, H.C. (2000) Modelling torque generation in the bacterial flagellar motor. Biophys. J. 78:P2310

14.  Ryu, W.S., Berry, R.M. and Berg, H.C. (2000) Torque generating units of the flagellar motor of Escherichia coli have a high duty ratio.  Nature. 403:444-447.

13.  Berry, R.M. (2000) Bacterial flagella: flagellar motor. in Nature Encyclopedia of Life Sciences, Macmillan Reference Ltd.

12.  Berry, R.M. (2000) Theories of Rotary Motors.  Philos. Trans. R. Soc. Lond. B. Biol. Sci. 355:503-511.

11.  Berry, R.M. and Armitage, J.P.  (2000). Response kinetics of tethered Rhodobacter sphaeroides to changes in light intensity. Biophys. J. 78:1207-1215.

10.  Berry, R.M. and Armitage, J.P.  (1999). The bacterial flagella motor. Adv. Microb. Physiol. 41:291-337.

9.      Berry, R.M. and Berg H.C.  (1999). Torque generation by the flagellar motor of Escherichia coli while driven backwards.  Biophys J. 76:580-587.

8.      Berry, R.M. and Berg H.C.  (1997)  Absence of a barrier to backwards rotation in the bacterial flagellar motor, demonstrated with optical tweezers.  Proc. Natl. Acad. Sci. USA.  94:14433-14437. 

7.      Berry, R.M. and Berg H.C.  (1996)  Torque generated by the bacterial flagellar motor close to stall  Biophys. J.  71:3501-3510.

6.      Berry, R.M., Turner, L and Berg, H.C. (1995)  Mechanical limits of bacterial flagellar motors probed by electrorotation.  Biophys. J.   69:280-286.

5.      Berry, R.M. and Nowak, M.A. (1994).  Defective escape mutants of HIV.  J. Theor. Biol.   171:387-395.

4.      Berry, R.M. (1993).  Torque and switching in the bacterial flagellar motor: an electrostatic model.  Biophys. J.  64:961-973.

3.      Berry, R.M. and Edmonds, D.T. (1993).  Correlated ion flux through parallel pores: Application to channel subconductance states.  J. Membrane. Biol.  133:77-84.

2.      Berry, R. and Edmonds, D.T. (1992).  Carrier-like behaviour from a static but electrically responsive model pore.  J. Theor. Biol.  154:249-260.

1.      Edmonds, D.T. and Berry, R. (1991).  The proton ladder, a static mechanism for ion/proton coports and counterports.  Eur. Biophys. J.  20:241-245.