The Gearbox of the Bacterial Flagellar Motor Switch

Pandini, Alessandro; Morcos, Faruck; Khan, Shahid

doi:10.1016/j.str.2016.05.012

The Gearbox of the Bacterial Flagellar Motor Switch

Journal Article · Fri Jul 01 04:00:00 EDT 2016 · Structure

DOI:https://doi.org/10.1016/j.str.2016.05.012· OSTI ID:1623722

Pandini, Alessandro ^[1]; Morcos, Faruck ^[2]; Khan, Shahid ^[3]

Brunel Univ., Middlesex (United Kingdom). Dept. of Computer Science and Synthetic Biology; The Francis Crick Inst., London (United Kingdom). Computational Cell and Molecular Biology; DOE/OSTI
Univ. of Texas at Dallas, Richardson, TX (United States). Dept. of Biological Sciences
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biology Consortium

Switching of flagellar motor rotation sense dictates bacterial chemotaxis. Multi-subunit FliM-FliG rotor rings couple signal protein binding in FliM with reversal of a distant FliG C-terminal (FliGC) helix involved in stator contacts. Subunit dynamics were examined in conformer ensembles generated by molecular simulations from the X-ray structures. Principal component analysis extracted collective motions. Interfacial loop immobilization by complex formation coupled elastic fluctuations of the FliM middle (FliMM) and FliG middle (FliGM) domains. Coevolved mutations captured interfacial dynamics as well as contacts. FliGM rotation was amplified via two central hinges to the FliGC helix. Intrinsic flexibility, reported by the FliGMC ensembles, reconciled conformers with opposite FliGC helix orientations. FliG domain stacking deformed the inter-domain linker and reduced flexibility; but conformational changes were not triggered by engineered linker deletions that cause a rotation-locked phenotype. These facts suggest that binary rotation states arise from conformational selection by stacking interactions.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1623722

Journal Information:: Structure, Journal Name: Structure Journal Issue: 7 Vol. 24; ISSN 0969-2126

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (50)

Prediction of protein conformational freedom from distance constraints de Groot, B. L.; van Aalten, D. M. F.; Scheek, R. M. Proteins: Structure, Function, and Genetics, Vol. 29, Issue 2 https://doi.org/10.1002/(SICI)1097-0134(199710)29:2<240::AID-PROT11>3.0.CO;2-O	journal	October 1997
Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy: Optimization of Designed Armadillo Repeat Proteins Alfarano, Pietro; Varadamsetty, Gautham; Ewald, Christina Protein Science, Vol. 21, Issue 9 https://doi.org/10.1002/pro.2117	journal	August 2012
Essential dynamics of proteins Amadei, Andrea; Linssen, Antonius B. M.; Berendsen, Herman J. C. Proteins: Structure, Function, and Genetics, Vol. 17, Issue 4 https://doi.org/10.1002/prot.340170408	journal	December 1993
Charged residues of the rotor protein FliG essential for torque generation in the flagellar motor of Escherichia coli Lloyd, Scott A.; Blair, David F. Journal of Molecular Biology, Vol. 266, Issue 4 https://doi.org/10.1006/jmbi.1996.0836	journal	March 1997
Overproduced Salmonella typhimurium flagellar motor switch complexes Lux, Renate; Kar, Niladri; Khan, Shahid Journal of Molecular Biology, Vol. 298, Issue 4 https://doi.org/10.1006/jmbi.2000.3703	journal	May 2000
The consistency of large concerted motions in proteins in molecular dynamics simulations de Groot, B. L.; van Aalten, D. M.; Amadei, A. Biophysical Journal, Vol. 71, Issue 4 https://doi.org/10.1016/S0006-3495(96)79372-4	journal	October 1996
Populational Heterogeneity vs. Temporal Fluctuation in Escherichia coli Flagellar Motor Switching Bai, Fan; Che, Yong-Suk; Kami-ike, Nobunori Biophysical Journal, Vol. 105, Issue 9 https://doi.org/10.1016/j.bpj.2013.09.043	journal	November 2013
Switching of Bacterial Flagellar Motors Triggered by Mutant FliG Lele, Pushkar P.; Berg, Howard C. Biophysical Journal, Vol. 108, Issue 5 https://doi.org/10.1016/j.bpj.2015.02.004	journal	March 2015
The Phylogenetic Signature Underlying ATP Synthase c-Ring Compliance Pandini, Alessandro; Kleinjung, Jens; Taylor, Willie R. Biophysical Journal, Vol. 109, Issue 5 https://doi.org/10.1016/j.bpj.2015.07.005	journal	September 2015
Nanorotors and self-assembling macromolecular machines: The torque ring of the bacterial flagellar motor Stock, Daniela; Namba, Keiichi; Lee, Lawrence K. Current Opinion in Biotechnology, Vol. 23, Issue 4 https://doi.org/10.1016/j.copbio.2012.01.008	journal	August 2012
Structure of the Rotor of the Bacterial Flagellar Motor Revealed by Electron Cryomicroscopy and Single-particle Image Analysis Suzuki, Hirofumi; Yonekura, Koji; Namba, Keiichi Journal of Molecular Biology, Vol. 337, Issue 1 https://doi.org/10.1016/j.jmb.2004.01.034	journal	March 2004
A Molecular Mechanism of Bacterial Flagellar Motor Switching Dyer, Collin M.; Vartanian, Armand S.; Zhou, Hongjun Journal of Molecular Biology, Vol. 388, Issue 1 https://doi.org/10.1016/j.jmb.2009.02.004	journal	April 2009
Ultrasensitivity of an Adaptive Bacterial Motor Yuan, Junhua; Berg, Howard C. Journal of Molecular Biology, Vol. 425, Issue 10 https://doi.org/10.1016/j.jmb.2013.02.016	journal	May 2013
Assembly States of FliM and FliG within the Flagellar Switch Complex Sircar, Ria; Borbat, Peter P.; Lynch, Michael J. Journal of Molecular Biology, Vol. 427, Issue 4 https://doi.org/10.1016/j.jmb.2014.12.009	journal	February 2015
Geometry-Based Sampling of Conformational Transitions in Proteins Seeliger, Daniel; Haas, Jürgen; de Groot, Bert L. Structure, Vol. 15, Issue 11 https://doi.org/10.1016/j.str.2007.09.017	journal	November 2007
Multiple Conformations of the FliG C-Terminal Domain Provide Insight into Flagellar Motor Switching Lam, Kwok-Ho; Ip, Wing-Sang; Lam, Yun-Wah Structure, Vol. 20, Issue 2 https://doi.org/10.1016/j.str.2011.11.020	journal	February 2012
Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins Sfriso, Pedro; Duran-Frigola, Miquel; Mosca, Roberto Structure, Vol. 24, Issue 1 https://doi.org/10.1016/j.str.2015.10.025	journal	January 2016
Bending motions and internal motions in the myosin rod Highsmith, Stefan; Wang, Chun Chen; Zero, Karl Biochemistry, Vol. 21, Issue 6 https://doi.org/10.1021/bi00535a013	journal	March 1982
Structural Insights into the Interaction between the Bacterial Flagellar Motor Proteins FliF and FliG Levenson, Robert; Zhou, Hongjun; Dahlquist, Frederick W. Biochemistry, Vol. 51, Issue 25 https://doi.org/10.1021/bi3004582	journal	June 2012
Rotation Triggers Nucleotide-Independent Conformational Transition of the Empty β Subunit of F ₁ -ATPase Czub, Jacek; Grubmüller, Helmut Journal of the American Chemical Society, Vol. 136, Issue 19 https://doi.org/10.1021/ja500120m	journal	May 2014
Structure of the torque ring of the flagellar motor and the molecular basis for rotational switching Lee, Lawrence K.; Ginsburg, Michael A.; Crovace, Claudia Nature, Vol. 466, Issue 7309 https://doi.org/10.1038/nature09300	journal	August 2010
Domain-swap polymerization drives the self-assembly of the bacterial flagellar motor Baker, Matthew A. B.; Hynson, Robert M. G.; Ganuelas, Lorraine A. Nature Structural & Molecular Biology, Vol. 23, Issue 3 https://doi.org/10.1038/nsmb.3172	journal	February 2016
Insufficiently dehydrated hydrogen bonds as determinants of protein interactions Fernandez, A.; Scheraga, H. A. Proceedings of the National Academy of Sciences, Vol. 100, Issue 1 https://doi.org/10.1073/pnas.0136888100	journal	December 2002
Structure of FliM provides insight into assembly of the switch complex in the bacterial flagella motor Park, S. -Y.; Lowder, B.; Bilwes, A. M. Proceedings of the National Academy of Sciences, Vol. 103, Issue 32 https://doi.org/10.1073/pnas.0602811103	journal	August 2006
Hierarchies, multiple energy barriers, and robustness govern the fracture mechanics of -helical and beta-sheet protein domains Ackbarow, T.; Chen, X.; Keten, S. Proceedings of the National Academy of Sciences, Vol. 104, Issue 42 https://doi.org/10.1073/pnas.0705759104	journal	October 2007
Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stability Guzmán, Dora L.; Randall, Arlo; Baldi, Pierre Proceedings of the National Academy of Sciences, Vol. 107, Issue 5 https://doi.org/10.1073/pnas.0905796107	journal	January 2010
Chemotaxis signaling protein CheY binds to the rotor protein FliN to control the direction of flagellar rotation in Escherichia coli Sarkar, M. K.; Paul, K.; Blair, D. Proceedings of the National Academy of Sciences, Vol. 107, Issue 20 https://doi.org/10.1073/pnas.1000935107	journal	May 2010
A molecular mechanism of direction switching in the flagellar motor of Escherichia coli Paul, K.; Brunstetter, D.; Titen, S. Proceedings of the National Academy of Sciences, Vol. 108, Issue 41 https://doi.org/10.1073/pnas.1110111108	journal	October 2011
Direct-coupling analysis of residue coevolution captures native contacts across many protein families Morcos, F.; Pagnani, A.; Lunt, B. Proceedings of the National Academy of Sciences, Vol. 108, Issue 49 https://doi.org/10.1073/pnas.1111471108	journal	November 2011
Coevolutionary signals across protein lineages help capture multiple protein conformations Morcos, F.; Jana, B.; Hwa, T. Proceedings of the National Academy of Sciences, Vol. 110, Issue 51 https://doi.org/10.1073/pnas.1315625110	journal	December 2013
Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection Morcos, F.; Schafer, N. P.; Cheng, R. R. Proceedings of the National Academy of Sciences, Vol. 111, Issue 34 https://doi.org/10.1073/pnas.1413575111	journal	August 2014
From residue coevolution to protein conformational ensembles and functional dynamics Sutto, Ludovico; Marsili, Simone; Valencia, Alfonso Proceedings of the National Academy of Sciences, Vol. 112, Issue 44 https://doi.org/10.1073/pnas.1508584112	journal	October 2015
Binding of the Escherichia coli response regulator CheY to its target measured in vivo by fluorescence resonance energy transfer Sourjik, V.; Berg, H. C. Proceedings of the National Academy of Sciences, Vol. 99, Issue 20 https://doi.org/10.1073/pnas.192463199	journal	September 2002
Electrostatic interactions between rotor and stator in the bacterial flagellar motor Zhou, J.; Lloyd, S. A.; Blair, D. F. Proceedings of the National Academy of Sciences, Vol. 95, Issue 11 https://doi.org/10.1073/pnas.95.11.6436	journal	May 1998
Structure of Flagellar Motor Proteins in Complex Allows for Insights into Motor Structure and Switching Vartanian, Armand S.; Paz, Aviv; Fortgang, Emily A. Journal of Biological Chemistry, Vol. 287, Issue 43 https://doi.org/10.1074/jbc.C112.378380	journal	August 2012
Binding of the Chemotaxis Response Regulator CheY to the Isolated, Intact Switch Complex of the Bacterial Flagellar Motor Sagi, Yael; Khan, Shahid; Eisenbach, Michael Journal of Biological Chemistry, Vol. 278, Issue 28 https://doi.org/10.1074/jbc.M303201200	journal	July 2003
GSATools: analysis of allosteric communication and functional local motions using a structural alphabet Pandini, Alessandro; Fornili, Arianna; Fraternali, Franca Bioinformatics, Vol. 29, Issue 16 https://doi.org/10.1093/bioinformatics/btt326	journal	June 2013
MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins Jones, David T.; Singh, Tanya; Kosciolek, Tomasz Bioinformatics, Vol. 31, Issue 7 https://doi.org/10.1093/bioinformatics/btu791	journal	November 2014
Crystal structure of the middle and C-terminal domains of the flagellar rotor protein FliG Brown, P. N. The EMBO Journal, Vol. 21, Issue 13 https://doi.org/10.1093/emboj/cdf332	journal	July 2002
The Pfam protein families database Finn, Robert D.; Mistry, Jaina; Tate, John Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp985	journal	November 2009
Characterisation of Shigella Spa33 and Thermotoga FliM/N reveals a new model for C-ring assembly in T3SS: Uniform C-ring assembly by NF- and flagellar-T3SS McDowell, Melanie A.; Marcoux, Julien; McVicker, Gareth Molecular Microbiology, Vol. 99, Issue 4 https://doi.org/10.1111/mmi.13267	journal	December 2015
The Three-Dimensional Structure of the Flagellar Rotor from a Clockwise-Locked Mutant of Salmonella enterica Serovar Typhimurium Thomas, Dennis R.; Francis, Noreen R.; Xu, Chen Journal of Bacteriology, Vol. 188, Issue 20 https://doi.org/10.1128/JB.00552-06	journal	October 2006
Genetic and behavioral analysis of flagellar switch mutants of Salmonella typhimurium Magariyama, Y.; Yamaguchi, S.; Aizawa, S. Journal of Bacteriology, Vol. 172, Issue 8 https://doi.org/10.1128/jb.172.8.4359-4369.1990	journal	August 1990
Conformational Spread: The Propagation of Allosteric States in Large Multiprotein Complexes Bray, Dennis; Duke, Thomas Annual Review of Biophysics and Biomolecular Structure, Vol. 33, Issue 1 https://doi.org/10.1146/annurev.biophys.33.110502.132703	journal	June 2004
Structural alphabets derived from attractors in conformational space Pandini, Alessandro; Fornili, Arianna; Kleinjung, Jens BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-97	journal	January 2010
Structural Insight into the Rotational Switching Mechanism of the Bacterial Flagellar Motor Minamino, Tohru; Imada, Katsumi; Kinoshita, Miki PLoS Biology, Vol. 9, Issue 5 https://doi.org/10.1371/journal.pbio.1000616	journal	May 2011
Detection of Functional Modes in Protein Dynamics Hub, Jochen S.; de Groot, Bert L. PLoS Computational Biology, Vol. 5, Issue 8 https://doi.org/10.1371/journal.pcbi.1000480	journal	August 2009
Conformational Spread in the Flagellar Motor Switch: A Model Study Ma, Qi; Nicolau, Dan V.; Maini, Philip K. PLoS Computational Biology, Vol. 8, Issue 5 https://doi.org/10.1371/journal.pcbi.1002523	journal	May 2012
Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation Ollikainen, Noah; Kortemme, Tanja PLoS Computational Biology, Vol. 9, Issue 11 https://doi.org/10.1371/journal.pcbi.1003313	journal	November 2013
Coevolved Mutations Reveal Distinct Architectures for Two Core Proteins in the Bacterial Flagellar Motor Pandini, Alessandro; Kleinjung, Jens; Rasool, Shafqat PLOS ONE, Vol. 10, Issue 11 https://doi.org/10.1371/journal.pone.0142407	journal	November 2015

Cited By (9)

A structural model of flagellar filament switching across multiple bacterial species Wang, Fengbin; Burrage, Andrew M.; Postel, Sandra Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01075-5	journal	October 2017
Rotational direction of flagellar motor from the conformation of FliG middle domain in marine Vibrio Nishikino, Tatsuro; Hijikata, Atsushi; Miyanoiri, Yohei Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-35902-6	journal	December 2018
Characterization of C-ring component assembly in flagellar motors from amino acid coevolution dos Santos, Ricardo Nascimento; Khan, Shahid; Morcos, Faruck Royal Society Open Science, Vol. 5, Issue 5 https://doi.org/10.1098/rsos.171854	journal	May 2018
Effect of a clockwise-locked deletion in FliG on the FliG ring structure of the bacterial flagellar motor Kinoshita, Miki; Namba, Keiichi; Minamino, Tohru Genes to Cells, Vol. 23, Issue 3 https://doi.org/10.1111/gtc.12565	journal	February 2018
The role of a cytoplasmic loop of MotA in load-dependent assembly and disassembly dynamics of the MotA/B stator complex in the bacterial flagellar motor: Characterization of Salmonella slow motile MotA mutants Pourjaberi, Seyedeh Noorolhoda Shajari; Terahara, Naoya; Namba, Keiichi Molecular Microbiology, Vol. 106, Issue 4 https://doi.org/10.1111/mmi.13843	journal	September 2017
Protein ensembles link genotype to phenotype Nussinov, Ruth; Tsai, Chung-Jung; Jang, Hyunbum PLOS Computational Biology, Vol. 15, Issue 6 https://doi.org/10.1371/journal.pcbi.1006648	journal	June 2019
Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II Pandini, Alessandro; Schulman, Howard; Khan, Shahid PLOS Computational Biology, Vol. 15, Issue 5 https://doi.org/10.1371/journal.pcbi.1006796	journal	May 2019
Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II Pandini, Alessandro; Schulman, Howard; Khan, Shahid The Francis Crick Institute https://doi.org/10.25418/crick.11558742	text	January 2020
Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II Pandini, Alessandro; Schulman, Howard; Khan, Shahid The Francis Crick Institute https://doi.org/10.25418/crick.11558742.v1	text	January 2020

Similar Records

Insight into adaptive remodeling of the rotor ring complex of the bacterial flagellar motor

Journal Article · Sun Jan 14 23:00:00 EST 2018 · Biochemical and Biophysical Research Communications · OSTI ID:23127441

Exchange of rotor components in functioning bacterial flagellar motor

Journal Article · Fri Mar 26 00:00:00 EDT 2010 · Biochemical and Biophysical Research Communications · OSTI ID:22202432

Structure of FliM Provides Insight into Assembly of the Switch Complex in the Bacterial Flagella Motor

Journal Article · Sat Dec 31 23:00:00 EST 2005 · Proc Natl Acad Sci USA · OSTI ID:914286

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
Biophysics
Cell Biology

The Gearbox of the Bacterial Flagellar Motor Switch

Citation Formats

References (50)

Cited By (9)

Similar Records

Related Subjects