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Mechanism of Bacterial Signal Transduction Revealed by Molecular Dynamics of Tsr Dimers and Trimers of Dimers in Lipid Vesicles
2012
PLoS Computational Biology
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Simulations of the models in a 70 nm diameter vesicle with a biologically realistic lipid mixture reveal specific lipid interactions and oligomerisation of the trimer of dimers. ...
We present a molecular model of the entire Tsr dimer, and examine its behaviour using coarse-grained molecular dynamics and elastic network modelling. ...
Acknowledgments We thank the Oxford Computing Centre for computer time, and AA Watson, D Parton, and S Khalid for their interest and helpful comments on the manuscript.
Author Contributions ...
doi:10.1371/journal.pcbi.1002685
pmid:23028283
pmcid:PMC3447960
fatcat:papvyfl2tffgddmdznea4jsysq
Interdimer zipping in the chemoreceptor signaling domain revealed by molecular dynamics simulations
[article]
2019
bioRxiv
pre-print
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Furthermore, molecular mechanisms of signal transduction that are likely to involve inter-dimer interactions are not fully understood. ...
Here we apply all-atom, microsecond-time scale molecular dynamics simulations of the Tsr trimer of dimers atomic model in order to obtain further insight into potential interactions within the chemoreceptor ...
Hall BA, Armitage JP, & Sansom MS (2012) Mechanism of bacterial signal transduction revealed by molecular dynamics of Tsr dimers and trimers of dimers in lipid vesicles. ...
doi:10.1101/745117
fatcat:c75pv55r5za77f4tqzkwj4xweq
CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling
2015
eLife
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Using all-atom molecular dynamics simulations, we further reveal a distinctive conformational change in CheA. ...
Chemotactic responses in bacteria require large, highly ordered arrays of sensory proteins to mediate the signal transduction that ultimately controls cell motility. ...
Large-scale molecular dynamics simulations were performed on the Blue Waters supercomputer, financed by the National Science Foundation (awards OCI-0725070 and ACI-1238993).
Additional information ...
doi:10.7554/elife.08419
pmid:26583751
fatcat:lserwqslkzasvff3khuclrbgsq
Three-Dimensional Electron Microscopic Imaging of Membrane Invaginations in Escherichia coli Overproducing the Chemotaxis Receptor Tsr
2004
Journal of Bacteriology
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such receptor aggregates could play an important role in signal transduction during bacterial chemotaxis. ...
Here we used electron tomographic imaging to determine the molecular architecture of Escherichia coli cells engineered to overproduce the bacterial chemotaxis receptor Tsr. ...
ACKNOWLEDGMENTS We thank Anas Chalah for assistance with preparation of membranes and Stanton Lee for generous assistance with recording tomograms. ...
doi:10.1128/jb.186.15.5052-5061.2004
pmid:15262942
pmcid:PMC451663
fatcat:qoje4rvy7nhefkghs5ae6nomh4
Thermodynamic Analysis of Protein-Membrane Interactions: The case of Octameric Mitochondrial Creatine Kinase
2010
Biophysical Journal
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Our hypothesis is: the failure of mitochondrial inner membrane morphology might be due to very basic and purely physical mechanism -the deterioration of mechanical (visco-elastic) properties of the lipid ...
In other words, the Amyloid-beta (1-42) could induce the lipid bilayer incapacity to support the dynamics of shape changes underlying (and inherent to) mitochondrial inner membrane normal functioning. ...
Through comparative modeling and map-constrained molecular dynamics simulations, we obtained the assembly structures of tsr organized in a two dimensional array. ...
doi:10.1016/j.bpj.2009.12.2059
fatcat:gaoiilwyavdk3akmp4jpc3ycoq
Preformed Soluble Chemoreceptor Trimers That Mimic Cellular Assembly States and Activate CheA Autophosphorylation
2015
Biochemistry
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Bacterial chemoreceptors associate with the histidine kinase CheA and coupling protein CheW to form extended membrane arrays that receive and transduce environmental signals. ...
A receptor trimers-of-dimers resides at each vertex of the hexagonal protein lattice. CheA is fully activated and regulated when it is integrated into the receptor assembly. ...
T he molecular signal transduction pathway intrinsic to bacterial chemotaxis is known for high sensitivity, dynamic range, and signal gain. 1−4 The chemotaxis detection system is comprised of ordered membrane ...
doi:10.1021/bi501570n
pmid:25967982
pmcid:PMC4772074
fatcat:5y3nq2yo4fh23dfah6ac7oqpdq
Synthetic Multivalent Ligands as Probes of Signal Transduction
2006
Angewandte Chemie International Edition
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assembly in signal transduction. ...
[74] Powerful new imaging methods have been used to visualize immune synapses formed in vitro and in vivo; these studies reveal that dynamic changes in protein localization and organization can occur ...
doi:10.1002/anie.200502794
pmid:16557636
pmcid:PMC2842921
fatcat:wzt42goao5faxnwsklulxnlte4
Transmembrane signaling in bacterial chemoreceptors
2001
TIBS -Trends in Biochemical Sciences. Regular ed
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This transmembrane signaling is being investigated by novel strategies, which have revealed a remarkably subtle conformational signal carried by a signaling helix that spans the entire length of the >350 ...
Multiple, independent lines of evidence indicate that, in the periplasmic and transmembrane domains, conformational signaling is a piston-type sliding of the signaling helix towards the cytoplasm. ...
Acknowledgments Support provided by NIH Grant GM40731 (to J.J.F.) and GM29963 (to G.L.H.). ...
doi:10.1016/s0968-0004(00)01770-9
pmid:11295559
pmcid:PMC2895674
fatcat:cxvs7c53g5hzrmsjh4formqou4
Nanodiscs in Membrane Biochemistry and Biophysics
2017
Chemical Reviews
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Membrane proteins play a most important part in metabolism, signaling, cell motility, transport, development, and many other biochemical and biophysical processes which constitute fundamentals of life ...
by Nanodiscs for structural and mechanistic studies of membrane proteins. ...
Acknowledgments Research was supported by grants from NIH GM33775, GM31756, GM110428 and GM118145. ...
doi:10.1021/acs.chemrev.6b00690
pmid:28177242
pmcid:PMC5805400
fatcat:siraoshiivfnlbadvbdl4u4wvi
Complete structure of the core signalling unit of the E. coli chemosensory array in an optimised minicell strain
[article]
2019
bioRxiv
pre-print
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This map, combined with previously determined high resolution structures and molecular dynamics simulations, yields an atomistic model of the membrane-bound CSU and enables spatial localisation of its ...
Our work thus offers a solid structural basis for interpretation of existing data and design of new experiments to elucidate signalling mechanisms within the CSU and larger array. ...
. 338 The complete Tsr model was embedded in an atomistic lipid bilayer and subjected to an 339 extensive structural equilibration using molecular dynamics simulation. ...
doi:10.1101/723692
fatcat:7e63ohc6u5gf5challyc6nqz2e
Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain
2020
Nature Communications
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This map, combined with previously determined high resolution structures and molecular dynamics simulations, yields a molecular model of the transmembrane core signalling unit and enables spatial localisation ...
Our work thus offers a solid structural basis for the interpretation of a wide range of existing data and the design of further experiments to elucidate signalling mechanisms within the core signalling ...
Molecular dynamics simulations were performed on the Blue Waters supercomputer, which is supported by the National Science Foundation (OCI-0725070 and ACI-1238993) and the state of Illinois as part of ...
doi:10.1038/s41467-020-14350-9
pmid:32029744
pmcid:PMC7005262
fatcat:tp3pbmktkrefvpf67ofmus6g6y
Effects of Solubilization on the Structure and Function of the Sensory Rhodopsin II/Transducer Complex
2006
Journal of Molecular Biology
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Lipid-protein interactions are known to play a crucial role in structure and physiological activity of integral membrane proteins. ...
In this study, a comparison of structural and kinetic data obtained for the archaebacterial photoreceptor/transducer complex from Natronomonas pharaonis (NpSRII/NpHtrII) in detergent-solubilized and lipid-reconstituted ...
Beier for his help with the modeling and visualization of the HAMP domain, and A. Gö ppner for technical assistance. ...
doi:10.1016/j.jmb.2005.12.015
pmid:16410012
fatcat:lq4wsmvbandnzb3v74dehb3ul4
第57回年会予稿集
2019
Seibutsu Butsuri
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We revealed by single-molecule fluorescence imaging that wildtype UvrD unwinds DNA in the form of an oligomer (dimer or trimer) (Biophys. J. 2013). ...
We revealed by single-molecule fluorescence imaging that wildtype UvrD unwinds DNA in the form of an oligomer (dimer or trimer) (Biophys. J. 2013). ...
In this study, to reveal the detailed mechanism of Ub transfer by full length E6AP E3 ligase, we tried to observe structural dynamics of full length E6AP E3 ligase using HS-AFM. 3Pos189 Kinesin transport ...
doi:10.2142/biophys.59.s1
fatcat:rsudhlmaanetrhmdxjgsiyorme
Ankyrin-Like with Transmembrane Domains 1
[chapter]
2018
Encyclopedia of Signaling Molecules
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Acknowledgments This work was supported by the following grants from the National Institutes of Health: 5R01DK105542 (J.D.S.) and 4P01DK05441 (J.D.S.). ...
Acknowledgments The work was supported by grants of the CONACYT 252942, 2015-02-1320, SEP-PRODEP-913026-1461211, and Universidad Autónoma Metropolitana Iztapalapa. ...
The PH domain is present in a wide variety of proteins involved in the regulation of cytoskeletal dynamics and signal transduction (Yan et al. 2005) . ...
doi:10.1007/978-3-319-67199-4_100213
fatcat:5df5d57dvngs5bwxwm4dkhgqr4
Adenyl Cyclase
[chapter]
2018
Encyclopedia of Signaling Molecules
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Acknowledgments This work was supported by the following grants from the National Institutes of Health: 5R01DK105542 (J.D.S.) and 4P01DK05441 (J.D.S.). ...
Acknowledgments The work was supported by grants of the CONACYT 252942, 2015-02-1320, SEP-PRODEP-913026-1461211, and Universidad Autónoma Metropolitana Iztapalapa. ...
The PH domain is present in a wide variety of proteins involved in the regulation of cytoskeletal dynamics and signal transduction (Yan et al. 2005) . ...
doi:10.1007/978-3-319-67199-4_100131
fatcat:antda47zovgqpibqeo53gsh3wa
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