Filters








34 Hits in 9.1 sec

Mechanism of Bacterial Signal Transduction Revealed by Molecular Dynamics of Tsr Dimers and Trimers of Dimers in Lipid Vesicles

Benjamin A. Hall, Judith P. Armitage, Mark S. P. Sansom, Marco Punta
2012 PLoS Computational Biology  
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]

Marharyta G. Petukh, Davi R. Ortega, Jerome Baudry, Igor B. Zhulin
2019 bioRxiv   pre-print
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

C Keith Cassidy, Benjamin A Himes, Frances J Alvarez, Jun Ma, Gongpu Zhao, Juan R Perilla, Klaus Schulten, Peijun Zhang
2015 eLife  
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

J. Lefman, P. Zhang, T. Hirai, R. M. Weis, J. Juliani, D. Bliss, M. Kessel, E. Bos, P. J. Peters, S. Subramaniam
2004 Journal of Bacteriology  
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

Malgorzata Tokarska-Schlattner, Uwe Schlattner
2010 Biophysical Journal  
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

Anna R. Greenswag, Xiaoxiao Li, Peter P. Borbat, Dipanjan Samanta, Kylie J. Watts, Jack H. Freed, Brian R. Crane
2015 Biochemistry  
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

Laura L. Kiessling, Jason E. Gestwicki, Laura E. Strong
2006 Angewandte Chemie International Edition  
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

Joseph J. Falke, Gerald L. Hazelbauer
2001 TIBS -Trends in Biochemical Sciences. Regular ed  
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

Ilia G. Denisov, Stephen G. Sligar
2017 Chemical Reviews  
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]

Alister Burt, C. Keith Cassidy, Peter Ames, Maria Bacia-Verloop, Megghane Baulard, Karine Huard, Zaida Luthey-Schulten, Ambroise Desfosses, Phillip J. Stansfeld, William Margolin, John S. Parkinson, Irina Gutsche
2019 bioRxiv   pre-print
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

Alister Burt, C. Keith Cassidy, Peter Ames, Maria Bacia-Verloop, Megghane Baulard, Karine Huard, Zaida Luthey-Schulten, Ambroise Desfosses, Phillip J. Stansfeld, William Margolin, John S. Parkinson, Irina Gutsche
2020 Nature Communications  
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

Johann P. Klare, Enrica Bordignon, Meike Doebber, Jörg Fitter, Jana Kriegsmann, Igor Chizhov, Heinz-Jürgen Steinhoff, Martin Engelhard
2006 Journal of Molecular Biology  
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  
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  
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  
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
« Previous Showing results 1 — 15 out of 34 results