Research Topics
| Dennis BraySummaryAffiliation: University of Cambridge Country: UK Publications
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Detail Information
Publications
A spatially extended stochastic model of the bacterial chemotaxis signalling pathwayThomas S Shimizu
Department of Zoology, University of Cambridge, UK
J Mol Biol 329:291-309. 2003..The model also has some of the properties of a cellular automaton and shows an unexpected emergence of spatial patterns of methylation within the receptor lattice...
How the "melting" and "freezing" of protein molecules may be used in cell signalingDennis Bray
Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
ACS Chem Biol 3:89-91. 2008..We discuss the thermodynamic basis for this effect and argue that the "freezing" or "melting" of protein structure may be the language of signaling...
Computer-based analysis of the binding steps in protein complex formationD Bray
Department of Zoology, Downing Street, Cambridge CB2 3EJ, United Kingdom
Proc Natl Acad Sci U S A 94:13493-8. 1997..On the basis of this study, we suggest that the prozone phenomenon will occur widely in living cells and that it could be a crucial factor in the regulation of protein complex formation...- Receptor clustering as a cellular mechanism to control sensitivityD Bray
Department of Zoology, University of Cambridge, UK
Nature 393:85-8. 1998..A mechanism of this kind can account quantitatively for the sensitivity and response range of E. coli to aspartate... - Signaling complexes: biophysical constraints on intracellular communicationD Bray
Department of Zoology, University of Cambridge, United Kingdom
Annu Rev Biophys Biomol Struct 27:59-75. 1998..The importance of diffusion in controlling the numbers and locations of signaling complexes is discussed, as is the special role played by membranes in signaling pathways... - Genomics. Molecular prodigalityDennis Bray
Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
Science 299:1189-90. 2003 - Signal amplification in a lattice of coupled protein kinasesJacki P Goldman
Department of Physiology, Development, and Neuroscience, University of Cambridge, UK
Mol Biosyst 5:1853-9. 2009..We test this idea with detailed, molecular-based stochastic simulations and show that it gives an accurate reproduction of signalling in this system, including ligand-specific adaptation... - Balls and chains--a mesoscopic approach to tethered protein domainsBernhard Windisch
Department of Physics, Cavendish Laboratory, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
Biophys J 91:2383-92. 2006..The possible biological significance of these and other results is discussed... - The cell as a thermostat: how much does it know?Dennis Bray
Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
Adv Exp Med Biol 736:193-8. 2012..This information is far richer than anything carried by a thermostat and closer to the 'knowledge' that higher animals have about the world... - The chemotactic behavior of computer-based surrogate bacteriaDennis Bray
Department of Physiology, Development, and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, United Kingdom
Curr Biol 17:12-9. 2007..In many species of bacteria, this occurs when extracellular signals are detected by transmembrane receptors and relayed to flagellar motors, which control the cell's swimming behavior... - Simulated diffusion of phosphorylated CheY through the cytoplasm of Escherichia coliKaren Lipkow
Department of Anatomy, University of Cambridge, Downing St, Cambridge CB2 3DY, United Kingdom
J Bacteriol 187:45-53. 2005..These and other results are left as predictions for future experiments... - Binding and diffusion of CheR molecules within a cluster of membrane receptorsMatthew D Levin
Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
Biophys J 82:1809-17. 2002..We explore the possible consequences of this motion, which we term "molecular brachiation", for chemotactic adaptation and suggest that a similar mechanism may be operative in other large assemblies of protein molecules... - Conformational spread: the propagation of allosteric states in large multiprotein complexesDennis Bray
Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
Annu Rev Biophys Biomol Struct 33:53-73. 2004..We suggest that conformational spread could provide the basis of a solid-state "circuitry" in a living cell, able to integrate biochemical and biophysical events over hundreds of protein molecules... - Molecular model of a lattice of signalling proteins involved in bacterial chemotaxisT S Shimizu
1 Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
Nat Cell Biol 2:792-6. 2000..This structure creates separate compartments for adaptation and downstream signalling, and indicates a possible basis for the spread of activity within the cluster... - Modelling the bacterial chemotaxis receptor complexThomas Simon Shimizu
Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
Novartis Found Symp 247:162-77; discussion 177-81, 198-206, 244-52. 2002..The adaptation reactions may also exploit the proximity of receptor molecules, and a hypothetical mechanism by which this may occur is currently being tested... - Flexible peptides and cytoplasmic gelsDennis Bray
Department of Anatomy, University of Cambridge, Cambridge CB2 3DY, UK
Genome Biol 6:106. 2005..Unstructured, flexible polypeptides are likely to be functionally important and may cause local cytoplasmic regions to become gel-like... - Heightened sensitivity of a lattice of membrane receptorsT A Duke
Institut Curie, Physico Chimie Curie, Section de Recherche, 26 Rue d Ulm, 75231 Paris Cedex 05, France
Proc Natl Acad Sci U S A 96:10104-8. 1999..These and other properties should make a lattice of conformationally coupled receptors ideally suited to act as a "nose" by which a cell can detect and respond to extracellular stimuli... - Origins of individual swimming behavior in bacteriaM D Levin
Department of Zoology, University of Cambridge, United Kingdom
Biophys J 74:175-81. 1998..We also make predictions for the swimming behaviors of mutant strains lacking the adaptational mechanism that can be tested experimentally... - A computer program for the analysis of protein complex formationS Lay
Comput Appl Biosci 13:439-44. 1997..The program also finds the equilibrium state of the system, using either default starting concentrations and Kd values or data supplied by the user... - Size and composition of membrane protein clusters predicted by Monte Carlo analysisJacki Goldman
Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
Eur Biophys J 33:506-12. 2004..Our results suggest that the self-assembly of microdomains might require a critical level of subunits and that for optimal co-aggregation, proteins should be present in the membrane in the correct stoichiometric ratios... - Stochastic simulation of chemical reactions with spatial resolution and single molecule detailSteven S Andrews
Department of Zoology, University of Cambridge, UK
Phys Biol 1:137-51. 2004..Capabilities of these methods are demonstrated with simulations of a simple bimolecular reaction and the Lotka-Volterra system... - Bacterial chemotaxis and the question of gainDennis Bray
Department of Zoology, University of Cambridge, Cambridge, United Kingdom
Proc Natl Acad Sci U S A 99:7-9. 2002 - Molecular networks: the top-down viewDennis Bray
Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
Science 301:1864-5. 2003..Network theory can give a useful overview of how a biological system works. But to make testable predictions, we need the details...