Dennis Bray

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. ncbi request reprint A spatially extended stochastic model of the bacterial chemotaxis signalling pathway
    Thomas S Shimizu
    Department of Zoology, University of Cambridge, UK
    J Mol Biol 329:291-309. 2003
  2. doi request reprint How the "melting" and "freezing" of protein molecules may be used in cell signaling
    Dennis Bray
    Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
    ACS Chem Biol 3:89-91. 2008
  3. pmc Computer-based analysis of the binding steps in protein complex formation
    D Bray
    Department of Zoology, Downing Street, Cambridge CB2 3EJ, United Kingdom
    Proc Natl Acad Sci U S A 94:13493-8. 1997
  4. ncbi request reprint Receptor clustering as a cellular mechanism to control sensitivity
    D Bray
    Department of Zoology, University of Cambridge, UK
    Nature 393:85-8. 1998
  5. ncbi request reprint Signaling complexes: biophysical constraints on intracellular communication
    D Bray
    Department of Zoology, University of Cambridge, United Kingdom
    Annu Rev Biophys Biomol Struct 27:59-75. 1998
  6. ncbi request reprint Genomics. Molecular prodigality
    Dennis Bray
    Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
    Science 299:1189-90. 2003
  7. doi request reprint Signal amplification in a lattice of coupled protein kinases
    Jacki P Goldman
    Department of Physiology, Development, and Neuroscience, University of Cambridge, UK
    Mol Biosyst 5:1853-9. 2009
  8. pmc Balls and chains--a mesoscopic approach to tethered protein domains
    Bernhard Windisch
    Department of Physics, Cavendish Laboratory, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
    Biophys J 91:2383-92. 2006
  9. doi request reprint 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
  10. pmc Simulated diffusion of phosphorylated CheY through the cytoplasm of Escherichia coli
    Karen Lipkow
    Department of Anatomy, University of Cambridge, Downing St, Cambridge CB2 3DY, United Kingdom
    J Bacteriol 187:45-53. 2005

Collaborators

Detail Information

Publications24

  1. ncbi request reprint A spatially extended stochastic model of the bacterial chemotaxis signalling pathway
    Thomas 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...
  2. doi request reprint How the "melting" and "freezing" of protein molecules may be used in cell signaling
    Dennis 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...
  3. pmc Computer-based analysis of the binding steps in protein complex formation
    D 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...
  4. ncbi request reprint Receptor clustering as a cellular mechanism to control sensitivity
    D 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...
  5. ncbi request reprint Signaling complexes: biophysical constraints on intracellular communication
    D 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...
  6. ncbi request reprint Genomics. Molecular prodigality
    Dennis Bray
    Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
    Science 299:1189-90. 2003
  7. doi request reprint Signal amplification in a lattice of coupled protein kinases
    Jacki 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...
  8. pmc Balls and chains--a mesoscopic approach to tethered protein domains
    Bernhard 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...
  9. doi request reprint 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...
  10. pmc Simulated diffusion of phosphorylated CheY through the cytoplasm of Escherichia coli
    Karen 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...
  11. ncbi request reprint The chemotactic behavior of computer-based surrogate bacteria
    Dennis 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...
  12. pmc Binding and diffusion of CheR molecules within a cluster of membrane receptors
    Matthew 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...
  13. ncbi request reprint Conformational spread: the propagation of allosteric states in large multiprotein complexes
    Dennis 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...
  14. ncbi request reprint Molecular model of a lattice of signalling proteins involved in bacterial chemotaxis
    T 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...
  15. pmc Flexible peptides and cytoplasmic gels
    Dennis 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...
  16. ncbi request reprint Modelling the bacterial chemotaxis receptor complex
    Thomas 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...
  17. pmc Heightened sensitivity of a lattice of membrane receptors
    T 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...
  18. pmc Origins of individual swimming behavior in bacteria
    M 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...
  19. ncbi request reprint A computer program for the analysis of protein complex formation
    S Lay
    Comput Appl Biosci 13:439-44. 1997
    ..We needed an efficient way to explore the binding reactions leading to protein complexes of known composition and structure...
  20. doi request reprint The propagation of allosteric states in large multiprotein complexes
    Dennis Bray
    Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DT, UK
    J Mol Biol 425:1410-4. 2013
    ..A similar mechanism could potentially provide a universal mechanism of integration within living cells...
  21. ncbi request reprint Stochastic simulation of chemical reactions with spatial resolution and single molecule detail
    Steven 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...
  22. ncbi request reprint Size and composition of membrane protein clusters predicted by Monte Carlo analysis
    Jacki 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...
  23. pmc Bacterial chemotaxis and the question of gain
    Dennis Bray
    Department of Zoology, University of Cambridge, Cambridge, United Kingdom
    Proc Natl Acad Sci U S A 99:7-9. 2002
  24. ncbi request reprint Molecular networks: the top-down view
    Dennis 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...