Mark S P Sansom

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. pmc Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale
    Matthieu Chavent
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Curr Opin Struct Biol 40:8-16. 2016
  2. pmc Interfacial activation of M37 lipase: A multi-scale simulation study
    Nathalie Willems
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Biochim Biophys Acta . 2016
  3. pmc Computational virology: From the inside out
    Tyler Reddy
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Biochim Biophys Acta 1858:1610-8. 2016
  4. pmc Interactions of the EGFR juxtamembrane domain with PIP2-containing lipid bilayers: Insights from multiscale molecular dynamics simulations
    Khairul Bariyyah Abd Halim
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Biochim Biophys Acta 1850:1017-25. 2015
  5. pmc Membrane stiffness is modified by integral membrane proteins
    Philip W Fowler
    Department of Biochemistry, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK
    Soft Matter 12:7792-7803. 2016
  6. pmc Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion
    Tyler Reddy
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Structure 23:584-97. 2015
  7. pmc PIP(2)-binding site in Kir channels: definition by multiscale biomolecular simulations
    Phillip J Stansfeld
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Biochemistry 48:10926-33. 2009
  8. pmc Transmembrane helix dynamics of bacterial chemoreceptors supports a piston model of signalling
    Benjamin A Hall
    Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    PLoS Comput Biol 7:e1002204. 2011
  9. pmc Finding a needle in a haystack: the role of electrostatics in target lipid recognition by PH domains
    Craig N Lumb
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    PLoS Comput Biol 8:e1002617. 2012
  10. pmc Conformational changes in talin on binding to anionic phospholipid membranes facilitate signaling by integrin transmembrane helices
    Antreas C Kalli
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    PLoS Comput Biol 9:e1003316. 2013

Detail Information

Publications124 found, 100 shown here

  1. pmc Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale
    Matthieu Chavent
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Curr Opin Struct Biol 40:8-16. 2016
    ..Current methods allow near atomic resolution simulations of small membrane organelles, and of enveloped viruses to be performed, revealing key aspects of their structure and functionally important dynamics...
  2. pmc Interfacial activation of M37 lipase: A multi-scale simulation study
    Nathalie Willems
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Biochim Biophys Acta . 2016
    ..The exposure of hydrophobic residues within lid and active site flap regions (residues 94-110) during the activation process provides insights into the functional effect of hydrophobic surfaces on lipase activation...
  3. pmc Computational virology: From the inside out
    Tyler Reddy
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Biochim Biophys Acta 1858:1610-8. 2016
    ..This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. ..
  4. pmc Interactions of the EGFR juxtamembrane domain with PIP2-containing lipid bilayers: Insights from multiscale molecular dynamics simulations
    Khairul Bariyyah Abd Halim
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Biochim Biophys Acta 1850:1017-25. 2015
    ..The EGFR juxtamembrane (JM) domain is involved in the mechanism of activation of the receptor, interacting with the anionic lipid phosphatidylinositol 4,5-bisphosphate (PIP2) in the intracellular leaflet of the cell membrane...
  5. pmc Membrane stiffness is modified by integral membrane proteins
    Philip W Fowler
    Department of Biochemistry, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK
    Soft Matter 12:7792-7803. 2016
    ..Our results suggest that integral membrane proteins can have different effects, and in the case of the bacterial outer membrane protein, BtuB, the greater the density of protein, the larger the reduction in stiffness...
  6. pmc Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion
    Tyler Reddy
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Structure 23:584-97. 2015
    ..Our simulations indicate that viral spike proteins do not aggregate and thus are competent for multivalent immunoglobulin G interactions. ..
  7. pmc PIP(2)-binding site in Kir channels: definition by multiscale biomolecular simulations
    Phillip J Stansfeld
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Biochemistry 48:10926-33. 2009
    ..Polar contacts in the coarse-grained simulations corresponded to long-lived electrostatic and H-bonding interactions between the channel and PIP(2) in the atomistic simulations, enabling identification of key side chains...
  8. pmc Transmembrane helix dynamics of bacterial chemoreceptors supports a piston model of signalling
    Benjamin A Hall
    Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    PLoS Comput Biol 7:e1002204. 2011
    ..2000 simulations in total. Overall, this analysis supports a swinging-piston model of transmembrane signalling by Tar and related chemoreceptors...
  9. pmc Finding a needle in a haystack: the role of electrostatics in target lipid recognition by PH domains
    Craig N Lumb
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    PLoS Comput Biol 8:e1002617. 2012
    ..These studies demonstrate a computational framework which addresses lipid recognition within a cell membrane environment, offering a link between structural and cell biological characterisation...
  10. pmc Conformational changes in talin on binding to anionic phospholipid membranes facilitate signaling by integrin transmembrane helices
    Antreas C Kalli
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    PLoS Comput Biol 9:e1003316. 2013
    ....
  11. pmc Multiscale simulations reveal conserved patterns of lipid interactions with aquaporins
    Phillip J Stansfeld
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Structure 21:810-9. 2013
    ..Rather Aqps exhibit a more broadly conserved protein/lipid interface, suggestive of interchange between annular and bulk lipids, instead of a fixed annular "shell" of lipids...
  12. pmc The structure of the talin/integrin complex at a lipid bilayer: an NMR and MD simulation study
    Antreas C Kalli
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Structure 18:1280-8. 2010
    ..Our studies suggest that the perturbed orientation of talin relative to the membrane in the F2 mutant would be expected to in turn perturb talin/integrin interactions...
  13. pmc Biophysical and computational studies of membrane penetration by the GRP1 pleckstrin homology domain
    Craig N Lumb
    Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
    Structure 19:1338-46. 2011
    ..This supports a "dual-recognition" model of binding, with specific GRP1-PH-PI(3,4,5)P(3) interactions supplemented by interactions of loop regions with the lipid bilayer...
  14. pmc How does a voltage sensor interact with a lipid bilayer? Simulations of a potassium channel domain
    Zara A Sands
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
    Structure 15:235-44. 2007
    ..As a consequence of this, the electrostatic field is "focused" across the center of the bilayer...
  15. pmc Insights into how nucleotide-binding domains power ABC transport
    Simon Newstead
    Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College London, London, UK
    Structure 17:1213-22. 2009
    ..This result has important implications for our understanding of the mechanism of power generation in ABC transporters, because the unwinding of this free energy ensures that the opening of these two NBDs is also powered...
  16. pmc Interactions between a voltage sensor and a toxin via multiscale simulations
    Chze Ling Wee
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Biophys J 98:1558-65. 2010
    ..Overall, the results show that serial multiscale MD simulations may be used to model a two-stage process of protein-bilayer and protein-protein interactions within a membrane...
  17. doi request reprint Coarse-grained simulation: a high-throughput computational approach to membrane proteins
    Mark S P Sansom
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U K
    Biochem Soc Trans 36:27-32. 2008
    ..Both CG and AT simulations predict considerable local bilayer deformation by the voltage sensor domain of the potassium channel KvAP...
  18. pmc Conformational dynamics of the ligand-binding domain of inward rectifier K channels as revealed by molecular dynamics simulations: toward an understanding of Kir channel gating
    Shozeb Haider
    Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
    Biophys J 88:3310-20. 2005
    ..It is of interest that loss of exact rotational symmetry has also been suggested to play a role in gating in the bacterial Kir homolog, KirBac1.1, and in the nicotinic acetylcholine receptor channel...
  19. pmc Anionic phospholipid interactions with the potassium channel KcsA: simulation studies
    Sundeep S Deol
    Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
    Biophys J 90:822-30. 2006
    ..Overall, this study suggests that simulations can help identify and characterize sites for specific lipid interactions on a membrane protein surface...
  20. ncbi request reprint Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa
    Syma Khalid
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Proteins 63:6-15. 2006
    ..Overall, the behavior of the OprF model in simulations supports the suggestion that this molecule is comparable to OmpA. The simulations help to explain the mechanism of formation of low conductance pores within the outer membrane...
  21. pmc Potassium channel, ions, and water: simulation studies based on the high resolution X-ray structure of KcsA
    Carmen Domene
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Biophys J 85:2787-800. 2003
    ..A preliminary comparison of the use of particle mesh Ewald versus cutoff protocols for the treatment of long-range electrostatics suggests some difference in the kinetics of ion translocation within the filter...
  22. pmc Molecular dynamics simulation of the M2 helices within the nicotinic acetylcholine receptor transmembrane domain: structure and collective motions
    Andrew Hung
    Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
    Biophys J 88:3321-33. 2005
    ..Normal mode analyses using the anisotropic network model reveal collective motions similar to those identified by principal components analyses...
  23. pmc Increased ATPase activity produced by mutations at arginine-1380 in nucleotide-binding domain 2 of ABCC8 causes neonatal diabetes
    Heidi de Wet
    Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, United Kingdom
    Proc Natl Acad Sci U S A 104:18988-92. 2007
    ..Molecular modeling studies supported this idea. Because mutant channels were inhibited less strongly by MgATP, this would increase K(ATP) currents in pancreatic beta cells, thus reducing insulin secretion and producing diabetes...
  24. pmc A mutation (R826W) in nucleotide-binding domain 1 of ABCC8 reduces ATPase activity and causes transient neonatal diabetes
    Heidi de Wet
    Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
    EMBO Rep 9:648-54. 2008
    ..Channel inhibition by MgATP was reduced, leading to an increase in resting whole-cell currents. In pancreatic beta cells, this would lead to less insulin secretion and thereby diabetes...
  25. pmc Molecular dynamics simulations of the bacterial outer membrane protein FhuA: a comparative study of the ferrichrome-free and bound states
    José D Faraldo-Gómez
    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
    Biophys J 85:1406-20. 2003
    ..These simulations are among the longest that have been performed on a complex membrane protein. However, a simple analysis of sampling reveals that the description of protein motions is far from complete...
  26. pmc Lipid-protein interactions of integral membrane proteins: a comparative simulation study
    Sundeep S Deol
    Department of Biochemistry, and Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
    Biophys J 87:3737-49. 2004
    ..Overall, these simulations present a dynamic picture of lipid-protein interactions: there are a number of more specific interactions but even these fluctuate on an approximately 1- to 5-ns timescale...
  27. pmc A universally conserved residue in the SUR1 subunit of the KATP channel is essential for translating nucleotide binding at SUR1 into channel opening
    Heidi de Wet
    Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
    J Physiol 590:5025-36. 2012
    ..Interestingly, this effect was dependent on the functional integrity of the NBDs. These results therefore suggest that SUR1 modulates both nucleotide inhibition and activation of the KATP channel...
  28. ncbi request reprint A prokaryotic glutamate receptor: homology modelling and molecular dynamics simulations of GluR0
    Yalini Arinaminpathy
    Department of Biochemistry, The University of Oxford, The Rex Richards Building, South Parks Road, OX1 3QU Oxford, UK
    FEBS Lett 553:321-7. 2003
    ..In the intact receptor the opening of this gate will be controlled by interactions with the extramembranous ligand-binding domains...
  29. ncbi request reprint Ion channel gating: insights via molecular simulations
    Oliver Beckstein
    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    FEBS Lett 555:85-90. 2003
    ..Simulations of a simple outer membrane protein, OmpA, indicate that a gate may also be formed by interactions of charged side chains within a pore, as is also the case in ClC channels...
  30. pmc OmpT: molecular dynamics simulations of an outer membrane enzyme
    Marc Baaden
    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Biophys J 87:2942-53. 2004
    ..The simulations appear to reveal the presence of specific lipid interaction sites on the surface of the OmpT barrel. This reveals the ability of extended MD simulations to provide meaningful information on protein-lipid interactions...
  31. pmc Nucleotide-dependent conformational changes in HisP: molecular dynamics simulations of an ABC transporter nucleotide-binding domain
    Jeff D Campbell
    Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
    Biophys J 87:3703-15. 2004
    ..These results support the mechanism for ATP-induced conformational transitions derived from the crystal structures of other NBDs...
  32. ncbi request reprint Molecular dynamics simulation approaches to K channels: conformational flexibility and physiological function
    Alessandro Grottesi
    Department of Biochemistry, University of Oxford, Oxford OX 3QU, United Kingdom
    IEEE Trans Nanobioscience 4:112-20. 2005
    ..Based on these and other simulations, a molecular model for gating of inward rectifier K channel gating is presented...
  33. doi request reprint Interaction of monotopic membrane enzymes with a lipid bilayer: a coarse-grained MD simulation study
    Kia Balali-Mood
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Biochemistry 48:2135-45. 2009
    ..Deeper insertion seems to correlate with a greater number of basic residues in the "foot" whereby a monotopic protein interacts with the membrane...
  34. ncbi request reprint Focus on Kir6.2: a key component of the ATP-sensitive potassium channel
    Shozeb Haider
    Department of Biochemistry, University of Oxford, UK
    J Mol Cell Cardiol 38:927-36. 2005
    ..We speculate on how some mutations lead to neurological disease and why no obvious cardiac symptoms are observed. We also consider the implications of these studies for type-2 diabetes...
  35. pmc Reduced lateral mobility of lipids and proteins in crowded membranes
    Joseph E Goose
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    PLoS Comput Biol 9:e1003033. 2013
    ..The increase in protein concentration also resulted in a decrease in the anomalous diffusion exponent α of the lipid. Formation of extended clusters and networks of proteins led to compartmentalisation of lipids in extreme cases...
  36. ncbi request reprint Molecular dynamics simulations of GlpF in a micelle vs in a bilayer: conformational dynamics of a membrane protein as a function of environment
    George Patargias
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
    J Phys Chem B 109:575-82. 2005
    ..Aromatic side chains (Trp, Tyr) and basic side chains (Arg, Lys) play an important role in both protein-detergent (OG) and protein-lipid (DMPC) interactions...
  37. ncbi request reprint Three hydrolases and a transferase: comparative analysis of active-site dynamics via the BioSimGrid database
    Kaihsu Tai
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
    J Mol Graph Model 25:896-902. 2007
    ..Overall, these results demonstrate the potential of a comparative MD approach to analysis of enzyme function. This approach could be extended to a wider range of enzymes using current high throughput MD simulation and database methods...
  38. ncbi request reprint Transmembrane helix-helix interactions: comparative simulations of the glycophorin a dimer
    Jonathan M Cuthbertson
    Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, UK
    Biochemistry 45:14298-310. 2006
    ..These results demonstrate the ability of extended molecular dynamics simulations in a lipid bilayer environment to refine membrane protein structures or models derived from experimental data obtained in protein/detergent micelles...
  39. ncbi request reprint Molecular dynamics simulations and membrane protein structure quality
    Anthony Ivetac
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
    Eur Biophys J 37:403-9. 2008
    ..We therefore propose that MD could become a useful quality control tool for membrane protein structural biology. In particular, it provides a way in which to explore the global conformational stability of a model membrane protein fold...
  40. pmc Gating at both ends and breathing in the middle: conformational dynamics of TolC
    Loredana Vaccaro
    Department of Biochemistry, University of Oxford, Oxford OX13QU, United Kingdom
    Biophys J 95:5681-91. 2008
    ..The motions observed in the atomistic simulations are also seen in coarse-grained simulations in which the protein tertiary structure is represented by an elastic network model...
  41. ncbi request reprint Setting up and optimization of membrane protein simulations
    José D Faraldo-Gómez
    Laboratory of Molecular Biophysics, Department of Biochemistry, The Rex Richards Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Eur Biophys J 31:217-27. 2002
    ..The results show that the drift from the initial structure is less in the latter case, especially for KcsA and for the non-core secondary structural elements (i.e. surface loops) of both proteins...
  42. ncbi request reprint Potassium channels: structures, models, simulations
    Mark S P Sansom
    Laboratory of Molecular Biophysics, Department of Biochemistry, The University of Oxford, The Rex Richards Building, South Parks Road, Oxford, UK
    Biochim Biophys Acta 1565:294-307. 2002
    ..Progress in this area is explored via two examples: inward rectifier (Kir) and voltage-gated (Kv) potassium channels. A brief account of structural studies of ancillary domains and subunits of K channels is provided...
  43. pmc The intrinsic flexibility of the Kv voltage sensor and its implications for channel gating
    Zara A Sands
    Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
    Biophys J 90:1598-606. 2006
    ..The flexible S3a region may in turn act to help restore the paddle to its initial conformation upon repolarization...
  44. ncbi request reprint Simulations of a protein translocation pore: SecY
    Shozeb Haider
    Department of Biochemistry, University of Oxford, UK
    Biochemistry 45:13018-24. 2006
    ..The simulation results also indicate that hydrophobic gating at the central pore ring prevents leakage of water and ions through the channel in the absence of a translocating peptide...
  45. ncbi request reprint Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers
    Katherine Cox
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
    Eur Biophys J 37:131-41. 2008
    ....
  46. doi request reprint Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer
    Peter J Bond
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX13QU, UK
    Biochemistry 47:11321-31. 2008
    ..The results indicated that a transmembrane orientation was favored by about -70 kT...
  47. pmc A helix heterodimer in a lipid bilayer: prediction of the structure of an integrin transmembrane domain via multiscale simulations
    Antreas C Kalli
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Structure 19:1477-84. 2011
    ..The αIIb/β3 interface was more flexible than that of, e.g., glycophorin A. This is suggestive of a role for alternative packing modes of the TM helices in transbilayer signaling...
  48. pmc Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations
    Daniel L Parton
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    PLoS Comput Biol 9:e1003034. 2013
    ..This may also represent a general mechanism for the targeting of TM proteins to rafts in the plasma membrane, which is of functional importance in a wide range of cellular processes...
  49. pmc Lipid bilayer deformation and the free energy of interaction of a Kv channel gating-modifier toxin
    Chze Ling Wee
    Department of Biochemistry and Computing Laboratory, University of Oxford, Oxford, United Kingdom
    Biophys J 95:3816-26. 2008
    ..In particular, one should allow for local deformations that may arise due to the spatial array of charged and hydrophobic elements of an interfacially located membrane protein...
  50. doi request reprint One membrane protein, two structures and six environments: a comparative molecular dynamics simulation study of the bacterial outer membrane protein PagP
    Katherine Cox
    Department of Biochemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, UK
    Mol Membr Biol 26:205-14. 2009
    ..In simulations starting from the X-ray structure in lipid bilayer, the L1 and L2 loops move towards one another, leading to the formation of a putative active site by residues H33, D76 and S77 coming closer together...
  51. pmc A conserved tryptophan at the membrane-water interface acts as a gatekeeper for Kir6.2/SUR1 channels and causes neonatal diabetes when mutated
    Roope Mannikko
    Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
    J Physiol 589:3071-83. 2011
    ..In the other state, it is flipped out, enabling movement of TM2. We therefore hypothesise that W68 may act as a molecular'gatekeeper' for Kir channels...
  52. pmc Control of KirBac3.1 potassium channel gating at the interface between cytoplasmic domains
    Lejla Zubcevic
    From the Biological Physics Group, Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, United Kingdom
    J Biol Chem 289:143-51. 2014
    ..These results provide a structural explanation for the activatory effect of this mutation and provide a greater insight into the role of the CTD in Kir channel gating. ..
  53. ncbi request reprint Homology modelling and molecular dynamics simulations: comparative studies of human aquaporin-1
    Richard J Law
    Laboratory of Molecular Biophysics, Department of Biochemistry, The University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
    Eur Biophys J 33:477-89. 2004
    ..These simulations suggest that homology models based on bacterial homologues may be used to derive functionally relevant information on the structural dynamics of mammalian transport proteins...
  54. ncbi request reprint The alpha7 nicotinic acetylcholine receptor: molecular modelling, electrostatics, and energetics
    Shiva Amiri
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Mol Membr Biol 22:151-62. 2005
    ..These studies illustrate how molecular models of members of the nicotinic receptor superfamily of channels may be used to study structure-function relationships...
  55. ncbi request reprint Comparative molecular dynamics--similar folds and similar motions?
    Andrew Pang
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Proteins 61:809-22. 2005
    ..Thus, large-scale conformational changes do indeed appear to be conserved across this fold architecture, but smaller conformational motions appear to reflect the differences in sequence and local fold...
  56. ncbi request reprint MD simulations of Mistic: conformational stability in detergent micelles and water
    Emi Psachoulia
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Biochemistry 45:9053-8. 2006
    ..These results suggest that Mistic may not be a stable integrated membrane protein but rather that it may undergo a conformational change upon interaction with a membrane or membrane-like environment...
  57. ncbi request reprint Molecular dynamics simulations of inwardly rectifying (Kir) potassium channels: a comparative study
    Shozeb Haider
    Department of Biochemistry, University of Oxford, UK
    Biochemistry 46:3643-52. 2007
    ....
  58. ncbi request reprint Identification of a functionally important negatively charged residue within the second catalytic site of the SUR1 nucleotide-binding domains
    Jeff D Campbell
    University Laboratory of Physiology, University of Oxford, Parks Rd, Oxford, OX1 3PT, UK
    Diabetes 53:S123-7. 2004
    ..Our model should be useful for designing experiments aimed at elucidating the relationship between the structure and function of the KATP channel...
  59. ncbi request reprint Coarse-grained molecular dynamics simulations of membrane proteins and peptides
    Peter J Bond
    Department of Biochemistry, University of Oxford, South Parks Road Oxford, OX1 3QU, UK
    J Struct Biol 157:593-605. 2007
    ..Taken together, these results demonstrate the utility of CG-MD simulations for studies of membrane/protein interactions...
  60. pmc OmpA: a pore or not a pore? Simulation and modeling studies
    Peter J Bond
    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
    Biophys J 83:763-75. 2002
    ..A gating mechanism is proposed to explain its documented channel properties, involving a flickering isomerization of Arg138, forming alternate salt bridges with Glu52 (closed state) and Glu128 (open state)...
  61. ncbi request reprint Extending the structure of an ABC transporter to atomic resolution: modeling and simulation studies of MsbA
    Jeff D Campbell
    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
    Biochemistry 42:3666-73. 2003
    ..This suggests that the MsbA crystal dimer may not correspond to the MsbA dimer in vivo. An alternative model of the dimer is discussed in the context of available experimental data...
  62. ncbi request reprint Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer
    Peter J Bond
    Laboratory of Molecular Biophysics, Department of Biochemistry, The University of Oxford, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK
    J Mol Biol 329:1035-53. 2003
    ..This may explain the experimentally observed channel formation by OmpA...
  63. ncbi request reprint Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein
    Andrew Pang
    Laboratory of Molecular Biophysics, Department of Biochemistry, The University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    FEBS Lett 550:168-74. 2003
    ..The essential dynamics analysis of GlnBP also revealed a third class of motion which suggests a mechanism for signal transmission in GluRs...
  64. pmc Outer membrane protein G: Engineering a quiet pore for biosensing
    Min Chen
    Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
    Proc Natl Acad Sci U S A 105:6272-7. 2008
    ..We used this mutant for the detection of adenosine diphosphate at the single-molecule level, after equipping the porin with a cyclodextrin molecular adapter, thereby demonstrating its potential for use in stochastic sensing applications...
  65. pmc Mechanism of bacterial signal transduction revealed by molecular dynamics of Tsr dimers and trimers of dimers in lipid vesicles
    Benjamin A Hall
    Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    PLoS Comput Biol 8:e1002685. 2012
    ..The results indicate a mechanism whereby small motions of a single helix can be amplified through HAMP domain packing, to initiate large changes in the whole receptor structure...
  66. ncbi request reprint Vstx1, a modifier of Kv channel gating, localizes to the interfacial region of lipid bilayers
    Daniele Bemporad
    Department of Biochemistry, The University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Biochemistry 45:11844-55. 2006
    ....
  67. pmc The interaction of phospholipase A2 with a phospholipid bilayer: coarse-grained molecular dynamics simulations
    Chze Ling Wee
    Department of Biochemistry and Computing Laboratory, University of Oxford, Oxford, United Kingdom
    Biophys J 95:1649-57. 2008
    ....
  68. pmc Structures of ABCB10, a human ATP-binding cassette transporter in apo- and nucleotide-bound states
    Chitra A Shintre
    Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
    Proc Natl Acad Sci U S A 110:9710-5. 2013
    ..These structures indicate that ABC transporters may exist in an open-inwards conformation when nucleotide is bound. We discuss ways in which this observation can be aligned with the current views on mechanisms of ABC transporters...
  69. ncbi request reprint A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA
    Marc Baaden
    Department of Biochemistry, University of Oxford, South Parks Road Oxford, OX1 3QU, UK
    J Mol Biol 331:177-89. 2003
    ..The observed collapse of the substrate-binding cleft may explain the experimentally observed occurrence of multiple dimer conformations of OMPLA, one of which is fully active while the other shows significantly reduced activity...
  70. ncbi request reprint KcsA closed and open: modelling and simulation studies
    John Holyoake
    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
    Eur Biophys J 33:238-46. 2004
    ..Helix kink and swivel motion is observed at the molecular hinge formed by residue G99 of the M2 helix. This motion is more substantial for the open- than for the closed-state model of the channel...
  71. ncbi request reprint Lipid/protein interactions and the membrane/water interfacial region
    Carmen Domene
    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    J Am Chem Soc 125:14966-7. 2003
    ....
  72. ncbi request reprint Membrane protein structure quality in molecular dynamics simulation
    Richard J Law
    Laboratory of Molecular Biophysics, Department of Biochemistry, The University of Oxford, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK
    J Mol Graph Model 24:157-65. 2005
    ..MD stability was shown to be a good indicator for the quality of structures. The quality was also shown to be dependent on the resolution at which the structures were determined...
  73. pmc Conformation and environment of channel-forming peptides: a simulation study
    Jennifer M Johnston
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom OX1 3QU
    Biophys J 90:1855-64. 2006
    ..This study provides a first atomic resolution comparison of the structure and dynamics of NK4-M2GlyR-p22 peptides in membrane and membrane-mimetic environments, paralleling NMR and functional studies of these peptides...
  74. ncbi request reprint Molecular dynamics simulations of a bacterial autotransporter: NalP from Neisseria meningitidis
    Syma Khalid
    Department of Biochemistry, University of Oxford, Oxford, UK
    Mol Membr Biol 23:499-508. 2006
    ....
  75. ncbi request reprint OmpA: gating and dynamics via molecular dynamics simulations
    Syma Khalid
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
    Biochim Biophys Acta 1778:1871-80. 2008
    ..Simulation studies have been extended to comparative models of OmpA homologues from Pseudomonas aeruginosa (OprF) and Pasteurella multocida (PmOmpA), the latter model including the periplasmic C-terminal domain...
  76. pmc Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel
    Timothy Carpenter
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Biophys J 95:3790-801. 2008
    ..These simulations alongside comparison with recent x-ray (3BKD) and NMR (2RLF) structures of the M2 bundle suggest that the model yielded by CG-MD may correspond to a closed state of the channel...
  77. doi request reprint Ion channel gates: comparative analysis of energy barriers
    Kaihsu Tai
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
    Eur Biophys J 38:347-54. 2009
    ..In general, the method is more useful when the channel is wider; for narrower channels, the flexibility of the protein may allow otherwise-unsurmountable energetic barriers to be overcome...
  78. doi request reprint CGDB: a database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations
    Alan P Chetwynd
    Department of Biochemistry, University of Oxford, UK
    Mol Membr Biol 25:662-9. 2008
    ..Introducing anionic lipids into a DPPC bilayer containing the KvAP voltage sensor does not affect the extent of bilayer distortion...
  79. doi request reprint Molecular modeling and simulation studies of ion channel structures, dynamics and mechanisms
    Kaihsu Tai
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Methods Cell Biol 90:233-65. 2008
    ..Molecular dynamics simulations and free-energy calculations provide information on the thermodynamics and kinetics of channel function...
  80. pmc Membrane insertion of a voltage sensor helix
    Chze Ling Wee
    Department of Biochemistry, University of Oxford, United Kingdom
    Biophys J 100:410-9. 2011
    ..We show that the unique combination of charged and hydrophobic residues in S4 allows it to insert stably into the membrane...
  81. ncbi request reprint Ion channel structures: a review of recent progress
    Carmen Domene
    University of Oxford, Laboratory of Molecular Biophysics, Department of Biochemistry, South Parks Road, Oxford, OX1 3QU, UK
    Curr Opin Drug Discov Devel 6:611-9. 2003
    ..Structures of ligand binding domains provide some clues as to how ligand-induced conformational changes control channel gating, but further experimental and computational studies are required before a full picture emerges...
  82. pmc Asymmetric switching in a homodimeric ABC transporter: a simulation study
    Jussi Aittoniemi
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    PLoS Comput Biol 6:e1000762. 2010
    ..This finding strengthens recent suggestions that the interplay of a consensus and a degenerate NBS in eukaroytic ABC proteins pre-determines the sequence of hydrolysis at the two NBSs...
  83. pmc K(+) versus Na(+) ions in a K channel selectivity filter: a simulation study
    Indira H Shrivastava
    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
    Biophys J 83:633-45. 2002
    ..In our simulations the selectivity filter exhibits significant flexibility in response to changes in ion/protein interactions, with a somewhat greater distortion induced by Na(+) than by K(+) ions...
  84. pmc Filter flexibility in a mammalian K channel: models and simulations of Kir6.2 mutants
    Charlotte E Capener
    Laboratory of Molecular Biophysics, Department of Biochemistry, Rex Richards Building, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
    Biophys J 84:2345-56. 2003
    ..This suggests filter distortion may be a possible general model for determining the conductance of K channels...
  85. doi request reprint Biomimetic design of a brush-like nanopore: simulation studies
    Prapasiri Pongprayoon
    Department of Biochemistry, University of Oxford, Oxford, UK
    J Phys Chem B 116:462-8. 2012
    ..These studies indicate that a locally accurate biomimetic design has captured the essentials of the structure/function relationship of the parent protein...
  86. ncbi request reprint MD simulations of spontaneous membrane protein/detergent micelle formation
    Peter J Bond
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    J Am Chem Soc 126:15948-9. 2004
    ..We confirm that the end structures of the self-assembled micelles are similar to those from their preformed counterparts, with each micelle presenting a bilayerlike environment to the enclosed protein...
  87. ncbi request reprint Nucleotide binding to the homodimeric MJ0796 protein: a computational study of a prokaryotic ABC transporter NBD dimer
    Jeff D Campbell
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    FEBS Lett 579:4193-9. 2005
    ..However, if ADP is present at one binding site then both NBD-NBD and protein-ATP interactions are enhanced at the opposite site...
  88. ncbi request reprint The influence of geometry, surface character, and flexibility on the permeation of ions and water through biological pores
    Oliver Beckstein
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Phys Biol 1:42-52. 2004
    ..An increase in temperature has the same effect, and we hypothesize that both effects can be explained by a decrease in the effective solvent-surface attraction which in turn leads to an increase in the solvent-wall surface free energy...
  89. pmc Insertion and assembly of membrane proteins via simulation
    Peter J Bond
    Department of Biochemistry, University of Oxford, UK
    J Am Chem Soc 128:2697-704. 2006
    ..Thus, coarse-grained methods may help to define mechanisms of membrane protein (re)folding and will prove suitable for simulation of larger scale dynamic rearrangements of biological membranes...
  90. doi request reprint Conformational dynamics of the mitochondrial ADP/ATP carrier: a simulation study
    Jennifer M Johnston
    Department of Biochemistry, University of Oxford, Oxford, UK
    Mol Membr Biol 25:506-17. 2008
    ..Overall, the simulations support a transport mechanism in which flexibility about the proline hinges enables a transition between a 'closed' and an 'open' pore-like state of the carrier protein...
  91. pmc Interaction of diverse voltage sensor homologs with lipid bilayers revealed by self-assembly simulations
    Younes Mokrab
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Biophys J 100:875-84. 2011
    ..In conclusion, our results suggest common interactions with phospholipids for various VS homologs, providing insights into the molecular basis of their stabilization in the membrane and how they are altered by lipid modification...
  92. doi request reprint Multiscale simulations of the antimicrobial peptide maculatin 1.1: water permeation through disordered aggregates
    Daniel L Parton
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
    J Phys Chem B 116:8485-93. 2012
    ..The aggregates are dynamically disordered structures, and water flux occurs through irregular, fluctuating channels. The results are discussed in relation to experimental data and other simulations of antimicrobial peptides...
  93. pmc Filter flexibility and distortion in a bacterial inward rectifier K+ channel: simulation studies of KirBac1.1
    Carmen Domene
    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU United Kingdom
    Biophys J 87:256-67. 2004
    ..The simulation data also provide evidence for interactions of the "slide" (pre-M1) helix of KirBac with phospholipid headgroups...
  94. ncbi request reprint Molecular dynamics simulations of the ligand-binding domain of an N-methyl-D-aspartate receptor
    Samantha L Kaye
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
    J Biol Chem 281:12736-42. 2006
    ....
  95. doi request reprint A role for Leu118 of loop E in agonist binding to the alpha 7 nicotinic acetylcholine receptor
    Shiva Amiri
    Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
    Mol Pharmacol 73:1659-67. 2008
    ..Together, the results indicate a role for Leu118 in influencing agonist actions on alpha7 nAChRs...
  96. doi request reprint Coarse-grained MD simulations of membrane protein-bilayer self-assembly
    Kathryn A Scott
    Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
    Structure 16:621-30. 2008
    ..We demonstrate that this method can be used to predict accurately the protein position in the bilayer for membrane proteins with a range of different sizes and architectures...
  97. doi request reprint PX- and FYVE-mediated interactions with membranes: simulation studies
    Emi Psachoulia
    Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
    Biochemistry 48:5090-5. 2009
    ..The simulations agree well with available biophysical data, suggesting this computational method may be used to predict protein-bilayer interactions for other PI-binding proteins...
  98. pmc Peptide nanopores and lipid bilayers: interactions by coarse-grained molecular-dynamics simulations
    Jochen W Klingelhoefer
    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Biophys J 96:3519-28. 2009
    ..Furthermore, both nanopore size and key residue types (e.g., tryptophan) seem to influence the level of protein tilt, emphasizing the reciprocal nature of nanopore-lipid bilayer interactions...
  99. doi request reprint Ion-blocking sites of the Kir2.1 channel revealed by multiscale modeling
    Kaihsu Tai
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
    Biochemistry 48:8758-63. 2009
    ..Interaction sites for spermine are formed by Asp255, Glu299, and Glu224. Entropic factors seem to favor interactions of spermine within the center of the cytoplasmic domain...