Shin Ho Chung

Summary

Affiliation: Australian National University
Country: Australia

Publications

  1. pmc Study of ionic currents across a model membrane channel using Brownian dynamics
    S H Chung
    Protein Dynamics Unit, Department of Chemistry, Research School of Physical Sciences, Australian National University, Canberra, A C T 0200, Australia
    Biophys J 75:793-809. 1998
  2. pmc Conduction properties of KcsA measured using brownian dynamics with flexible carbonyl groups in the selectivity filter
    Shin Ho Chung
    Research School of Biological Sciences, Australian National University, Canberra, Australia
    Biophys J 93:44-53. 2007
  3. ncbi request reprint Recent advances in ion channel research
    Shin Ho Chung
    Protein Dynamics Unit, Department of Physics, Faculty of Sciences, Australian National University, Canberra, Australia
    Biochim Biophys Acta 1565:267-86. 2002
  4. ncbi request reprint Ion channels: recent progress and prospects
    Shin Ho Chung
    Department of Theoretical Physics, Research School of Physical Sciences, Australian National University, Canberra, ACT 0200, Australia
    Eur Biophys J 31:283-93. 2002
  5. pmc Modeling diverse range of potassium channels with Brownian dynamics
    Shin Ho Chung
    Department of Physics, The Faculty of Sciences, Australian National University, Canberra, ACT 0200, Australia
    Biophys J 83:263-77. 2002
  6. pmc Conducting-state properties of the KcsA potassium channel from molecular and Brownian dynamics simulations
    Shin Ho Chung
    Department of Physics, Faculty of Sciences, Australian National University, Canberra, ACT 0200, Australia
    Biophys J 82:628-45. 2002
  7. ncbi request reprint Predicting channel function from channel structure using Brownian dynamics simulations
    S H Chung
    Department of Chemistry, Research School of Physical Sciences, Australian National University, Canberra, Australian Capital Territory
    Clin Exp Pharmacol Physiol 28:89-94. 2001
  8. pmc Permeation of ions across the potassium channel: Brownian dynamics studies
    S H Chung
    Protein Dynamics Unit, Department of Chemistry, Research School of Physical Sciences, Australian National University, Canberra, ACT 0200, Australia
    Biophys J 77:2517-33. 1999
  9. pmc The fast gating mechanism in ClC-0 channels
    David Bisset
    Department of Theoretical Physics, Research School of Physical Sciences, The Australian National University, Canberra, Australia
    Biophys J 89:179-86. 2005
  10. pmc Conduction mechanisms of chloride ions in ClC-type channels
    Ben Corry
    Department of Theoretical Physics, Research School of Physical Sciences, The Australian National University, Canberra, Australia
    Biophys J 86:846-60. 2004

Collaborators

Detail Information

Publications54

  1. pmc Study of ionic currents across a model membrane channel using Brownian dynamics
    S H Chung
    Protein Dynamics Unit, Department of Chemistry, Research School of Physical Sciences, Australian National University, Canberra, A C T 0200, Australia
    Biophys J 75:793-809. 1998
    ..We discuss the implications of these findings for the transport of ions across the membrane and the structure of ion channels...
  2. pmc Conduction properties of KcsA measured using brownian dynamics with flexible carbonyl groups in the selectivity filter
    Shin Ho Chung
    Research School of Biological Sciences, Australian National University, Canberra, Australia
    Biophys J 93:44-53. 2007
    ..The method we utilized here can be extended to allow the movement of glutamate or aspartate side chains lining the selectivity filters of other ionic channels...
  3. ncbi request reprint Recent advances in ion channel research
    Shin Ho Chung
    Protein Dynamics Unit, Department of Physics, Faculty of Sciences, Australian National University, Canberra, Australia
    Biochim Biophys Acta 1565:267-86. 2002
    ..Here we present simplified accounts of the competing permeation theories and then discuss their application to the potassium, gramicidin A and calcium channels...
  4. ncbi request reprint Ion channels: recent progress and prospects
    Shin Ho Chung
    Department of Theoretical Physics, Research School of Physical Sciences, Australian National University, Canberra, ACT 0200, Australia
    Eur Biophys J 31:283-93. 2002
    ....
  5. pmc Modeling diverse range of potassium channels with Brownian dynamics
    Shin Ho Chung
    Department of Physics, The Faculty of Sciences, Australian National University, Canberra, ACT 0200, Australia
    Biophys J 83:263-77. 2002
    ..Finally, the conductance exhibits the saturation property observed experimentally. We discuss the implications of these findings on the transport of ions across the potassium channels and membrane channels in general...
  6. pmc Conducting-state properties of the KcsA potassium channel from molecular and Brownian dynamics simulations
    Shin Ho Chung
    Department of Physics, Faculty of Sciences, Australian National University, Canberra, ACT 0200, Australia
    Biophys J 82:628-45. 2002
    ..Our simulation results reproduce several experimental observations, including the current-voltage curves, conductance-concentration relationships, and outward rectification of currents...
  7. ncbi request reprint Predicting channel function from channel structure using Brownian dynamics simulations
    S H Chung
    Department of Chemistry, Research School of Physical Sciences, Australian National University, Canberra, Australian Capital Territory
    Clin Exp Pharmacol Physiol 28:89-94. 2001
    ..3. We then show how some of the salient features of ion channels can be deduced by following the positions of ions at each discrete step over many millions of time steps...
  8. pmc Permeation of ions across the potassium channel: Brownian dynamics studies
    S H Chung
    Protein Dynamics Unit, Department of Chemistry, Research School of Physical Sciences, Australian National University, Canberra, ACT 0200, Australia
    Biophys J 77:2517-33. 1999
    ..The conductance exhibits the saturation property observed experimentally. We discuss the implications of these findings for the transport of ions across the potassium channels and membrane channels in general...
  9. pmc The fast gating mechanism in ClC-0 channels
    David Bisset
    Department of Theoretical Physics, Research School of Physical Sciences, The Australian National University, Canberra, Australia
    Biophys J 89:179-86. 2005
    ..Finally, we use Brownian dynamics simulations to demonstrate the influence of membrane potential and external Cl- concentration on channel open probability...
  10. pmc Conduction mechanisms of chloride ions in ClC-type channels
    Ben Corry
    Department of Theoretical Physics, Research School of Physical Sciences, The Australian National University, Canberra, Australia
    Biophys J 86:846-60. 2004
    ..Finally, we demonstrate that a ClC-0 homology model created from an alternative sequence alignment fails to replicate any of the experimental observations...
  11. pmc Reservoir boundaries in Brownian dynamics simulations of ion channels
    Ben Corry
    Department of Theoretical Physics, Research School of Physical Sciences, Australian National University, Canberra, Australian Capital Territory 0200, Australia
    Biophys J 82:1975-84. 2002
    ..Our results confirm that the treatment of the reservoir boundaries is mostly irrelevant to the conductance properties of an ion channel as long as the reservoirs are large enough...
  12. pmc Homology model of the GABAA receptor examined using Brownian dynamics
    Megan O'Mara
    Department of Theoretical Physics, Research School of Physical Sciences, Australian National University, Canberra, Australia
    Biophys J 88:3286-99. 2005
    ..Finally, we simulate the gamma2 K289M epilepsy inducing mutation and examine Cl(-) ion permeation through the mutant receptor...
  13. pmc Gramicidin A channel as a test ground for molecular dynamics force fields
    Toby W Allen
    Department of Physics, Faculty of Science, Australian National University, Canberra, ACT, Australia
    Biophys J 84:2159-68. 2003
    ..The present results, taken together with many earlier studies, highlights the shortcomings of the standard force fields used in MD simulations of ion channels and calls for construction of more appropriate force fields for this purpose...
  14. pmc Dielectric self-energy in Poisson-Boltzmann and Poisson-Nernst-Planck models of ion channels
    Ben Corry
    Department of Theoretical Physics, Research School of Physical Sciences, Australian National University, Canberra, Australia
    Biophys J 84:3594-606. 2003
    ..Thus, further work is required if these continuum theories are to be reliably salvaged for quantitative studies of biological ion channels in all situations...
  15. doi request reprint Conductance properties of the inwardly rectifying channel, Kir3.2: molecular and Brownian dynamics study
    Tamsyn A Hilder
    Computational Biophysics Group, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
    Biochim Biophys Acta 1828:471-8. 2013
    ..The depth of the potential of mean force encountered by tertiapin is -16.1kT, thus indicating that the channel will be half-blocked by 0.4μM of the toxin...
  16. doi request reprint Synthetic cation-selective nanotube: permeant cations chaperoned by anions
    Tamsyn A Hilder
    Computational Biophysics Group, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
    J Chem Phys 134:045103. 2011
    ..The cation-anion selectivity ratio ranges from 8 to 25, depending on the ionic concentrations in the reservoirs...
  17. doi request reprint Brownian dynamics study of flux ratios in sodium channels
    Taira Vora
    Research School of Biological Sciences, The Australian National University, Canberra, Australia
    Eur Biophys J 38:45-52. 2008
    ....
  18. pmc Synthetic chloride-selective carbon nanotubes examined by using molecular and stochastic dynamics
    Tamsyn A Hilder
    Research School of Biology, Australian National University, Canberra, Australia
    Biophys J 99:1734-42. 2010
    ..The pore is normally occupied by two ions, and the rate-limiting step in conduction is the time taken for the resident ion near the exit gate to move out of the energy well...
  19. ncbi request reprint A model of sodium channels
    Taira Vora
    Department of Theoretical Physics, Research School of Physical Sciences, Australian National University, Canberra, A C T 0200, Australia
    Biochim Biophys Acta 1668:106-16. 2005
    ..Our model closely reproduces a range of experimental data including the current-voltage curves, current-concentration curves and blockage of monovalent ions by divalent ions...
  20. pmc Continuum electrostatics fails to describe ion permeation in the gramicidin channel
    Scott Edwards
    Protein Dynamics Unit, Department of Physics, Faculty of Science, Australian National University, Canberra, A C T 0200, Australia
    Biophys J 83:1348-60. 2002
    ..They also offer a convenient starting point for studying structure-function relationships in modified gramicidin channels...
  21. doi request reprint Computational modeling of transport in synthetic nanotubes
    Tamsyn A Hilder
    Computational Biophysics Group, Research School of Biology, Australian National University, Canberra, Australia
    Nanomedicine 7:702-9. 2011
    ....
  22. doi request reprint Rigid body Brownian dynamics as a tool for studying ion channel blockers
    Dan Gordon
    Research School of Biology, Australian National University, Canberra, Australia
    J Phys Chem B 116:1933-41. 2012
    ..The computational molecular modeling technique we introduce here can provide detailed insights into ligand-channel interactions and can be used for rapidly screening potential blocker molecules...
  23. doi request reprint Efficacy of external tetraethylammonium block of the KcsA potassium channel: molecular and Brownian dynamics studies
    David Bisset
    Research School of Biological Sciences, Australian National University, Australia
    Biochim Biophys Acta 1778:2273-82. 2008
    ..7 angstroms, irrespective of orientation of their aromatic rings...
  24. pmc Brownian dynamics theory for predicting internal and external blockages of tetraethylammonium in the KcsA potassium channel
    Matthew Hoyles
    Research School of Biological Sciences, The Australian National University, Canberra, Australia
    Biophys J 94:366-78. 2008
    ....
  25. ncbi request reprint Estimating the dielectric constant of the channel protein and pore
    Jin Aun Ng
    Research School of Biological Sciences, Australian National University, Canberra, Australia
    Eur Biophys J 37:213-22. 2008
    ..From the algorithm we obtain an optimum value of 2 for the protein dielectric constant and 64 for the pore dielectric constant...
  26. doi request reprint Salt rejection and water transport through boron nitride nanotubes
    Tamsyn A Hilder
    Computational Biophysics Group, Research School of Biology Australian National University, ACT 0200, Australia
    Small 5:2183-90. 2009
    ..Furthermore, ions continue to be rejected under the influence of high hydrostatic pressures up to 612 MPa. When the nanotube radius is increased to 4.14 A the tube becomes cation-selective, and at 5.52 A the tube becomes anion-selective...
  27. ncbi request reprint Generalized Langevin models of molecular dynamics simulations with applications to ion channels
    Dan Gordon
    Computational Biophysics Group, Research School of Biological Science, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
    J Chem Phys 131:134102. 2009
    ..Using our techniques and systematically changing the PMF, we are able to reverse engineer a modified PMF which gives a current-voltage curve closely matching experimental results...
  28. pmc Molecular dynamics simulations of scorpion toxin recognition by the Ca(2+)-activated potassium channel KCa3.1
    Rong Chen
    Research School of Biology, Australian National University, Canberra, Australia Electronic address
    Biophys J 105:1829-37. 2013
    ..1 than that of the wild-type. This study provides insight into the key molecular determinants for the high-affinity binding of peptide toxins to KCa3.1, and demonstrates the power of computational methods in the design of novel toxins...
  29. ncbi request reprint Brownian dynamics investigation into the conductance state of the MscS channel crystal structure
    Taira Vora
    Department of Theoretical Physics, Research School of Physical Sciences, The Australian National University, Canberra, A C T 0200, Australia
    Biochim Biophys Acta 1758:730-7. 2006
    ..Widening the hydrophobic region of the pore by 2.5 Angstrom however, increases the channel conductance to over 200 pS suggesting that only a minimal conformational change is required to gate the pore...
  30. pmc Effect of gating modifier toxins on membrane thickness: implications for toxin effect on gramicidin and mechanosensitive channels
    Rong Chen
    Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
    Toxins (Basel) 5:456-71. 2013
    ..It is found that the bilayer is about 2 Å thinner upon the binding of a GsMTx4 monomer. Such a thinning effect of GsMTx4 on membranes may explain its potentiation effect on gramicidin and mechanosensitive channels...
  31. pmc Binding modes of μ-conotoxin to the bacterial sodium channel (NaVAb)
    Rong Chen
    Computational Biophysics Group, Research School of Biology, Australian National University, Canberra, Australia
    Biophys J 102:483-8. 2012
    ..We construct the profile of potential of mean force for the unbinding of PIIIA from the channel, and predict that PIIIA blocks the bacterial sodium channel with subnanomolar affinity...
  32. pmc Permeation and block of the Kv1.2 channel examined using brownian and molecular dynamics
    Dan Gordon
    Research School of Biology, Australian National University, Canberra, Australia
    Biophys J 101:2671-8. 2011
    ..We thus show that the experimental observations on the voltage-gated channel, including the toxin-channel interaction, can reliably be replicated by using the two widely used computational tools...
  33. pmc A model of the glycine receptor deduced from Brownian dynamics studies
    Megan O'Mara
    Department of Theoretical Physics, Research School of Physical Sciences, Australian National University, Canberra 0200, Australia
    Proc Natl Acad Sci U S A 100:4310-5. 2003
    ..These results illustrate the key structural features and underlying mechanism for charge selectivity in the glycine receptor...
  34. pmc Conduction of Na+ and K+ through the NaK channel: molecular and Brownian dynamics studies
    Taira Vora
    Research School of Biological Sciences, Australian National University, Canberra, Australia
    Biophys J 95:1600-11. 2008
    ....
  35. pmc Computational methods of studying the binding of toxins from venomous animals to biological ion channels: theory and applications
    Dan Gordon
    Research School of Biology, The Australian National University, Acton, ACT 0200, Australia
    Physiol Rev 93:767-802. 2013
    ..Finally, we discuss prospects for future developments in the field...
  36. pmc Modeling the binding of three toxins to the voltage-gated potassium channel (Kv1.3)
    Rong Chen
    Research School of Biology, Australian National University, Canberra, Australia
    Biophys J 101:2652-60. 2011
    ..We pinpoint the residues in the toxins and the channel that are critical for the formation of the stable venom-channel complexes...
  37. ncbi request reprint Algorithm for rigid-body Brownian dynamics
    Dan Gordon
    Computational Biophysics Group, Research School of Biology, The Australian National University, Acton, ACT, Australia
    Phys Rev E Stat Nonlin Soft Matter Phys 80:066703. 2009
    ..We intend to use the algorithm to model the interaction between biological ion channels and other channel blocker molecules, but it may also have applicability to modeling other small particles such as colloids or nanoparticles...
  38. doi request reprint Conduction and block of inward rectifier K+ channels: predicted structure of a potent blocker of Kir2.1
    Tamsyn A Hilder
    Computational Biophysics Group, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
    Biochemistry 52:967-74. 2013
    ..7 nM). This potent blocker of Kir2.1 may serve as a structural template from which potent compounds for the treatment of various diseases mediated by this channel subfamily, such as cardiac arrhythmia, can be developed...
  39. pmc Structural basis of the selective block of Kv1.2 by maurotoxin from computer simulations
    Rong Chen
    Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
    PLoS ONE 7:e47253. 2012
    ..Potential of mean force calculations show that MTx blocks Kv1.1, Kv1.2 and Kv1.3 with an IC(50) value of 6 µM, 0.6 nM and 18 µM, respectively...
  40. doi request reprint Binding modes and functional surface of anti-mammalian scorpion α-toxins to sodium channels
    Rong Chen
    Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
    Biochemistry 51:7775-82. 2012
    ..Our models demonstrate that the functional surface of anti-mammalian scorpion α-toxins is centered on the linker-domain, similar to that of β-toxins...
  41. pmc Computational design of a carbon nanotube fluorofullerene biosensor
    Tamsyn A Hilder
    Computational Biophysics Group, Research School of Biology, Australian National University, Acton, ACT 0200, Australia
    Sensors (Basel) 12:13720-35. 2012
    ..Assuming a tight seal is formed between the two reservoirs, such a biosensor would be able to detect one channel opening and thus one molecule of analyte making it a highly sensitive detection design...
  42. pmc Multi-ion versus single-ion conduction mechanisms can yield current rectification in biological ion channels
    Tamsyn A Hilder
    Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
    J Biol Phys 40:109-19. 2014
    ..We pose the question as to whether the same mechanism could be at play in inwardly rectifying potassium channels...
  43. ncbi request reprint Complex structures between the N-type calcium channel (CaV2.2) and ω-conotoxin GVIA predicted via molecular dynamics
    Rong Chen
    Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
    Biochemistry 52:3765-72. 2013
    ..The similar IC50 values calculated for the different binding modes demonstrate that GVIA can inhibit CaV2.2 with alternative binding modes. Such a multiple-binding mode mechanism may be common for ω-conotoxins. ..
  44. pmc Mechanism of μ-conotoxin PIIIA binding to the voltage-gated Na+ channel NaV1.4
    Rong Chen
    Research School of Biology, Australian National University, Canberra, ACT, Australia
    PLoS ONE 9:e93267. 2014
    ..4 mimicking NaV channels resistant to μ-conotoxins and tetrodotoxin is constructed and the binding of PIIIA to this mutant channel examined. The double mutation causes the affinity of PIIIA to reduce by two orders of magnitude. ..
  45. pmc Binding of hanatoxin to the voltage sensor of Kv2.1
    Rong Chen
    Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
    Toxins (Basel) 4:1552-64. 2012
    ..Overall, our calculations reproduce a wide range of experimental data, and suggest that HaTx1 binds to the S3b-S4a paddle of Kv2.1 from S2 and S3 helices...
  46. doi request reprint Engineering a potent and specific blocker of voltage-gated potassium channel Kv1.3, a target for autoimmune diseases
    Rong Chen
    Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
    Biochemistry 51:1976-82. 2012
    ..We show that the IC(50) values predicted for three toxins and three channels match closely with experiment. Kv1.3 is half-blocked by 0.2 pM mutant OSK1; it is >10000-fold more specific for this channel than for Kv1.1 and Kv1.2...
  47. doi request reprint Boron nitride nanotubes selectively permeable to cations or anions
    Tamsyn A Hilder
    Computational Biophysics Group, Research School of Biology, Australian National University, ACT 2601, Australia
    Small 5:2870-5. 2009
    ..These engineered nanotubes have potential applications as sensitive biosensors, antibiotics, or filtration devices...
  48. doi request reprint Conserved functional surface of antimammalian scorpion β-toxins
    Rong Chen
    Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
    J Phys Chem B 116:4796-800. 2012
    ..Our calculations suggest that the functional surface of Cn2 and Css4 is primarily formed by the loop between positions 8 and 18, centered on the two charged residues Lys13 and Glu15. ..
  49. ncbi request reprint Adaptive learning algorithms for nernst potential and I-V curves in nerve cell membrane ion channels modeled as hidden Markov models
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC, Canada
    IEEE Trans Nanobioscience 2:266-78. 2003
    ..Numerical examples illustrate the performance of the algorithms on computer-generated synthetic data...
  50. ncbi request reprint Influence of protein flexibility on the electrostatic energy landscape in gramicidin A
    Ben Corry
    Chemistry, School of Biomedical and Chemical Sciences, The University of Western Australia Crawley, WA 6009, Australia
    Eur Biophys J 34:208-16. 2005
    ..Thus, even when protein atoms are allowed to move, the dielectric model used in our electrostatic calculations breaks down when modeling the gramicidin channel...
  51. ncbi request reprint Brownian dynamics simulation for modeling ion permeation across bionanotubes
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    IEEE Trans Nanobioscience 4:102-11. 2005
    ..We illustrate how BD simulations are used to unravel the permeation dynamics in two biological ion channels-the KcsA K+ channel and CIC Cl- channel...
  52. ncbi request reprint Adaptive Brownian dynamics simulation for estimating potential mean force in ion channel permeation
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver V6T 1Z4, Canada
    IEEE Trans Nanobioscience 5:126-38. 2006
    ..Numerical simulations on the gramicidin ion channel show that the algorithm yields the potential of mean force profile that accurately reproduces experimental observations...
  53. ncbi request reprint Electrostatic basis of valence selectivity in cationic channels
    Ben Corry
    Chemistry, School of Biomedical and Chemical Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
    Biochim Biophys Acta 1711:72-86. 2005
    ..On the other hand, the calcium channel binds them less strongly such that they can be destabilized by the repulsion of another incoming divalent ion, but not by the lesser repulsion from monovalent ions...
  54. ncbi request reprint Adaptive Brownian dynamics for shape estimation of sodium ion channels
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver V6T 1Z4, Canada
    J Nanosci Nanotechnol 7:2273-82. 2007
    ..Brownian dynamics simulations emulate the propagation of individual ions through the sodium channel nanotube at a femto time second time scale and Angstrom unit (10(-10) meter) spatial scale...