Kishani M Ranatunga

Imperial College London, London, ENG, United Kingdom

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Publications (15)50.62 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Understanding the nature of the interaction of the plant alkaloid ryanodine with its receptor channel (RyR) is important to aid interpretation of physiological studies and provide structure-function information about RyR. We present here the first quantitative description of the relative single-channel kinetic effects of a single-point mutation in RyR2. We exploit the well-characterized ryanoid 8beta-amino-9alpha-hydroxyryanodine that displays reversible kinetics with RyR2. We explicitly show that the effect of the Q4863A mutation is to increase the apparent dissociation constant by increasing the apparent dissociation rate of the ryanoid. The voltage-dependence of the interaction displays no change. We infer that Q4863 is not involved with the voltage-drop but is able to influence ryanoid-bound structural changes. We discuss structural mechanisms by which this mutation could affect ryanoid interaction.
    Molecular Membrane Biology 01/2007; 24(3):185-93. · 3.13 Impact Factor
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    ABSTRACT: The specific, high-affinity interaction of the plant toxin ryanodine with its molecular target the ryanodine receptor channel (RyR) has been instrumental in RyR research. Alanine scanning of putative pore regions of mouse RyR2 has highlighted the amino acid Gln4863, predicted to lie within trans-membrane helix TM10, as an important determinant of ryanodine binding. We have investigated the effects of several ryanodine derivatives, guanidinopropionylryanodine, 21-p-nitrobenzoylamino-9alpha-hydroxyryanodine, 8beta-amino-9alpha-hydroxyryanodine, and 21-amino-9alpha-hydroxyryanodine, with the mouse Q4863A RyR2 mutant at the single-channel level. Our results demonstrate that the rate of dissociation of all ryanoids investigated is increased by the mutation. The modification of channel function after ryanoid binding is qualitatively similar for wild-type and mutant, but in several cases, single-channel conductances were increased with Q4863A. These novel findings have been interpreted within the framework of existing comparative molecular field analysis studies on ryanoids. We suggest that replacement of a glutamine by an alanine residue at position 4863 causes RyR2 to simultaneously alter interactions with both ends of the ryanoid molecule.
    Molecular Pharmacology 10/2005; 68(3):840-6. · 4.41 Impact Factor
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    ABSTRACT: 1. Block of the human two-pore domain potassium (2-PK) channel TREK-1 by fluoxetine (Prozac) and its active metabolite, norfluoxetine, was investigated using whole-cell patch-clamp recording of currents through recombinant channels in tsA 201 cells. 2. Fluoxetine produced a concentration-dependent inhibition of TREK-1 current that was reversible on wash. The IC50 for block was 19 microM. Block by fluoxetine was voltage-independent. Fluoxetine (100 microM) produced an 84% inhibition of TREK-1 currents, but only a 31% block of currents through a related 2-PK channel, TASK-3. 3. Norfluoxetine was a more potent inhibitor of TREK-1 currents with an IC50 of 9 microM. Block by norfluoxetine was also voltage-independent. 4. Truncation of the C-terminus of TREK-1 (delta89) resulted in a loss of channel function, which could be restored by intracellular acidification or the mutation E306A. The mutation E306A alone increased basal TREK-1 current and resulted in a loss of the slow phase of TREK-1 activation. 5. Progressive deletion of the C-terminus of TREK-1 had no effect on the inhibition of the channel by fluoxetine. The E306A mutation, on the other hand, reduced the magnitude of fluoxetine inhibition, with 100 microM producing only a 40% inhibition. 6. It is concluded that fluoxetine and norfluoxetine are potent inhibitors of TREK-1. Block of TREK-1 by fluoxetine may have important consequences when the drug is used clinically in the treatment of depression.
    British Journal of Pharmacology 04/2005; 144(6):821-9. · 5.07 Impact Factor
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    ABSTRACT: Potassium (K) channels have a key role in the regulation of neuronal excitability. Over a hundred different subunits encoding distinct K channel subtypes have been identified so far. A major challenge is to relate these many different channel subunits to the functional K currents observed in native neurons. In this review, we have concentrated on cerebellar granule neurons (CGNs). We have considered each of the three principal super families of K channels in turn, namely, the six transmembrane domain, voltage-gated super family, the two transmembrane domain, inward-rectifier super family and the four transmembrane domain, leak channel super family. For each super family, we have identified the subunits that are expressed in CGNs and related the properties of these expressed channel subunits to the functional currents seen in electrophysiological recordings from these neurons. In some cases, there are strong molecular candidates for proteins underlying observed currents. In other cases the correlation is less clear. We show that at least 26 potassium channel alpha subunits are moderately or strongly expressed in CGNs. Nevertheless, a good empirical model of CGN function has been obtained with just six distinct K conductances. The transient KA current in CGNs, seems due to expression of Kv4.2 channels or Kv4.2/4.3 heteromers, while the KCa current is due to expression of large-conductance slo channels. The G-protein activated KIR current is probably due to heteromeric expression of KIR3.1 and KIR3.2. Perhaps KIR2.2 subunits underlie the KIR current when it is constitutively active. The leak conductance can be attributed to TASK-1 and or TASK-3 channels. With less certainty, the IK-slow current may be due to expression of one or more members of the KCNQ or EAG family. Lastly, the delayed-rectifier Kv current has as many as six different potential contributors from the extensive Kv family of alpha subunits. Since many of these subunits are highly regulated by neurotransmitters, physiological regulators and, often, auxiliary subunits, the resulting electrical properties of CGNs may be highly dynamic and subject to constant fine-tuning.
    The Cerebellum 02/2003; 2(1):11-25. · 2.60 Impact Factor
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    ABSTRACT: A homology model of the pore domain of the Shaker K+ channel has been constructed using a bacterial K+ channel, KcsA, as a template structure. The model is in agreement with mutagenesis and sequence variability data. A number of structural features are conserved between the two channels, including a ring of tryptophan sidechains on the outer surface of the pore domain at the extracellular end of the helix bundle, and rings of acidic sidechains close to the extracellular mouth of the channel. One of these rings, that formed by four Asp447 sidechains at the mouth of the Shaker pore, is shown by pK(A) calculations to be incompletely ionized at neutral pH. The potential energy profile for a K+ ion moved along the central axis of the Shaker pore domain model selectivity filter reveals a shallow well, the depth of which is modulated by the ionization state of the Asp447 ring. This is more consistent with the high cation flux exhibited by the channel in its conductance value of 19 pS.
    European Biophysics Journal 09/2001; 30(4):295-303. · 2.27 Impact Factor
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    ABSTRACT: KcsA is a bacterial K+ channel that is gated by pH. Continuum dielectric calculations on the crystal structure of the channel protein embedded in a low dielectric slab suggest that side chains E71 and D80 of each subunit, which lie adjacent to the selectivity filter region of the channel, form a proton-sharing pair in which E71 is neutral (protonated) and D80 is negatively charged at pH 7. When K+ ions are introduced into the system at their crystallographic positions the pattern of proton sharing is altered. The largest perturbation is for a K+ ion at site S3, i.e., interacting with the carbonyls of T75 and V76. The presence of multiple K+ ions in the filter increases the probability of E71 being ionized and of D80 remaining neutral (i.e., protonated). The ionization states of the protein side chains influence the potential energy profile experienced by a K+ ion as it is translated along the pore axis. In particular, the ionization state of the E71-D80 proton-sharing pair modulates the shape of the potential profile in the vicinity of the selectivity filter. Such reciprocal effects of ion occupancy on side-chain ionization states, and of side-chain ionization states on ion potential energy profiles will complicate molecular dynamics simulations and related studies designed to calculate ion permeation energetics.
    Biophysical Journal 04/2001; 80(3):1210-9. · 3.67 Impact Factor
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    ABSTRACT: Ion channels mediate electrical excitability in neurons and muscle. Three-dimensional structures for model peptide channels and for a potassium (K+) channel have been combined with computer simulations to permit rigorous exploration of structure-function relations of channels. Water molecules and ions within transbilayer pores tend to diffuse more slowly than in bulk solutions. In the narrow selectivity filter of the bacterial K+ channel (i.e. the region of the channel that discriminates between different species of ions) a column of water molecules and K+ ions moves in a concerted fashion. By combining atomistic simulations (in which all atoms of the channel molecule, water and ions are treated explicitly) with continuum methods (in which the description of the channel system is considerably simplified) it is possible to simulate some of the physiological properties of channels.
    Trends in Biochemical Sciences 09/2000; 25(8):368-74. · 13.08 Impact Factor
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    ABSTRACT: A homology model has been generated for the pore-forming domain of Kir6.2, a component of an ATP-sensitive K channel, based on the x-ray structure of the bacterial channel KcsA. Analysis of the lipid-exposed and pore-lining surfaces of the model reveals them to be compatible with the known features of membrane proteins and Kir channels, respectively. The Kir6.2 homology model was used as the starting point for nanosecond-duration molecular dynamics simulations in a solvated phospholipid bilayer. The overall drift from the model structure was comparable to that seen for KcsA in previous similar simulations. Preliminary analysis of the interactions of the Kir6.2 channel model with K(+) ions and water molecules during these simulations suggests that concerted single-file motion of K(+) ions and water through the selectivity filter occurs. This is similar to such motion observed in simulations of KcsA. This suggests that a single-filing mechanism is conserved between different K channel structures and may be robust to changes in simulation details. Comparison of Kir6.2 and KcsA suggests some degree of flexibility in the filter, thus complicating models of ion selectivity based upon a rigid filter.
    Biophysical Journal 07/2000; 78(6):2929-42. · 3.67 Impact Factor
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    ABSTRACT: Multiple nanosecond duration molecular dynamics simulations on the pore-lining M2 helix of the nicotinic acetylcholine receptor reveal how its structure and dynamics change as a function of environment. In water, the M2 helix partially unfolds to form a molecular hinge in the vicinity of a central Leu residue that has been implicated in the mechanism of ion channel gating. In a phospholipid bilayer, either as a single transmembrane helix, or as part of a pentameric helix bundle, the M2 helix shows less flexibility, but still exhibits a kink in the vicinity of the central Leu. The single M2 helix tilts relative to the bilayer normal by 12 degrees, in agreement with recent solid state NMR data (Opella et al., Nat Struct Biol 6:374-379, 1999). The pentameric helix bundle, a model for the pore domain of the nicotinic receptor and for channels formed by M2 peptides in a bilayer, is remarkably stable over a 2-ns MD simulation in a bilayer, provided one adjusts the pK(A)s of ionizable residues to their calculated values (when taking their environment into account) before starting the simulation. The resultant transbilayer pore shows fluctuations at either mouth which transiently close the channel. Proteins 2000;39:47-55.
    Proteins Structure Function and Bioinformatics 05/2000; 39(1):47-55. · 3.34 Impact Factor
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    ABSTRACT: A homology model has been generated for the pore-forming domain of Kir6.2, a component of an ATP-sensitive K channel, based on the x-ray structure of the bacterial channel KcsA. Analysis of the lipid-exposed and pore-lining surfaces of the model reveals them to be compatible with the known features of membrane proteins and Kir channels, respectively. The Kir6.2 homology model was used as the starting point for nanosecond-duration molecular dynamics simulations in a solvated phospholipid bilayer. The overall drift from the model structure was comparable to that seen for KcsA in previous similar simulations. Preliminary analysis of the interactions of the Kir6.2 channel model with K ϩ ions and water molecules during these simulations suggests that concerted single-file motion of K ϩ ions and water through the selectivity filter occurs. This is similar to such motion observed in simulations of KcsA. This suggests that a single-filing mechanism is conserved between different K channel structures and may be robust to changes in simulation details. Comparison of Kir6.2 and KcsA suggests some degree of flexibility in the filter, thus complicating models of ion selectivity based upon a rigid filter.
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    ABSTRACT: The Poisson-Boltzmann equation was solved numerically for models of the pore regions of the Shaker K+ channel and of two glycoporins (LamB and ScrY) to yield electrostatic potential profiles along the pore axes. From these potential profiles, single-channel current-voltage (I–V) relations were calculated. The importance of a proper treatment of the ionisation state of two rings of aspartate sidechains at the mouth of the K+ channel pore emerged from such calculations. The calculated most likely state, in which only two of the eight aspartate sidechains were deprotonated, yielded better agreement with experimental conductance data. An approximate calculation of single-channel conductances based simply on pore geometry yielded very similar conductance values for the two glycoporins. This differed from an␣experimentally determined conductance ratio of ScrY:LamB=10:1. Preliminary electrostatics calculations appeared to reproduce the observed difference in conductance between the two glycoporins, confirming that single-channel conductance is determined by electrostatic as well as geometric considerations.
    Theoretical Chemistry Accounts 01/1999; 101(1):97-102. · 2.14 Impact Factor
  • I.D. Kerr, K.M. Ranatunga, M.S.P. Sansom
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    ABSTRACT: Molecular modelling studies of the transmembrane domain, and in particular of the pore-forming region, of voltage-gated K+ channels are reviewed. Sequence analysis methods are used to define transmembrane helices and their orientation within the intact channel protein. A detailed comparison is presented of three models (from different research groups) of the (H5)4 domain. These models have all been generated by systematic attempts to fit experimental data which identify pore-lining sidechains. The models are analysed in terms of pore radius profiles and predicted conductances, as well as the extent of their agreement with published mutagenesis data. An extended pore domain model, (S5-H5-S6)4, which includes the S5 and S6 helices packed around a bulged -barrel of (H5)4, is also described and analysed.
    Perspectives in Drug Discovery and Design 01/1999;
  • Ian D. Kerr, Kishani M. Ranatunga, Mark S.P. Sansom
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    ABSTRACT: Molecular modelling studies of the transmembrane domain, and in particular of the pore-forming region, of voltage-gated K+ channels are reviewed. Sequence analysis methods are used to define transmembrane helices and their orientation within the intact channel protein. A detailed comparison is presented of three models (from different research groups) of the (H5)4 domain. These models have all been generated by systematic attempts to fit experimental data which identify pore-lining sidechains. The models are analysed in terms of pore radius profiles and predicted conductances, as well as the extent of their agreement with published mutagenesis data. An extended pore domain model, (S5-H5-S6)4, which includes the S5 and S6 helices packed around a bulged -barrel of (H5)4, is also described and analysed.
    Perspectives in Drug Discovery and Design 12/1998; 15-16:187-214.
  • Biochemical Society Transactions 09/1998; 26(3):S301. · 2.59 Impact Factor
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    ABSTRACT: A model of the selectivity filter of a voltage-gated K+ (Kv) channel formed by an eight-stranded beta-barrel is compared with physiological properties of the channel. Continuum electrostatic calculations suggest that only two of the eight Asp sidechains at the extracellular mouth of the pore will ionise. A ring of four Tyr sidechains forms the narrowest region of the pore. Molecular dynamic simulations of the potential energy of a K+ ion as translated along the model pore indicate that the two ionised Asp sidechains and the hydroxyl groups of the Tyr sidechains stabilise the partially desolvated ion as it passes through the narrowest region.
    Biochimica et Biophysica Acta 04/1998; 1370(1):1-7. · 4.66 Impact Factor

Publication Stats

356 Citations
50.62 Total Impact Points

Institutions

  • 2001–2007
    • Imperial College London
      • Faculty of Medicine
      London, ENG, United Kingdom
  • 1998–2001
    • University of Oxford
      • • Department of Biochemistry
      • • Laboratory of Molecular Biophysics
      Oxford, ENG, United Kingdom