Abstract
The dynamic properties of shaker-type Kv1.1 ion channel in its open, closed, & two mutated (E325D & V408A) states embedded in DPPC membrane have been investigated using all-atom force field-based MD simulation. Here, we represent the detailed channel stability, gating environment of charge-carrying residues, salt bridge interaction among the voltage-sensing domains (VSDs), movement of S4 helix, and ion conduction of pore. At positive potential, the S4 helix undergoes lateral fluctuations in accordance with their gating motions found in every model. During transition from closed to active state conformation, charged residues of S4 move “up” across the membrane with an average tilt angle difference of 24°, which is more consistent with the paddle model of channel gating. The E325D mutation at C-terminal end of S4–S5 helical linker leads the channel to a rapid activated state by pushing the gating charge residues upward beside the VSDs resulting in more prominent tilt of S4. Similarly in V408A mutant model, disruption of hydrophobic gate at S6 C-terminal end takes place, which causes the violation of channel-active conformation by bringing the C-terminal end of S4 to its corresponding resting state. The ion permeation is observed only in open-state conformation.
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References
Adelman JP, Bond CT, Pessia M, Maylie J (1995) Episodic ataxia results from voltage-dependent potassium channels with altered functions. Neuron 15:1449–1454. doi:10.1016/0896-6273(95)90022-5
Aggarwal SK, MacKinnon R (1996) Contribution of the S4 segment to gating charge in the Shaker K+ channel. Neuron 16:1169–1177. doi:10.1016/S0896-6273(00)80143-9
Aqvist J, Luzhkov V (2000) Ion permeation mechanism of the potassium channel. Nature 404:881–884. doi:10.1038/35009114
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98:10037–10041. doi:10.1073/pnas.181342398
Banerjee A, Lee A, Campbell E, Mackinnon R (2013) Structure of a pore-blocking toxin in complex with a eukaryotic voltage-dependent K+ channel. Elife 2:e00594. doi:10.7554/eLife.00594
Berendsen HJC, Grigera JR, Straatsma TP (1987) The missing term in effective pair potentials. J Phys Chem 91:6269–6271. doi:10.1021/j100308a038
Berger O, Edholm O, Jähnig F (1997) Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys J 72:2002–2013. doi:10.1016/S0006-3495(97)78845-3
Bernèche S, Roux B (2000) Molecular dynamics of the KcsA K+ channel in a bilayer membrane. Biophys J 78:2900–2917. doi:10.1016/S0006-3495(00)76831-7
Bezanilla F (2000) The voltage sensor in voltage-dependent ion channels. Physiol Rev 80:555–592
Bezanilla F, Perozo E, Stefani E (1994) Gating of Shaker K+ channels: II. The components of gating currents and a model of channel activation. Biophys J 66:1011–1021. doi:10.1016/S0006-3495(94)80882-3
Bjelkmar P, Niemelä PS, Vattulainen I, Lindahl E (2009) Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channel. PLoS Comput Biol 5:e1000289. doi:10.1371/journal.pcbi.1000289
Browne DL, Gancher ST, Nutt JG, Brunt ER, Smith EA, Kramer P, Litt M (1994) Episodic ataxia/myokymia syndrome is associated with point mutations in the human potassium channel gene, KCNA1. Nat Genet 8:136–140. doi:10.1038/ng1094-136
Bucher D, Goaillard JM (2011) Beyond faithful conduction: short-term dynamics, neuromodulation, and long-term regulation of spike propagation in the axon. Prog Neurobiol 94:307–346. doi:10.1016/j.pneurobio.2011.06.001
Bussi G, Donadio D, Parrinello M (2007) Canonical sampling through velocity rescaling. J Chem Phys 126:014101. doi:10.1063/1.2408420
Campos FV, Chanda B, Roux B, Bezanilla F (2007) Two atomic constraints unambiguously position the S4 segment relative to S1 and S2 segments in the closed state of Shaker K channel. Proc Natl Acad Sci USA 104:7904–7909. doi:10.1073/pnas.0702638104
Chanda B, Asamoah OK, Blunck R, Roux B, Bezanilla F (2005) Gating charge displacement in voltage-gated ion channels involves limited transmembrane movement. Nature 436:852–856. doi:10.1038/nature03888
Chen X, Wang Q, Ni F, Ma J (2010) Structure of the full-length Shaker potassium channel Kv1.2 by normal-mode-based X-ray crystallographic refinement. Proc Natl Acad Sci USA 107:11352–11357. doi:10.1073/pnas.1000142107
Chovancova E et al (2012) CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures. PLoS Comput Biol 8:e1002708. doi:10.1371/journal.pcbi.1002708
Clayton GM, Altieri S, Heginbotham L, Unger VM, Morais-Cabral JH (2008) Structure of the transmembrane regions of a bacterial cyclic nucleotide-regulated channel. Proc Natl Acad Sci USA 105:1511–1515. doi:10.1073/pnas.0711533105
Conforti L, Millhorn DE (1997) Selective inhibition of a slow-inactivating voltage-dependent K+ channel in rat PC12 cells by hypoxia. J Physiol 502(Pt 2):293–305
Conforti L, Bodi I, Nisbet JW, Millhorn DE (2000) O2-sensitive K+ channels: role of the Kv1.2 α-subunit in mediating the hypoxic response. J Physiol 524(Pt 3):783–793. doi:10.1111/j.1469-7793.2000.00783.x
D’Adamo MC, Imbrici P, Sponcichetti F, Pessia M (1999) Mutations in the KCNA1 gene associated with episodic ataxia type-1 syndrome impair heteromeric voltage-gated K+ channel function. FASEB J 13:1335–1345. doi:10.1096/fj.1530-6860
Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092. doi:10.1063/1.464397
Debanne D, Campanac E, Bialowas A, Carlier E, Alcaraz G (2011) Axon physiology. Physiol Rev 91:555–602. doi:10.1152/physrev.00048.2009
Doyle DA et al (1998) The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280:69–77. doi:10.1126/science.280.5360.69
Eswar N, Eramian D, Webb B, Shen MY, Sali A (2008) Protein structure modeling with MODELLER. Methods Mol Biol 426:145–159. doi:10.1007/978-1-60327-058-8_8
Grissmer S et al (1994) Pharmacological characterization of five cloned voltage-gated K+ channels, types Kv1.1, 1.2, 1.3, 1.5, and 3.1, stably expressed in mammalian cell lines. Mol Pharmacol 45:1227–1234
Gutman GA et al (2005) International Union of Pharmacology. LIII. Nomenclature and molecular relationships of voltage-gated potassium channels. Pharmacol Rev 57:473–508. doi:10.1124/pr.57.4.10
Heginbotham L, MacKinnon R (1993) Conduction properties of the cloned Shaker K+ channel. Biophys J 65:2089–2096. doi:10.1016/S0006-3495(93)81244-X
Henrion U et al (2012) Tracking a complete voltage-sensor cycle with metal-ion bridges. Proc Natl Acad Sci USA 109:8552–8557. doi:10.1073/pnas.1116938109
Hess B, Bekker H, Berendsen HJ, Fraaije JG (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18:1463–1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463:AID-JCC4>3.0.CO;2-H
Hess B, Kutzner C, Van Der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435–447. doi:10.1021/ct700301q
Hille B (1992) Ionic channels of excitable membranes. Sinauer, Sunderland
Hille B (2001) Ion channels of excitable membranes. Sinauer Associates, Sunderland
Hodgkin AL, Huxley AF (1990) A quantitative description of membrane current and its application to conduction and excitation in nerve. Bull Math Biol 52:25–71. doi:10.1007/BF02459568
Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38. doi:10.1016/0263-7855(96)00018-5
Jensen MØ et al (2010) Principles of conduction and hydrophobic gating in K+ channels. Proc Natl Acad Sci USA 107:5833–5838. doi:10.1073/pnas.0911691107
Jensen MØ, Jogini V, Borhani DW, Leffler AE, Dror RO, Shaw DE (2012) Mechanism of voltage gating in potassium channels. Science 336:229–233. doi:10.1126/science.1216533
Jiang Y, Ruta V, Chen J, Lee A, MacKinnon R (2003) The principle of gating charge movement in a voltage-dependent K+ channel. Nature 423:42–48. doi:10.1038/nature01581
Jogini V, Roux B (2007) Dynamics of the Kv1.2 voltage-gated K+ channel in a membrane environment. Biophys J 93:3070–3082. doi:10.1529/biophysj.107.112540
Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL (2008) NCBI BLAST: a better web interface. Nucleic Acids Res 36:W5–W9. doi:10.1093/nar/gkn201
Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637. doi:10.1002/bip.360221211
Khalili-Araghi F, Jogini V, Yarov-Yarovoy V, Tajkhorshid E, Roux B, Schulten K (2010) Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel. Biophys J 98:2189–2198. doi:10.1016/j.bpj.2010.02.056
Larkin MA et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948. doi:10.1093/bioinformatics/btm404
Lee SY, Banerjee A, MacKinnon R (2009) Two separate interfaces between the voltage sensor and pore are required for the function of voltage-dependent K+ channels. PLoS Biol 7:e47. doi:10.1371/journal.pbio.1000047
Long SB, Campbell EB, Mackinnon R (2005) Crystal structure of a mammalian voltage-dependent Shaker family K+ channel. Science 309:897–903. doi:10.1126/science.1116269
Long SB, Tao X, Campbell EB, MacKinnon R (2007) Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment. Nature 450:376–382. doi:10.1038/nature06265
Mert T (2006) Kv1 channels in signal conduction of myelinated nerve fibers. Rev Neurosci 17:369–374. doi:10.1515/REVNEURO.2006.17.3.369
Milescu M, Bosmans F, Lee S, Alabi AA, Kim JI, Swartz KJ (2009) Interactions between lipids and voltage sensor paddles detected with tarantula toxins. Nat Struct Mol Biol 16:1080–1085. doi:10.1038/nsmb.1679
Nosé S (1984) A molecular dynamics method for simulations in the canonical ensemble. Mol Phy 52:255–268. doi:10.1080/00268978400101201
Papazian DM, Shao XM, Seoh SA, Mock AF, Huang Y, Wainstock DH (1995) Electrostatic interactions of S4 voltage sensor in Shaker K+ channel. Neuron 14:1293–1301. doi:10.1016/0896-6273(95)90276-7
Parrinello M, Rahman A (1981) Polymorphic transitions in single crystals: a new molecular dynamics method. J Appl Phys 52:7182–7190. doi:10.1063/1.328693
Pathak MM et al (2007) Closing in on the resting state of the Shaker K+ channel. Neuron 56:124–140. doi:10.1016/j.neuron.2007.09.023
Ruta V, Chen J, MacKinnon R (2005) Calibrated measurement of gating-charge arginine displacement in the KvAP voltage-dependent K+ channel. Cell 123:463–475. doi:10.1016/j.cell.2005.08.041
Seoh SA, Sigg D, Papazian DM, Bezanilla F (1996) Voltage-sensing residues in the S2 and S4 segments of the Shaker K+ channel. Neuron 16:1159–1167. doi:10.1016/S0896-6273(00)80142-7
Shealy RT, Murphy AD, Ramarathnam R, Jakobsson E, Subramaniam S (2003) Sequence-function analysis of the K+-selective family of ion channels using a comprehensive alignment and the KcsA channel structure. Biophys J 84:2929–2942. doi:10.1016/S0006-3495(03)70020-4
Sigworth FJ (1994) Voltage gating of ion channels. Q Rev Biophys 27:1–40. doi:10.1017/S0033583500002894
Smith-Maxwell CJ, Ledwell JL, Aldrich RW (1998) Role of the S4 in cooperativity of voltage-dependent potassium channel activation. J Gen Physiol 111:399–420. doi:10.1085/jgp.111.3.399
Soler-Llavina GJ, Chang TH, Swartz KJ (2006) Functional interactions at the interface between voltage-sensing and pore domains in the Shaker Kv channel. Neuron 52:623–634. doi:10.1016/j.neuron.2006.10.005
Starace DM, Bezanilla F (2001) Histidine scanning mutagenesis of basic residues of the S4 segment of the shaker K+ channel. J Gen Physiol 117:469–490. doi:10.1085/jgp.117.5.469
Swartz KJ (2004) Towards a structural view of gating in potassium channels. Nat Rev Neurosci 5:905–916. doi:10.1038/nrn1559
Swartz KJ (2008) Sensing voltage across lipid membranes. Nature 456:891–897. doi:10.1038/nature07620
Tao X, Lee A, Limapichat W, Dougherty DA, MacKinnon R (2010) A gating charge transfer center in voltage sensors. Science 328:67–73. doi:10.1126/science.1185954
Tiwari-Woodruff SK, Schulteis CT, Mock AF, Papazian DM (1997) Electrostatic interactions between transmembrane segments mediate folding of Shaker K+ channel subunits. Biophys J 72:1489–1500. doi:10.1016/S0006-3495(97)78797-6
Tiwari-Woodruff SK, Lin MA, Schulteis CT, Papazian DM (2000) Voltage-dependent structural interactions in the Shaker K+ channel. J Gen Physiol 115:123–138. doi:10.1085/jgp.115.2.123
Tombola F, Pathak MM, Isacoff EY (2005) Voltage-sensing arginines in a potassium channel permeate and occlude cation-selective pores. Neuron 45:379–388. doi:10.1016/j.neuron.2004.12.047
Tombola F, Pathak MM, Gorostiza P, Isacoff EY (2007) The twisted ion-permeation pathway of a resting voltage-sensing domain. Nature 445:546–549. doi:10.1038/nature05396
Treptow W, Tarek M (2006) Environment of the gating charges in the Kv1.2 Shaker potassium channel. Biophys J 90:L64–L66. doi:10.1529/biophysj.106.080754
Tu LW, Deutsch C (2010) A folding zone in the ribosomal exit tunnel for Kv1.3 helix formation. J Mol Biol 396:1346–1360. doi:10.1016/j.jmb.2009.12.059
Tusnady GE, Dosztanyi Z, Simon I (2005) TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates. Bioinformatics 21:1276–1277. doi:10.1093/bioinformatics/bti121
Villalba-Galea CA, Sandtner W, Starace DM, Bezanilla F (2008) S4-based voltage sensors have three major conformations. Proc Natl Acad Sci USA 105:17600–17607. doi:10.1073/pnas.0807387105
Zagotta WN, Hoshi T, Aldrich RW (1994) Shaker potassium channel gating. III: evaluation of kinetic models for activation. J Gen Physiol 103:321–362. doi:10.1085/jgp.103.2.321
Zhou Y, MacKinnon R (2003) The occupancy of ions in the K+ selectivity filter: charge balance and coupling of ion binding to a protein conformational change underlie high conduction rates. J Mol Biol 333:965–975. doi:10.1016/j.jmb.2003.09.022
Zhou M, MacKinnon R (2004) A mutant KcsA K+ channel with altered conduction properties and selectivity filter ion distribution. J Mol Biol 338:839–846. doi:10.1016/j.jmb.2004.03.020
Zhu J et al (2003) Allowed N-glycosylation sites on the Kv1.2 potassium channel S1-S2 linker: implications for linker secondary structure and the glycosylation effect on channel function. Biochem J 375:769–775. doi:10.1042/BJ20030517
Zuberi SM et al (1999) A novel mutation in the human voltage-gated potassium channel gene (Kv1.1) associates with episodic ataxia type 1 and sometimes with partial epilepsy. Brain 122(Pt 5):817–825. doi:10.1093/brain/122.5.817
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The authors are thankful to Mr. Suman Kumar Nandy for his valuable suggestions and for reading the manuscript carefully. The whole study was supported by Grants from BTIS net programme of DBT, Ministry of Science & Technology, Government of India, New Delhi and DST purse programme.
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Bhuyan, R., Seal, A. Conformational Dynamics of Shaker-Type Kv1.1 Ion Channel in Open, Closed, and Two Mutated States. J Membrane Biol 248, 241–255 (2015). https://doi.org/10.1007/s00232-014-9764-7
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DOI: https://doi.org/10.1007/s00232-014-9764-7