Modelling the effect of a GHz electric field on the dynamics of K⁺ ions in KcsA potassium channel

REFERENCES

• HilleB. Ionic channels of excitable membranes. 3rd ed.Sunderland, MA: Sinauer Associates; 2001.
   Google Scholar
• DoyleDA, Morais-CabralJ, PfuetznerRA, KuoA, GulbisJM, CohenSL, ChaitBT, MacKinnonR. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science. 1998;280:69–77.
   PubMed Web of Science ®Google Scholar
• ZhouYF, Morais-CabralJH, KaufmanA, MacKinnonR. Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 Å resolution. Nature. 2001;414:43–48.
   PubMed Web of Science ®Google Scholar
• Morais-CabralJH, ZhouYF, MacKinnonR. Energetic optimization of ion conduction rate by the K+ selectivity filter. Nature. 2001;414:37–42.
   PubMed Web of Science ®Google Scholar
• ZhouY, MacKinnonR. 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. 2003;333:965–975.
   PubMed Web of Science ®Google Scholar
• ClaphamDE. At last, the structure of an ion-selective channel. Nat Struc Biol. 1998;5:342–344.
   PubMedGoogle Scholar
• GwanJF, BaumgaertnerA. Cooperative transport in a potassium ion channel. Chem Phys J.2007;127:045103-1–045103-10.
   Google Scholar
• ShrivastavaIH, TielemanDP, BigginPC, SansomMSP. K+ versus Na Ions in a K channel selectivity filter: a simulation study. Biophys J. 2002;83:633–645.
   PubMed Web of Science ®Google Scholar
• NoskovSY, BernecheS, RouxB. Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature. 2004;431:830–834.
   PubMed Web of Science ®Google Scholar
• EgwolfB, RouxB. Ion selectivity of the KcsA channel: a perspective from multi-ion free energy landscapes. J Mol Biol. 2010;401:831–842.
   PubMed Web of Science ®Google Scholar
• FuriniS, DomeneC. A typical mechanism of conduction in potassium channels. Proc Natl Acad Sci USA. 2009;106(38):16074–16077.
   PubMed Web of Science ®Google Scholar
• DomeneC, FuriniS. Dynamics, energetics, and selectivity of the low-K+ KcsA channel structure. J Mol Biol. 2009;389(3):637–645.
   PubMed Web of Science ®Google Scholar
• FuriniS, BecksteinO, DomeneC. Permeation of water through the KcsA K+ channel. Proteins. 2009;74(2):437–448.
   PubMed Web of Science ®Google Scholar
• DomeneC, KleinML, BranduardiD, GervasioFL, ParrinelloM. Conformational changes and gating at the selectivity filter of potassium channels. J Am Chem Soc. 2008;130(29):9474–9480.
   PubMed Web of Science ®Google Scholar
• BigginPC, SmithGR, ShrivastavaIH, ChoeS, SansomMSP. Potassium and sodium ions in a potassium channel studied by molecular dynamics simulations. Biochim Biophys Acta. 2001;1510:1–9.
   PubMed Web of Science ®Google Scholar
• GuidoniL, TorreV, CarloniP. Water and Potassium dynamics inside the KcsA K Channel. FEBS Lett. 2000;477:37–42.
   PubMed Web of Science ®Google Scholar
• DomeneC. Molecular dynamics simulations of potassium channel. Cent Eur J Chem. 2007;5:635–671.
   Web of Science ®Google Scholar
• BoiteuxC, CompointM, HuetzP, RamseyerC, GirardetC. Analysis of the Sequence KWKWKK in the KcsA protein channel using molecular dynamics simulations. Internet Electron J Mol Des. 2005;4:235–248.
   Google Scholar
• Khalili-AraghiF, TajkhorshidE, SchultenK. Dynamics of K+ ion conduction through Kv1.2. Biophys J. 2006;91:72–74.
   Web of Science ®Google Scholar
• KuyucakS, AndersenS, ChungSH. Models of permeation in ion channels. Rep Prog Phys. 2001;64:1427–1472.
   Web of Science ®Google Scholar
• ChungSH, AllenTW, KuyucakS. Conducting-state properties of the KcsA potassium channel from molecular and Brownian Dynamics simulations. Biophys J. 2002;82:628–645.
   PubMed Web of Science ®Google Scholar
• MarshlRJ, TangY, SchnitzerJ, JacobssonE. Hierarchical approach to predicting permeation in ion channels. Biophys J. 2001;81:2473–2483.
   PubMed Web of Science ®Google Scholar
• BurykinA, SchutzCN, VillaJ, WarshelA. Simulations of ion current in realistic models of ion channels: the KcsA potassium channel. Proteins Struct Funct Genet. 2002;47:265–280.
   PubMed Web of Science ®Google Scholar
• AqvistJ, LuzhkovV. Ion permeation mechanism of the K+ channel. Nature. 2000;404:881–884.
   PubMed Web of Science ®Google Scholar
• BernecheS, RouxB. Energetics of ion conduction through the K channel. Nature. 2001;414:73–77.
   PubMed Web of Science ®Google Scholar
• BernecheS, RouxB. A microscopic view of ion conduction through the K channel. Proc Natl Acad Sci USA. 2003;100:8644–8648.
   PubMed Web of Science ®Google Scholar
• DomeneC, SansomMSP. A potassium channel, ions and water: simulation studies based on the high resolution X-ray structure of KcsA. Biophys J. 2003;85:2787–2800.
   PubMed Web of Science ®Google Scholar
• GarofoliS, JordanPC. Modelling permeation energetics in the KcsA potassium channel. Biophys J. 2003;84:2814–2830.
   PubMed Web of Science ®Google Scholar
• BastugT, KuyucakS. Comparative study of the energetics of ion permeation in Kv1.2 and KcsA potassium channels. Biophys J. 2011;100:629–636.
   PubMed Web of Science ®Google Scholar
• BucherD, RaugeiS, GuidoniL, PeraroMD, RothlisbergerU, CarloniP, KleinML. Polarization effects and charge transfer in the KcsA potassium channel. Biophys Chem. 2006;124:292–301.
   PubMed Web of Science ®Google Scholar
• IllingworthC, FuriniS, DomeneC. Polarization effects and selectivity in K+ channels. J Chem Theory Comput. 2010;6:3780–3792.
   Web of Science ®Google Scholar
• IllingworthC, DomeneC. Many body effects and simulations of ion channels. Proc R Soc A. 2009;465:1701–1716.
   Google Scholar
• LohrasebiA, MohamadiS, FadaieS, Rafii-TabarH. Modelling the influence of thermal effects induced by radio frequency electric field on the dynamics of the ATPase nanobiomolecular motors. Phys Med. 2012;28:221–229.
   PubMed Web of Science ®Google Scholar
• LinYS, LinJH, ChangCC. Molecular dynamics simulations of the rotary motor F0 under external electric fields across the membrane. Biophys J. 2010;98:1009–1017.
   PubMed Web of Science ®Google Scholar
• CornellWD, CieplakP, BaylyCI, GouldIR, Merz KM, Jr, FergusonDM, SpellmeyerDC, FoxT, CaldwellJW, KollmanPA. A second generation force field for the simulation of proteins, nucleic acids, and organic Molecules. J Am Chem Soc. 1995;117:5179–5197.
   Web of Science ®Google Scholar
• HessB, KutznerC, van der SpoelD, LindahlE. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comp. 2008;4(3):435–447.
   PubMed Web of Science ®Google Scholar
• VajralaV, ClaycombJR, SanabriaH, MillerJH, Jr. Effects of oscillatory electric fields on internal membranes: an analytical model. Biophys J. 2008;94:2043–2052.
   PubMed Web of Science ®Google Scholar
• MarbanE. Cardiac channelopathies. Nature. 2002;415:213–218.
   PubMed Web of Science ®Google Scholar