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Membrane protein PDB id
1jvm
Jmol
Contents
Protein chains
97 a.a. *
Ligands
TBA
Metals
_RB ×3
Waters ×1
* Residue conservation analysis
PDB id:
1jvm
Name: Membrane protein
Title: Kcsa potassium channel with tba (tetrabutylammonium) and rubidium
Structure: Voltage-gated potassium channel. Chain: a, b, c, d. Fragment: residues 1-125. Engineered: yes. Mutation: yes
Source: Streptomyces lividans. Organism_taxid: 1916. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PQS)
Resolution:
2.80Å     R-factor:   0.281     R-free:   0.302
Authors: J.H.Morais-Cabral,Y.Zhou,R.Mackinnon
Key ref:
J.H.Morais-Cabral et al. (2001). Energetic optimization of ion conduction rate by the K+ selectivity filter. Nature, 414, 37-42. PubMed id: 11689935 DOI: 10.1038/35102000
Date:
30-Aug-01     Release date:   05-Dec-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A334  (KCSA_STRLI) -  Voltage-gated potassium channel
Seq:
Struc: 		160 a.a.
97 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     voltage-gated potassium channel complex   1 term 
  Biological process     potassium ion transport   1 term 
  Biochemical function     voltage-gated potassium channel activity     1 term  

 

 
DOI no: 10.1038/35102000 Nature 414:37-42 (2001)
PubMed id: 11689935  
 
 
Energetic optimization of ion conduction rate by the K+ selectivity filter.
J.H.Morais-Cabral, Y.Zhou, R.MacKinnon.
 
  ABSTRACT  
 
The K+ selectivity filter catalyses the dehydration, transfer and rehydration of a K+ ion in about ten nanoseconds. This physical process is central to the production of electrical signals in biology. Here we show how nearly diffusion-limited rates are achieved, by analysing ion conduction and the corresponding crystallographic ion distribution in the selectivity filter of the KcsA K+ channel. Measurements with K+ and its slightly larger analogue, Rb+, lead us to conclude that the selectivity filter usually contains two K+ ions separated by one water molecule. The two ions move in a concerted fashion between two configurations, K+-water-K+-water (1,3 configuration) and water-K+-water-K+ (2,4 configuration), until a third ion enters, displacing the ion on the opposite side of the queue. For K+, the energy difference between the 1,3 and 2,4 configurations is close to zero, the condition of maximum conduction rate. The energetic balance between these configurations is a clear example of evolutionary optimization of protein function.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Binding sites for K+ ions in the KcsA K+ channel. a, Ribbon representation of the KcsA channel with the subunit closest to the viewer removed. Potassium ions (green spheres) bind at four locations in the selectivity filter (yellow) and in the water-filled cavity at the membrane centre (bottom ion). b, Close-up view of the selectivity filter in ball-and-stick representation, with the front and back subunits removed. The four K+ ions are numbered to indicate the location of binding sites in the filter; position 1 is closest to the extracellular solution and position 4 is closest to the cavity. Key amino acids forming the selectivity filter are shown. Pictures were prepared with GL-Render26,27. 		Figure 5.
Figure 5: The biologically important throughput cycle for K+ ions. a, Detailed description of the cycle connecting states B and C (Fig. 4a). The selectivity filter is depicted as five sets of four in-plane oxygen atoms (the top is outside the cell), with K+ ions and water molecules shown as green and red spheres, respectively. K+ ions undergo coordination by eight oxygen atoms when in the 1,3 and 2,4 configurations. Movement along either the concentration-independent path (bottom) or the concentration-dependent path (top) would involve octahedral coordination by six oxygen atoms, two provided by the intervening water molecules. b, The atomic structures of K+-selective antibiotics nonactin (right) and valinomycin (left) exhibit coordination by eight and six oxygen atoms, respectively5 -7.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2001, 414, 37-42) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21518828 A.Alam, and Y.Jiang (2011).
Structural studies of ion selectivity in tetrameric cation channels.
  J Gen Physiol, 137, 397-403.  
21518829 C.M.Nimigean, and T.W.Allen (2011).
Origins of ion selectivity in potassium channels from the perspective of channel block.
  J Gen Physiol, 137, 405-413.  
21247754 J.Wang, J.X.Qiu, C.Soto, and W.F.DeGrado (2011).
Structural and dynamic mechanisms for the function and inhibition of the M2 proton channel from influenza A virus.
  Curr Opin Struct Biol, 21, 68-80.  
21186363 S.Chakrapani, J.F.Cordero-Morales, V.Jogini, A.C.Pan, D.M.Cortes, B.Roux, and E.Perozo (2011).
On the structural basis of modal gating behavior in K(+) channels.
  Nat Struct Mol Biol, 18, 67-74.
PDB codes: 3or6 3or7
21376013 T.A.Liu, H.K.Chang, and R.C.Shieh (2011).
Extracellular K(+) elevates outward currents through Kir2.1 channels by increasing single-channel conductance.
  Biochim Biophys Acta, 1808, 1772-1778.  
21402935 W.W.Cheng, J.G.McCoy, A.N.Thompson, C.G.Nichols, and C.M.Nimigean (2011).
Mechanism for selectivity-inactivation coupling in KcsA potassium channels.
  Proc Natl Acad Sci U S A, 108, 5272-5277.
PDB code: 3ogc
21317882 Y.Cao, X.Jin, H.Huang, M.G.Derebe, E.J.Levin, V.Kabaleeswaran, Y.Pan, M.Punta, J.Love, J.Weng, M.Quick, S.Ye, B.Kloss, R.Bruni, E.Martinez-Hackert, W.A.Hendrickson, B.Rost, J.A.Javitch, K.R.Rajashankar, Y.Jiang, and M.Zhou (2011).
Crystal structure of a potassium ion transporter, TrkH.
  Nature, 471, 336-340.
PDB code: 3pjz
20018952 E.D.Burg, O.Platoshyn, I.F.Tsigelny, B.Lozano-Ruiz, B.K.Rana, and J.X.Yuan (2010).
Tetramerization domain mutations in KCNA5 affect channel kinetics and cause abnormal trafficking patterns.
  Am J Physiol Cell Physiol, 298, C496-C509.  
19940001 J.A.Lundbaek, S.A.Collingwood, H.I.Ingólfsson, R.Kapoor, and O.S.Andersen (2010).
Lipid bilayer regulation of membrane protein function: gramicidin channels as molecular force probes.
  J R Soc Interface, 7, 373-395.  
20613845 L.G.Cuello, V.Jogini, D.M.Cortes, A.C.Pan, D.G.Gagnon, O.Dalmas, J.F.Cordero-Morales, S.Chakrapani, B.Roux, and E.Perozo (2010).
Structural basis for the coupling between activation and inactivation gates in K(+) channels.
  Nature, 466, 272-275.
PDB code: 3hpl
20613835 L.G.Cuello, V.Jogini, D.M.Cortes, and E.Perozo (2010).
Structural mechanism of C-type inactivation in K(+) channels.
  Nature, 466, 203-208.  
19959477 M.Hirano, Y.Takeuchi, T.Aoki, T.Yanagida, and T.Ide (2010).
Rearrangements in the KcsA cytoplasmic domain underlie its gating.
  J Biol Chem, 285, 3777-3783.  
20231479 M.Ã.˜.Jensen, D.W.Borhani, K.Lindorff-Larsen, P.Maragakis, V.Jogini, M.P.Eastwood, R.O.Dror, and D.E.Shaw (2010).
Principles of conduction and hydrophobic gating in K+ channels.
  Proc Natl Acad Sci U S A, 107, 5833-5838.  
  20513757 R.O.Dror, M.Ã.˜.Jensen, D.W.Borhani, and D.E.Shaw (2010).
Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations.
  J Gen Physiol, 135, 555-562.  
20571950 S.B.Choi, J.U.Kim, H.Joo, and C.K.Min (2010).
Identification and characterization of a novel bacterial ATP-sensitive K+ channel.
  J Microbiol, 48, 325-330.  
  20805578 S.Oiki, M.Iwamoto, and T.Sumikama (2010).
A mesoscopic approach to understanding the mechanisms underlying the ion permeation on the discrete-state diagram.
  J Gen Physiol, 136, 363-365.  
20676101 S.Ye, Y.Li, and Y.Jiang (2010).
Novel insights into K+ selectivity from high-resolution structures of an open K+ channel pore.
  Nat Struct Mol Biol, 17, 1019-1023.
PDB codes: 3ldc 3ldd 3lde
19098915 A.Alam, and Y.Jiang (2009).
Structural analysis of ion selectivity in the NaK channel.
  Nat Struct Mol Biol, 16, 35-41.
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  19803500 A.G.Komarov, K.M.Linn, J.J.Devereaux, and F.I.Valiyaveetil (2009).
Modular strategy for the semisynthesis of a K+ channel: investigating interactions of the pore helix.
  ACS Chem Biol, 4, 1029-1038.  
19946269 A.N.Thompson, I.Kim, T.D.Panosian, T.M.Iverson, T.W.Allen, and C.M.Nimigean (2009).
Mechanism of potassium-channel selectivity revealed by Na(+) and Li(+) binding sites within the KcsA pore.
  Nat Struct Mol Biol, 16, 1317-1324.
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19339978 D.C.Gadsby (2009).
Ion channels versus ion pumps: the principal difference, in principle.
  Nat Rev Mol Cell Biol, 10, 344-352.  
19486671 D.L.Bostick, and C.L.Brooks (2009).
Statistical determinants of selective ionic complexation: ions in solvent, transport proteins, and other "hosts".
  Biophys J, 96, 4470-4492.  
19413965 J.P.Lees-Miller, J.O.Subbotina, J.Guo, V.Yarov-Yarovoy, S.Y.Noskov, and H.J.Duff (2009).
Interactions of H562 in the S5 helix with T618 and S621 in the pore helix are important determinants of hERG1 potassium channel structure and function.
  Biophys J, 96, 3600-3610.  
19805261 S.Furini, and C.Domene (2009).
Atypical mechanism of conduction in potassium channels.
  Proc Natl Acad Sci U S A, 106, 16074-16077.  
19774294 S.Kraszewski, C.Boiteux, C.Ramseyer, and C.Girardet (2009).
Determination of the charge profile in the KcsA selectivity filter using ab initio calculations and molecular dynamics simulations.
  Phys Chem Chem Phys, 11, 8606-8613.  
19167299 S.Tayefeh, T.Kloss, M.Kreim, M.Gebhardt, D.Baumeister, B.Hertel, C.Richter, H.Schwalbe, A.Moroni, G.Thiel, and S.M.Kast (2009).
Model development for the viral Kcv potassium channel.
  Biophys J, 96, 485-498.  
19033439 S.Wang, Y.Alimi, A.Tong, C.G.Nichols, and D.Enkvetchakul (2009).
Differential roles of blocking ions in KirBac1.1 tetramer stability.
  J Biol Chem, 284, 2854-2860.  
19968368 Y.W.Jung, B.Lu, and M.Mascagni (2009).
A computational study of ion conductance in the KcsA K(+) channel using a Nernst-Planck model with explicit resident ions.
  J Chem Phys, 131, 215101.  
19032804 A.Inanobe, N.Kamiya, S.Murakami, Y.Fukunishi, H.Nakamura, and Y.Kurachi (2008).
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  J Physiol Sci, 58, 459-470.  
18842165 A.Ohsaga, Y.Murata, Y.Kondo, R.Hira, and Y.Maruyama (2008).
Asymmetry of Rb(+) Conduction Emerged under Bi-Ionic Conditions in Epithelial Maxi-K(+) Channels.
  J Physiol Sci, 58, 363-369.  
18421473 A.Roller, G.Natura, H.Bihler, C.L.Slayman, and A.Bertl (2008).
Functional consequences of leucine and tyrosine mutations in the dual pore motifs of the yeast K(+) channel, Tok1p.
  Pflugers Arch, 456, 883-896.  
  18378799 I.Schroeder, and U.P.Hansen (2008).
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  J Gen Physiol, 131, 365-378.  
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  Acta Biochim Biophys Sin (Shanghai), 40, 539-553.  
18604229 K.M.Waldhauser, K.Brecht, S.Hebeisen, H.R.Ha, D.Konrad, D.Bur, and S.Krähenbühl (2008).
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  Br J Pharmacol, 155, 585-595.  
18252769 K.Sheppard, J.Yuan, M.J.Hohn, B.Jester, K.M.Devine, and D.Söll (2008).
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  Nucleic Acids Res, 36, 1813-1825.  
18772896 L.Csanády, and J.A.Mindell (2008).
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  EMBO Rep, 9, 960-965.  
17905851 M.Andér, V.B.Luzhkov, and J.Aqvist (2008).
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  Biophys J, 94, 820-831.  
18658223 Q.Ma, E.Pavlov, T.Britvina, G.W.Zamponi, and R.J.French (2008).
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  Biophys J, 95, 4266-4276.  
18266681 T.Ikrar, H.Hanawa, H.Watanabe, S.Okada, Y.Aizawa, M.M.Ramadan, S.Komura, F.Yamashita, M.Chinushi, and Y.Aizawa (2008).
A double-point mutation in the selectivity filter site of the KCNQ1 potassium channel results in a severe phenotype, LQT1, of long QT syndrome.
  J Cardiovasc Electrophysiol, 19, 541-549.  
18594804 T.Vora, B.Corry, and S.H.Chung (2008).
Brownian dynamics study of flux ratios in sodium channels.
  Eur Biophys J, 38, 45-52.  
17415597 C.Boiteux, S.Kraszewski, C.Ramseyer, and C.Girardet (2007).
Ion conductance vs. pore gating and selectivity in KcsA channel: modeling achievements and perspectives.
  J Mol Model, 13, 699-713.  
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Dipole-induced vortex ratchets in superconducting films with arrays of micromagnets.
  Phys Rev Lett, 98, 117005.  
17052164 C.M.Armstrong (2007).
Life among the axons.
  Annu Rev Physiol, 69, 1.  
17526571 D.Boda, W.Nonner, M.Valiskó, D.Henderson, B.Eisenberg, and D.Gillespie (2007).
Steric selectivity in Na channels arising from protein polarization and mobile side chains.
  Biophys J, 93, 1960-1980.  
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  Biophys J, 93, 4159-4172.  
  17438120 G.Panyi, and C.Deutsch (2007).
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  J Gen Physiol, 129, 403-418.  
  17591987 I.Schroeder, and U.P.Hansen (2007).
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  J Gen Physiol, 130, 83-97.  
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  17535958 R.Olcese (2007).
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  J Gen Physiol, 129, 457-459.  
  17938230 S.Chakrapani, J.F.Cordero-Morales, and E.Perozo (2007).
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  J Gen Physiol, 130, 465-478.  
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Insight into the origins of the barrier-less knock-on conduction in the KcsA channel: molecular dynamics simulations and ab initio calculations.
  Phys Chem Chem Phys, 9, 1219-1225.  
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Structural and thermodynamic properties of selective ion binding in a K+ channel.
  PLoS Biol, 5, e121.
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17362089 T.BaÅŸtuÄŸ, and S.Kuyucak (2007).
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  J Chem Phys, 126, 105103.  
17534481 X.Liang, D.J.Campopiano, and P.J.Sadler (2007).
Metals in membranes.
  Chem Soc Rev, 36, 968-992.  
17676362 X.S.Liu, M.Zhang, M.Jiang, D.M.Wu, and G.N.Tseng (2007).
Probing the interaction between KCNE2 and KCNQ1 in their transmembrane regions.
  J Membr Biol, 216, 117-127.  
17038321 A.Raybaud, Y.Dodier, P.Bissonnette, M.Simoes, D.G.Bichet, R.Sauvé, and L.Parent (2006).
The role of the GX9GX3G motif in the gating of high voltage-activated Ca2+ channels.
  J Biol Chem, 281, 39424-39436.  
16572166 C.C.de Souza Silva, J.Van de Vondel, M.Morelle, and V.V.Moshchalkov (2006).
Controlled multiple reversals of a ratchet effect.
  Nature, 440, 651-654.  
  16847099 E.C.Ray, and C.Deutsch (2006).
A trapped intracellular cation modulates K+ channel recovery from slow inactivation.
  J Gen Physiol, 128, 203-217.  
16868853 E.J.Mapes, and M.F.Schumaker (2006).
Framework models of ion permeation through membrane channels and the generalized King-Altman method.
  Bull Math Biol, 68, 1429-1460.  
17095703 F.I.Valiyaveetil, M.Leonetti, T.W.Muir, and R.Mackinnon (2006).
Ion selectivity in a semisynthetic K+ channel locked in the conductive conformation.
  Science, 314, 1004-1007.
PDB codes: 2ih1 2ih3
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Structural and functional consequences of an amide-to-ester substitution in the selectivity filter of a potassium channel.
  J Am Chem Soc, 128, 11591-11599.
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16565061 H.Omote, and M.K.Al-Shawi (2006).
Interaction of transported drugs with the lipid bilayer and P-glycoprotein through a solvation exchange mechanism.
  Biophys J, 90, 4046-4059.  
16809540 H.Oshikane, K.Sheppard, S.Fukai, Y.Nakamura, R.Ishitani, T.Numata, R.L.Sherrer, L.Feng, E.Schmitt, M.Panvert, S.Blanquet, Y.Mechulam, D.Söll, and O.Nureki (2006).
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  Science, 312, 1950-1954.
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17025587 H.W.de Haan, I.S.Tolokh, C.G.Gray, and S.Goldman (2006).
Nonequilibrium molecular dynamics calculation of the conductance of the KcsA potassium ion channel.
  Phys Rev E Stat Nonlin Soft Matter Phys, 74, 030905.  
16907122 I.S.Tolokh, S.Goldman, and C.G.Gray (2006).
Unified modeling of conductance kinetics for low- and high-conductance potassium ion channels.
  Phys Rev E Stat Nonlin Soft Matter Phys, 74, 011902.  
16299086 J.Bronson, O.S.Lee, and J.G.Saven (2006).
Molecular Dynamics Simulation of WSK-3, a Computationally Designed, Water-Soluble Variant of the Integral Membrane Protein KcsA.
  Biophys J, 90, 1156-1163.  
  16880266 J.G.Trapani, P.Andalib, J.F.Consiglio, and S.J.Korn (2006).
Control of single channel conductance in the outer vestibule of the Kv2.1 potassium channel.
  J Gen Physiol, 128, 231-246.  
16342124 J.R.Pfeifer, P.Reiss, and U.Koert (2006).
Crown ether-gramicidin hybrid ion channels: dehydration-assisted ion selectivity.
  Angew Chem Int Ed Engl, 45, 501-504.  
16339887 J.Zimmer, D.A.Doyle, and J.G.Grossmann (2006).
Structural characterization and pH-induced conformational transition of full-length KcsA.
  Biophys J, 90, 1752-1766.  
16432696 L.Ferrera, and O.Moran (2006).
Beta1-subunit modulates the Nav1.4 sodium channel by changing the surface charge.
  Exp Brain Res, 172, 139-150.  
16983068 M.Grabe, D.Bichet, X.Qian, Y.N.Jan, and L.Y.Jan (2006).
K+ channel selectivity depends on kinetic as well as thermodynamic factors.
  Proc Natl Acad Sci U S A, 103, 14361-14366.  
16815844 M.L.Renart, F.N.Barrera, M.L.Molina, J.A.Encinar, J.A.Poveda, A.M.Fernández, J.Gómez, and J.M.González-Ros (2006).
Effects of conducting and blocking ions on the structure and stability of the potassium channel KcsA.
  J Biol Chem, 281, 29905-29915.  
16460196 P.Huetz, C.Boiteux, M.Compoint, C.Ramseyer, and C.Girardet (2006).
Incidence of partial charges on ion selectivity in potassium channels.
  J Chem Phys, 124, 044703.  
16863470 P.J.Stansfeld, M.J.Sutcliffe, and J.S.Mitcheson (2006).
Molecular mechanisms for drug interactions with hERG that cause long QT syndrome.
  Expert Opin Drug Metab Toxicol, 2, 81-94.  
16814540 R.Dutzler (2006).
The ClC family of chloride channels and transporters.
  Curr Opin Struct Biol, 16, 439-446.  
17468961 R.J.O'Connell, C.Yuan, L.J.Johnston, O.Rinco, I.Probodh, and S.N.Treistman (2006).
Gating and conductance changes in BK(Ca) channels in bilayers are reciprocal.
  J Membr Biol, 213, 143-153.  
17073662 R.L.Brown, T.Strassmaier, J.D.Brady, and J.W.Karpen (2006).
The pharmacology of cyclic nucleotide-gated channels: emerging from the darkness.
  Curr Pharm Des, 12, 3597-3613.  
16877513 S.Furini, F.Zerbetto, and S.Cavalcanti (2006).
Application of the Poisson-Nernst-Planck theory with space-dependent diffusion coefficients to KcsA.
  Biophys J, 91, 3162-3169.  
16341087 S.Lobet, and R.Dutzler (2006).
Ion-binding properties of the ClC chloride selectivity filter.
  EMBO J, 25, 24-33.
PDB codes: 2exw 2exy 2ez0
16513790 S.M.Makary, T.W.Claydon, K.M.Dibb, and M.R.Boyett (2006).
Base of pore loop is important for rectification, activation, permeation, and block of Kir3.1/Kir3.4.
  Biophys J, 90, 4018-4034.  
16554793 W.N.Zagotta (2006).
Membrane biology: permutations of permeability.
  Nature, 440, 427-429.  
16980355 W.Treptow, and M.Tarek (2006).
K+ conduction in the selectivity filter of potassium channels is monitored by the charge distribution along their sequence.
  Biophys J, 91, L81-L83.  
15816177 A.Grottesi, C.Domene, S.Haider, and M.S.Sansom (2005).
Molecular dynamics simulation approaches to K channels: conformational flexibility and physiological function.
  IEEE Trans Nanobioscience, 4, 112-120.  
16133265 A.Roller, G.Natura, H.Bihler, C.L.Slayman, C.Eing, and A.Bertl (2005).
In the yeast potassium channel, Tok1p, the external ring of aspartate residues modulates both gating and conductance.
  Pflugers Arch, 451, 362-370.  
15869387 B.Roux (2005).
Ion conduction and selectivity in K(+) channels.
  Annu Rev Biophys Biomol Struct, 34, 153-171.  
15849255 D.Gradmann, and C.M.Boyd (2005).
Fast, triangular voltage clamp for recording and kinetic analysis of an ion transporter expressed in Xenopus oocytes.
  Biophys J, 89, 734-744.  
15756587 D.Gradmann, and C.M.Boyd (2005).
Apparent charge of binding site in ion-translocating enzymes: kinetic impact.
  Eur Biophys J, 34, 353-357.  
15556975 E.Kutluay, B.Roux, and L.Heginbotham (2005).
Rapid intracellular TEA block of the KcsA potassium channel.
  Biophys J, 88, 1018-1029.  
16157278 F.C.Chatelain, N.Alagem, Q.Xu, R.Pancaroglu, E.Reuveny, and D.L.Minor (2005).
The pore helix dipole has a minor role in inward rectifier channel function.
  Neuron, 47, 833-843.  
  16260841 H.Ando, M.Kuno, H.Shimizu, I.Muramatsu, and S.Oiki (2005).
Coupled K+-water flux through the HERG potassium channel measured by an osmotic pulse method.
  J Gen Physiol, 126, 529-538.  
15516518 H.K.Chang, S.H.Yeh, and R.C.Shieh (2005).
A ring of negative charges in the intracellular vestibule of Kir2.1 channel modulates K+ permeation.
  Biophys J, 88, 243-254.  
16224118 H.X.Zhou (2005).
How do biomolecular systems speed up and regulate rates?
  Phys Biol, 2, R1-25.  
15783357 I.S.Tolokh, I.I.Tolokh, H.C.Cho, N.D'Avanzo, P.H.Backx, S.Goldman, and C.G.Gray (2005).
Non-Michaelis-Menten kinetics model for conductance of low-conductance potassium ion channels.
  Phys Rev E Stat Nonlin Soft Matter Phys, 71, 021912.  
16456716 J.A.Hernández, and J.Fischbarg (2005).
A general channel model accounts for channel, carrier, counter-transport and co-transport kinetics.
  J Membr Biol, 206, 215-226.  
  15897293 J.Thompson, and T.Begenisich (2005).
Two stable, conducting conformations of the selectivity filter in Shaker K+ channels.
  J Gen Physiol, 125, 619-629.  
16474879 M.Compoint, C.Boiteux, P.Huetz, C.Ramseyer, and C.Girardet (2005).
Role of water molecules in the KcsA protein channel by molecular dynamics calculations.
  Phys Chem Chem Phys, 7, 4138-4145.  
15847489 M.Compoint, F.Picaud, C.Ramseyer, and C.Girardet (2005).
Targeted molecular dynamics of an open-state KcsA channel.
  J Chem Phys, 122, 134707.  
15852022 M.J.Lenaeus, M.Vamvouka, P.J.Focia, and A.Gross (2005).
Structural basis of TEA blockade in a model potassium channel.
  Nat Struct Mol Biol, 12, 454-459.
PDB codes: 2bob 2boc
  16129774 M.N.Krishnan, J.P.Bingham, S.H.Lee, P.Trombley, and E.Moczydlowski (2005).
Functional role and affinity of inorganic cations in stabilizing the tetrameric structure of the KcsA K+ channel.
  J Gen Physiol, 126, 271-283.  
  15824191 N.D'Avanzo, H.C.Cho, I.Tolokh, R.Pekhletski, I.Tolokh, C.Gray, S.Goldman, and P.H.Backx (2005).
Conduction through the inward rectifier potassium channel, Kir2.1, is increased by negatively charged extracellular residues.
  J Gen Physiol, 125, 493-503.  
16143634 N.Shin, H.Soh, S.Chang, D.H.Kim, and C.S.Park (2005).
Sodium permeability of a cloned small-conductance calcium-activated potassium channel.
  Biophys J, 89, 3111-3119.  
16210320 N.Tholema, M.Vor der Brüggen, P.Mäser, T.Nakamura, J.I.Schroeder, H.Kobayashi, N.Uozumi, and E.P.Bakker (2005).
All four putative selectivity filter glycine residues in KtrB are essential for high affinity and selective K+ uptake by the KtrAB system from Vibrio alginolyticus.
  J Biol Chem, 280, 41146-41154.  
15816175 P.C.Jordan (2005).
Semimicroscopic modeling of permeation energetics in ion channels.
  IEEE Trans Nanobioscience, 4, 94.  
16113726 R.Ida, and G.Wu (2005).
Solid-state 87Rb NMR signatures for rubidium cations bound to a G-quadruplex.
  Chem Commun (Camb), 0, 4294-4296.  
15816172 R.J.French, and G.W.Zamponi (2005).
Voltage-gated sodium and calcium channels in nerve, muscle, and heart.
  IEEE Trans Nanobioscience, 4, 58-69.  
15837197 S.Bernèche, and B.Roux (2005).
A gate in the selectivity filter of potassium channels.
  Structure, 13, 591-600.
PDB code: 1s33
  16316974 S.H.Yeh, H.K.Chang, and R.C.Shieh (2005).
Electrostatics in the cytoplasmic pore produce intrinsic inward rectification in kir2.1 channels.
  J Gen Physiol, 126, 551-562.  
15749783 S.Haider, A.Grottesi, B.A.Hall, F.M.Ashcroft, and M.S.Sansom (2005).
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.
  Biophys J, 88, 3310-3320.  
15816169 S.J.Korn, and J.G.Trapani (2005).
Potassium channels.
  IEEE Trans Nanobioscience, 4, 21-33.  
15783362 S.Mafé, and J.Pellicer (2005).
Ion conduction in the KcsA potassium channel analyzed with a minimal kinetic model.
  Phys Rev E Stat Nonlin Soft Matter Phys, 71, 022901.  
15945769 S.Mafé, J.Pellicer, and J.Cervera (2005).
Kinetic modeling of ion conduction in KcsA potassium channel.
  J Chem Phys, 122, 204712.  
15697580 S.Savel'ev, F.Marchesoni, and F.Nori (2005).
Interacting particles on a rocked ratchet: rectification by condensation.
  Phys Rev E Stat Nonlin Soft Matter Phys, 71, 011107.  
16035914 S.Savel'ev, and F.Nori (2005).
Controlling the motion of interacting particles: homogeneous systems and binary mixtures.
  Chaos, 15, 26112.  
  16043773 T.I.Brelidze, and K.L.Magleby (2005).
Probing the geometry of the inner vestibule of BK channels with sugars.
  J Gen Physiol, 126, 105-121.  
15980164 X.Wang, T.A.Ponoran, R.L.Rasmusson, D.S.Ragsdale, and B.Z.Peterson (2005).
Amino acid substitutions in the pore of the Ca(V)1.2 calcium channel reduce barium currents without affecting calcium currents.
  Biophys J, 89, 1731-1743.  
  15226365 A.Boccaccio, F.Conti, B.M.Olivera, and H.Terlau (2004).
Binding of kappa-conotoxin PVIIA to Shaker K+ channels reveals different K+ and Rb+ occupancies within the ion channel pore.
  J Gen Physiol, 124, 71-81.  
15240462 C.Domene, A.Grottesi, and M.S.Sansom (2004).
Filter flexibility and distortion in a bacterial inward rectifier K+ channel: simulation studies of KirBac1.1.
  Biophys J, 87, 256-267.  
15070737 D.Bichet, Y.F.Lin, C.A.Ibarra, C.S.Huang, B.A.Yi, Y.N.Jan, and L.Y.Jan (2004).
Evolving potassium channels by means of yeast selection reveals structural elements important for selectivity.
  Proc Natl Acad Sci U S A, 101, 4441-4446.  
14990473 D.L.Prole, and N.V.Marrion (2004).
Ionic permeation and conduction properties of neuronal KCNQ2/KCNQ3 potassium channels.
  Biophys J, 86, 1454-1469.  
  14981137 F.Gómez-Lagunas, C.V.Batista, T.Olamendi-Portugal, M.E.Ramírez-Domínguez, and L.D.Possani (2004).
Inhibition of the collapse of the Shaker K+ conductance by specific scorpion toxins.
  J Gen Physiol, 123, 265-279.  
15041654 H.Choi, and L.Heginbotham (2004).
Functional influence of the pore helix glutamate in the KcsA K+ channel.
  Biophys J, 86, 2137-2144.  
15446937 H.J.Woo, A.R.Dinner, and B.Roux (2004).
Grand canonical Monte Carlo simulations of water in protein environments.
  J Chem Phys, 121, 6392-6400.  
14747319 J.Cohen, and K.Schulten (2004).
Mechanism of anionic conduction across ClC.
  Biophys J, 86, 836-845.  
15447477 J.Piasecki, R.J.Allen, and J.P.Hansen (2004).
Kinetic models of ion transport through a nanopore.
  Phys Rev E Stat Nonlin Soft Matter Phys, 70, 021105.  
  15337818 J.W.Karpen (2004).
Ion channel structure and the promise of bacteria: cyclic nucleotide-gated channels in the queue.
  J Gen Physiol, 124, 199-201.  
  15078916 K.L.Németh-Cahalan, K.Kalman, and J.E.Hall (2004).
Molecular basis of pH and Ca2+ regulation of aquaporin water permeability.
  J Gen Physiol, 123, 573-580.  
15130477 M.A.Schumacher, M.Crum, and M.C.Miller (2004).
Crystal structures of apocalmodulin and an apocalmodulin/SK potassium channel gating domain complex.
  Structure, 12, 849-860.
PDB codes: 1qx5 1qx7
  14725766 N.Chakrabarti, E.Tajkhorshid, B.Roux, and R.Pomès (2004).
Molecular basis of proton blockage in aquaporins.
  Structure, 12, 65-74.  
15361618 S.Khademi, J.O'Connell, J.Remis, Y.Robles-Colmenares, L.J.Miercke, and R.M.Stroud (2004).
Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A.
  Science, 305, 1587-1594.
PDB codes: 1u77 1u7c 1u7g
15034178 S.M.Saparov, and P.Pohl (2004).
Beyond the diffusion limit: Water flow through the empty bacterial potassium channel.
  Proc Natl Acad Sci U S A, 101, 4805-4809.  
15169211 S.Savel'ev, F.Marchesoni, and F.Nori (2004).
Manipulating small particles in mixtures far from equilibrium.
  Phys Rev Lett, 92, 160602.  
15483608 S.Y.Noskov, S.Bernèche, and B.Roux (2004).
Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands.
  Nature, 431, 830-834.  
15111400 T.Chou (2004).
Water alignment, dipolar interactions, and multiple proton occupancy during water-wire proton transport.
  Biophys J, 86, 2827-2836.  
15189852 V.L.Dorman, and P.C.Jordan (2004).
Ionic permeation free energy in gramicidin: a semimicroscopic perspective.
  Biophys J, 86, 3529-3541.  
15454434 W.Welch, S.Rheault, D.J.West, and A.J.Williams (2004).
A model of the putative pore region of the cardiac ryanodine receptor channel.
  Biophys J, 87, 2335-2351.  
14977398 Z.Lu (2004).
Mechanism of rectification in inward-rectifier K+ channels.
  Annu Rev Physiol, 66, 103-129.  
12866052 A.Burykin, M.Kato, and A.Warshel (2003).
Exploring the origin of the ion selectivity of the KcsA potassium channel.
  Proteins, 52, 412-426.  
13679372 A.J.Labro, A.L.Raes, I.Bellens, N.Ottschytsch, and D.J.Snyders (2003).
Gating of shaker-type channels requires the flexibility of S6 caused by prolines.
  J Biol Chem, 278, 50724-50731.  
14581184 C.Domene, and M.S.Sansom (2003).
Potassium channel, ions, and water: simulation studies based on the high resolution X-ray structure of KcsA.
  Biophys J, 85, 2787-2800.  
12668443 C.E.Capener, P.Proks, F.M.Ashcroft, and M.S.Sansom (2003).
Filter flexibility in a mammalian K channel: models and simulations of Kir6.2 mutants.
  Biophys J, 84, 2345-2356.  
14618155 D.Bichet, F.A.Haass, and L.Y.Jan (2003).
Merging functional studies with structures of inward-rectifier K(+) channels.
  Nat Rev Neurosci, 4, 957-967.  
14675526 D.E.Clapham, R.MacKinnon, and P.Agre (2003).
Symmetry, selectivity, and the 2003 Nobel Prize.
  Cell, 115, 641-646.  
  12642596 D.Guo, Y.Ramu, A.M.Klem, and Z.Lu (2003).
Mechanism of rectification in inward-rectifier K+ channels.
  J Gen Physiol, 121, 261-275.  
  14581581 D.Guo, and Z.Lu (2003).
Interaction mechanisms between polyamines and IRK1 inward rectifier K+ channels.
  J Gen Physiol, 122, 485-500.  
14581200 D.Lu, P.Grayson, and K.Schulten (2003).
Glycerol conductance and physical asymmetry of the Escherichia coli glycerol facilitator GlpF.
  Biophys J, 85, 2977-2987.  
12689355 H.Shimizu, C.Toyoshima, and S.Oiki (2003).
Interaction between tetraethylammonium and permeant cations at the inactivation gate of the HERG potassium channel.
  Jpn J Physiol, 53, 25-34.  
  12695485 J.B.Park, H.J.Kim, P.D.Ryu, and E.Moczydlowski (2003).
Effect of phosphatidylserine on unitary conductance and Ba2+ block of the BK Ca2+-activated K+ channel: re-examination of the surface charge hypothesis.
  J Gen Physiol, 121, 375-397.  
  12566539 J.F.Consiglio, P.Andalib, and S.J.Korn (2003).
Influence of pore residues on permeation properties in the Kv2.1 potassium channel. Evidence for a selective functional interaction of K+ with the outer vestibule.
  J Gen Physiol, 121, 111-124.  
12629596 J.J.Gargus (2003).
Unraveling monogenic channelopathies and their implications for complex polygenic disease.
  Am J Hum Genet, 72, 785-803.  
  12885878 J.Thompson, and T.Begenisich (2003).
External TEA block of shaker K+ channels is coupled to the movement of K+ ions within the selectivity filter.
  J Gen Physiol, 122, 239-246.  
12665608 J.Thompson, and T.Begenisich (2003).
Functional identification of ion binding sites at the internal end of the pore in Shaker K+ channels.
  J Physiol, 549, 107-120.  
  12835471 K.Hui, D.McIntyre, and R.J.French (2003).
Conotoxins as sensors of local pH and electrostatic potential in the outer vestibule of the sodium channel.
  J Gen Physiol, 122, 63-79.  
14504281 K.M.Dibb, T.Rose, S.Y.Makary, T.W.Claydon, D.Enkvetchakul, R.Leach, C.G.Nichols, and M.R.Boyett (2003).
Molecular basis of ion selectivity, block, and rectification of the inward rectifier Kir3.1/Kir3.4 K(+) channel.
  J Biol Chem, 278, 49537-49548.  
12719213 M.B.Jackson (2003).
Subtle shades of permeability.
  Biophys J, 84, 2793-2794.  
12547775 M.Shahidullah, and M.Covarrubias (2003).
The link between ion permeation and inactivation gating of Kv4 potassium channels.
  Biophys J, 84, 928-941.  
12518045 P.Artigas, and D.C.Gadsby (2003).
Na+/K+-pump ligands modulate gating of palytoxin-induced ion channels.
  Proc Natl Acad Sci U S A, 100, 501-505.  
14754235 P.H.Nelson (2003).
Modeling the concentration-dependent permeation modes of the KcsA potassium ion channel.
  Phys Rev E Stat Nonlin Soft Matter Phys, 68, 061908.  
12649487 R.Dutzler, E.B.Campbell, and R.MacKinnon (2003).
Gating the selectivity filter in ClC chloride channels.
  Science, 300, 108-112.
PDB codes: 1ots 1ott 1otu
14622016 R.E.Middleton, M.Sanchez, A.R.Linde, R.M.Bugianesi, G.Dai, J.P.Felix, S.L.Koprak, M.J.Staruch, M.Bruguera, R.Cox, A.Ghosh, J.Hwang, S.Jones, M.Kohler, R.S.Slaughter, O.B.McManus, G.J.Kaczorowski, and M.L.Garcia (2003).
Substitution of a single residue in Stichodactyla helianthus peptide, ShK-Dap22, reveals a novel pharmacological profile.
  Biochemistry, 42, 13698-13707.  
12655069 S.C.Burdette, and S.J.Lippard (2003).
Meeting of the minds: metalloneurochemistry.
  Proc Natl Acad Sci U S A, 100, 3605-3610.  
12719216 S.Garofoli, and P.C.Jordan (2003).
Modeling permeation energetics in the KcsA potassium channel.
  Biophys J, 84, 2814-2830.  
12719220 T.BaÅŸtuÄŸ, and S.Kuyucak (2003).
Role of the dielectric constants of membrane proteins and channel water in ion permeation.
  Biophys J, 84, 2871-2882.  
12885642 U.Zachariae, V.Helms, and H.Engelhardt (2003).
Multistep mechanism of chloride translocation in a strongly anion-selective porin channel.
  Biophys J, 85, 954-962.  
  14610019 X.Gong, and P.Linsdell (2003).
Mutation-induced blocker permeability and multiion block of the CFTR chloride channel pore.
  J Gen Physiol, 122, 673-687.  
12679371 X.Gong, and P.Linsdell (2003).
Coupled movement of permeant and blocking ions in the CFTR chloride channel pore.
  J Physiol, 549, 375-385.  
12679372 X.Gong, and P.Linsdell (2003).
Molecular determinants and role of an anion binding site in the external mouth of the CFTR chloride channel pore.
  J Physiol, 549, 387-397.  
  12084770 A.Bucchi, M.Baruscotti, and D.DiFrancesco (2002).
Current-dependent block of rabbit sino-atrial node I(f) channels by ivabradine.
  J Gen Physiol, 120, 1.  
11948781 A.Burykin, C.N.Schutz, J.Villá, and A.Warshel (2002).
Simulations of ion current in realistic models of ion channels: the KcsA potassium channel.
  Proteins, 47, 265-280.  
12187317 A.S.Yu (2002).
Elucidating the structural basis of membrane transport protein function: light at the end of the channel?
  Curr Opin Nephrol Hypertens, 11, 523-526.  
12133841 B.Gilquin, J.Racapé, A.Wrisch, V.Visan, A.Lecoq, S.Grissmer, A.Ménez, and S.Gasparini (2002).
Structure of the BgK-Kv1.1 complex based on distance restraints identified by double mutant cycles. Molecular basis for convergent evolution of Kv1 channel blockers.
  J Biol Chem, 277, 37406-37413.  
11959495 B.Roux (2002).
Theoretical and computational models of ion channels.
  Curr Opin Struct Biol, 12, 182-189.  
  12198089 C.M.Nimigean, and C.Miller (2002).
Na+ block and permeation in a K+ channel of known structure.
  J Gen Physiol, 120, 323-335.  
  12045251 D.Kozono, M.Yasui, L.S.King, and P.Agre (2002).
Aquaporin water channels: atomic structure molecular dynamics meet clinical medicine.
  J Clin Invest, 109, 1395-1399.  
  12356854 F.M.Mullins, S.Z.Stepanovic, R.R.Desai, A.L.George, and J.R.Balser (2002).
Extracellular sodium interacts with the HERG channel at an outer pore site.
  J Gen Physiol, 120, 517-537.  
12414680 G.Li, and Q.Cui (2002).
A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase.
  Biophys J, 83, 2457-2474.  
12214225 G.Yellen (2002).
The voltage-gated potassium channels and their relatives.
  Nature, 419, 35-42.  
12062021 J.J.Rosenthal, and F.Bezanilla (2002).
Extensive editing of mRNAs for the squid delayed rectifier K+ channel regulates subunit tetramerization.
  Neuron, 34, 743-757.  
11818082 M.S.Sansom, and I.H.Shrivastava (2002).
Ion channels: frozen motion.
  Curr Biol, 12, R65-R67.  
12037552 M.Schumacher, and J.P.Adelman (2002).
Ion channels: an open and shut case.
  Nature, 417, 501-502.  
12324408 P.C.Biggin, and M.S.Sansom (2002).
Open-state models of a potassium channel.
  Biophys J, 83, 1867-1876.  
11959905 P.Mäser, Y.Hosoo, S.Goshima, T.Horie, B.Eckelman, K.Yamada, K.Yoshida, E.P.Bakker, A.Shinmyo, S.Oiki, J.I.Schroeder, and N.Uozumi (2002).
Glycine residues in potassium channel-like selectivity filters determine potassium selectivity in four-loop-per-subunit HKT transporters from plants.
  Proc Natl Acad Sci U S A, 99, 6428-6433.  
  11865020 R.F.Rakowski, D.C.Gadsby, and P.De Weer (2002).
Single ion occupancy and steady-state gating of Na channels in squid giant axon.
  J Gen Physiol, 119, 235-249.  
11988468 R.H.Spencer, and D.C.Rees (2002).
The alpha-helix and the organization and gating of channels.
  Annu Rev Biophys Biomol Struct, 31, 207-233.  
11907549 R.MacKinnon (2002).
Nothing automatic about ion-channel structures.
  Nature, 416, 261-262.  
  12149281 R.O.Blaustein (2002).
Kinetics of tethering quaternary ammonium compounds to K(+) channels.
  J Gen Physiol, 120, 203-216.  
12372287 R.Schönherr, L.M.Mannuzzu, E.Y.Isacoff, and S.H.Heinemann (2002).
Conformational switch between slow and fast gating modes: allosteric regulation of voltage sensor mobility in the EAG K+ channel.
  Neuron, 35, 935-949.  
  12084778 S.Ding, and R.Horn (2002).
Tail end of the s6 segment: role in permeation in shaker potassium channels.
  J Gen Physiol, 120, 87-97.  
12080118 S.H.Chung, T.W.Allen, and S.Kuyucak (2002).
Modeling diverse range of potassium channels with Brownian dynamics.
  Biophys J, 83, 263-277.  
12411513 Y.Murata, Y.Fujiwara, and Y.Kubo (2002).
Identification of a site involved in the block by extracellular Mg(2+) and Ba(2+) as well as permeation of K(+) in the Kir2.1 K(+) channel.
  J Physiol, 544, 665-677.  
11842204 Y.Shen, Y.Kong, and J.Ma (2002).
Intrinsic flexibility and gating mechanism of the potassium channel KcsA.
  Proc Natl Acad Sci U S A, 99, 1949-1953.  
  12407078 Z.Lu, A.M.Klem, and Y.Ramu (2002).
Coupling between voltage sensors and activation gate in voltage-gated K+ channels.
  J Gen Physiol, 120, 663-676.  
11723466 G.Yellen (2001).
Keeping K+ completely comfortable.
  Nat Struct Biol, 8, 1011-1013.  
  11738961 N.Baderman, J.Clough, J.Milburn, J.Owens, and B.Ramster (2001).
News in brief.
  Drug Discov Today, 6, 1249-1254.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.