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Contents |
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212 a.a.
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219 a.a.
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103 a.a.
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* Residue conservation analysis
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PDB id:
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| Name: |
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Membrane protein
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Title:
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Potassium channel kcsa-fab complex in low concentration of tl+
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Structure:
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Antibody fab fragment light chain. Chain: a. Antibody fab fragment heavy chain. Chain: b. Voltage-gated potassium channel. Chain: c. Engineered: yes. Mutation: yes
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Source:
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Mus musculus. House mouse. Organism_taxid: 10090. Streptomyces lividans. Organism_taxid: 1916. Gene: kcsa, skc1, sco7660, sc10f4.33. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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Dodecamer (from PDB file)
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Resolution:
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2.80Å
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R-factor:
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0.238
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R-free:
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0.273
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Authors:
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Y.Zhou,R.Mackinnon
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Key ref:
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Y.Zhou
and
R.MacKinnon
(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.
PubMed id:
DOI:
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Date:
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02-Oct-03
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Release date:
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25-Nov-03
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PROCHECK
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Headers
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References
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P01837
(IGKC_MOUSE) -
Immunoglobulin kappa constant from Mus musculus
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Seq:
Struc:
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107 a.a.
212 a.a.
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DOI no:
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J Mol Biol
333:965-975
(2003)
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PubMed id:
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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.
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Y.Zhou,
R.MacKinnon.
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ABSTRACT
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Potassium ions diffuse across the cell membrane in a single file through the
narrow selectivity filter of potassium channels. The crystal structure of the
KcsA K+ channel revealed the chemical structure of the selectivity filter, which
contains four binding sites for K+. In this study, we used Tl+ in place of K+ to
address the question of how many ions bind within the filter at a given time,
i.e. what is the absolute ion occupancy? By refining the Tl+ structure against
data to 1.9A resolution with an anomalous signal, we determined the absolute
occupancy of Tl+. Then, by comparing the electron density of Tl+ with that of
K+, Rb+ and Cs+, we estimated the absolute occupancy of these three ions. We
further analyzed how the ion occupancy affects the conformation of the
selectivity filter by analyzing the structure of KcsA at different
concentrations of Tl+. Our results indicate that the average occupancy for each
site in the selectivity filter is about 0.63 for Tl+ and 0.53 for K+. For K+,
Rb+ and Cs+, the total number of ions contained within four sites in the
selectivity filter is about two. At low concentrations of permeant ion, the
number of ions drops to one in association with a conformational change in the
selectivity filter. We conclude that electrostatic balance and coupling of ion
binding to a protein conformational change underlie high conduction rates in the
setting of high selectivity.
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Selected figure(s)
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Figure 5.
Figure 5. The selectivity filter conformation in A 3 mM
K+ or B 25 mM Tl+. Both structures are presented the
same way as in Figure 1B and C.
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Figure 7.
Figure 7. Transition between low- and high-ion
structures may be important for high conduction rates.
A, Experimentally observed conformational change
when the occupancy in the selectivity filter changes
from 1.0 to 2.0 ions. B, In a hypothetical case, the
selectivity filter is held in a pre-formed, high-ion
structure. Two ions will bind with lower affinity if
binding energy is used to perform work to change the
protein's conformation.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2003,
333,
965-975)
copyright 2003.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Alam,
and
Y.Jiang
(2011).
Structural studies of ion selectivity in tetrameric cation channels.
|
| |
J Gen Physiol,
137,
397-403.
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|
|
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|
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C.Boiteux,
and
S.Bernèche
(2011).
Absence of ion-binding affinity in the putatively inactivated low-[K+] structure of the KcsA potassium channel.
|
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Structure,
19,
70-79.
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|
|
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|
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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.
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Curr Opin Struct Biol,
21,
68-80.
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A.B.Waight,
J.Love,
and
D.N.Wang
(2010).
Structure and mechanism of a pentameric formate channel.
|
| |
Nat Struct Mol Biol,
17,
31-37.
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PDB codes:
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E.J.Denning,
and
T.B.Woolf
(2010).
Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations.
|
| |
Proteins,
78,
1105-1119.
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H.Yu,
S.Y.Noskov,
and
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(2010).
Two mechanisms of ion selectivity in protein binding sites.
|
| |
Proc Natl Acad Sci U S A,
107,
20329-20334.
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L.G.Cuello,
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D.M.Cortes,
and
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(2010).
Structural mechanism of C-type inactivation in K(+) channels.
|
| |
Nature,
466,
203-208.
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|
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|
|
|
M.Ã.˜.Jensen,
D.W.Borhani,
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V.Jogini,
M.P.Eastwood,
R.O.Dror,
and
D.E.Shaw
(2010).
Principles of conduction and hydrophobic gating in K+ channels.
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Proc Natl Acad Sci U S A,
107,
5833-5838.
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|
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P.J.Focke,
and
F.I.Valiyaveetil
(2010).
Studies of ion channels using expressed protein ligation.
|
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Curr Opin Chem Biol,
14,
797-802.
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|
|
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|
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S.Ye,
Y.Li,
and
Y.Jiang
(2010).
Novel insights into K+ selectivity from high-resolution structures of an open K+ channel pore.
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Nat Struct Mol Biol,
17,
1019-1023.
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PDB codes:
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A.Alam,
and
Y.Jiang
(2009).
Structural analysis of ion selectivity in the NaK channel.
|
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Nat Struct Mol Biol,
16,
35-41.
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PDB codes:
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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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PDB codes:
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B.Liu,
J.Yao,
Y.Wang,
H.Li,
and
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(2009).
Proton inhibition of unitary currents of vanilloid receptors.
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and
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(2009).
Concerted action of two cation filters in the aquaporin water channel.
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28,
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C.Miller,
and
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A provisional transport mechanism for a chloride channel-type Cl-/H+ exchanger.
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364,
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and
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(2009).
Statistical determinants of selective ionic complexation: ions in solvent, transport proteins, and other "hosts".
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| |
Biophys J,
96,
4470-4492.
|
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L.Wang,
A.T.Dennis,
P.Trieu,
F.Charron,
N.Ethier,
T.E.Hebert,
X.Wan,
and
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(2009).
Intracellular potassium stabilizes human ether-à-go-go-related gene channels for export from endoplasmic reticulum.
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| |
Mol Pharmacol,
75,
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P.D.Kiser,
G.H.Lorimer,
and
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Use of thallium to identify monovalent cation binding sites in GroEL.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun,
65,
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PDB code:
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S.Furini,
and
C.Domene
(2009).
Atypical mechanism of conduction in potassium channels.
|
| |
Proc Natl Acad Sci U S A,
106,
16074-16077.
|
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|
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S.Wang,
Y.Alimi,
A.Tong,
C.G.Nichols,
and
D.Enkvetchakul
(2009).
Differential Roles of Blocking Ions in KirBac1.1 Tetramer Stability.
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J Biol Chem,
284,
2854-2860.
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|
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Z.Kuras,
and
S.Grissmer
(2009).
Effect of K+ and Rb+ on the action of verapamil on a voltage-gated K+ channel, hKv1.3: implications for a second open state?
|
| |
Br J Pharmacol,
157,
757-768.
|
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|
|
|
|
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A.K.Lyashchenko,
and
G.R.Tibbs
(2008).
Ion binding in the open HCN pacemaker channel pore: fast mechanisms to shape "slow" channels.
|
| |
J Gen Physiol,
131,
227-243.
|
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|
|
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|
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D.Zhan,
F.R.Fan,
and
A.J.Bard
(2008).
The Kv channel blocker 4-aminopyridine enhances Ag+ uptake: a scanning electrochemical microscopy study of single living cells.
|
| |
Proc Natl Acad Sci U S A,
105,
12118-12122.
|
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|
|
|
|
|
I.Schroeder,
and
U.P.Hansen
(2008).
Tl+-induced micros gating of current indicates instability of the MaxiK selectivity filter as caused by ion/pore interaction.
|
| |
J Gen Physiol,
131,
365-378.
|
|
|
|
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|
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I.V.Khavrutskii,
M.Fajer,
and
J.A.McCammon
(2008).
Intrinsic Free Energy of the Conformational Transition of the KcsA Signature Peptide from Conducting to Nonconducting State.
|
| |
J Chem Theory Comput,
4,
1541-1554.
|
|
|
|
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|
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J.E.Contreras,
D.Srikumar,
and
M.Holmgren
(2008).
Gating at the selectivity filter in cyclic nucleotide-gated channels.
|
| |
Proc Natl Acad Sci U S A,
105,
3310-3314.
|
|
|
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|
|
J.Payandeh,
C.Li,
M.Ramjeesingh,
E.Poduch,
C.E.Bear,
and
E.F.Pai
(2008).
Probing structure-function relationships and gating mechanisms in the CorA Mg2+ transport system.
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| |
J Biol Chem,
283,
11721-11733.
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N.Suzuki,
Y.Yamazaki,
R.L.Brown,
Z.Fujimoto,
T.Morita,
and
H.Mizuno
(2008).
Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: implications for movement of the C-terminal cysteine-rich domain.
|
| |
Acta Crystallogr D Biol Crystallogr,
64,
1034-1042.
|
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PDB codes:
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O.Zaika,
C.C.Hernandez,
M.Bal,
G.P.Tolstykh,
and
M.S.Shapiro
(2008).
Determinants within the turret and pore-loop domains of KCNQ3 K+ channels governing functional activity.
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Biophys J,
95,
5121-5137.
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S.Varma,
and
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(2008).
Structural transitions in ion coordination driven by changes in competition for ligand binding.
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130,
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Y.Zhou,
and
J.E.Huettner
(2008).
Amino acid substitutions in the pore helix of GluR6 control inhibition by membrane fatty acids.
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J Gen Physiol,
132,
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and
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(2007).
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92,
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and
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Ion conductance vs. pore gating and selectivity in KcsA channel: modeling achievements and perspectives.
|
| |
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13,
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and
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Biophys J,
93,
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D.Boda,
W.Nonner,
M.Valiskó,
D.Henderson,
B.Eisenberg,
and
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(2007).
Steric selectivity in Na channels arising from protein polarization and mobile side chains.
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Biophys J,
93,
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D.Bucher,
L.Guidoni,
and
U.Rothlisberger
(2007).
The protonation state of the Glu-71/Asp-80 residues in the KcsA potassium channel: a first-principles QM/MM molecular dynamics study.
|
| |
Biophys J,
93,
2315-2324.
|
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D.L.Bostick,
and
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(2007).
Deprotonation by dehydration: the origin of ammonium sensing in the AmtB channel.
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PLoS Comput Biol,
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G.Gibor,
D.Yakubovich,
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N.Dascal,
D.E.Logothetis,
Y.Paas,
and
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An inactivation gate in the selectivity filter of KCNQ1 potassium channels.
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and
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I.Schroeder,
and
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Saturation and microsecond gating of current indicate depletion-induced instability of the MaxiK selectivity filter.
|
| |
J Gen Physiol,
130,
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M.Yeager,
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PDB code:
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| |
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PDB codes:
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A.Lange,
K.Giller,
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and
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J Gen Physiol,
128,
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C.M.Wilkens,
and
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(2006).
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D.Asthagiri,
L.R.Pratt,
and
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(2006).
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|
| |
J Chem Phys,
125,
24701.
|
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|
E.C.Ray,
and
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(2006).
A trapped intracellular cation modulates K+ channel recovery from slow inactivation.
|
| |
J Gen Physiol,
128,
203-217.
|
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|
F.I.Valiyaveetil,
M.Leonetti,
T.W.Muir,
and
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(2006).
Ion selectivity in a semisynthetic K+ channel locked in the conductive conformation.
|
| |
Science,
314,
1004-1007.
|
|
|
PDB codes:
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|
|
|
|
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|
F.I.Valiyaveetil,
M.Sekedat,
R.MacKinnon,
and
T.W.Muir
(2006).
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.
|
|
|
PDB codes:
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|
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|
|
I.S.Tolokh,
S.Goldman,
and
C.G.Gray
(2006).
Unified modeling of conductance kinetics for low- and high-conductance potassium ion channels.
|
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Where a reference describes a PDB structure, the PDB
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