-
1
-
-
0029666231
-
Nonselective and G-Beta/Gamma-Insensitive Weaver K+ Channels
-
Navarro B, Kennedy ME, Velimirovic B, Bhat D, Peterson AS, et al. (1996) Nonselective and G-Beta/Gamma-Insensitive Weaver K+ Channels. Science 272: 1950-1953.
-
(1996)
Science
, vol.272
, pp. 1950-1953
-
-
Navarro, B.1
Kennedy, M.E.2
Velimirovic, B.3
Bhat, D.4
Peterson, A.S.5
-
3
-
-
0015424492
-
Negative conductance caused by entry of sodium and cesium ions into the potassium channels of squid axons
-
Bezanilla F, Armstrong CM (1972) Negative conductance caused by entry of sodium and cesium ions into the potassium channels of squid axons. J Gen Physiol 60: 588-608.
-
(1972)
J Gen Physiol
, vol.60
, pp. 588-608
-
-
Bezanilla, F.1
Armstrong, C.M.2
-
4
-
-
33748263658
-
The potassium permeability of a giant nerve fibre
-
Hodgkin AL, Keynes RD (1955) The potassium permeability of a giant nerve fibre. J Physiol 128: 61-88.
-
(1955)
J Physiol
, vol.128
, pp. 61-88
-
-
Hodgkin, A.L.1
Keynes, R.D.2
-
5
-
-
0032478818
-
+ conduction and selectivity
-
DOI 10.1126/science.280.5360.69
-
Doyle DA, Cabral JM, Pfuetzner RA, Kuo A, Gulbis JM, et al. (1998) The structure of the potassium channel: molecular basis of K conduction and selectivity. Science 280: 69-77. (Pubitemid 28169082)
-
(1998)
Science
, vol.280
, Issue.5360
, pp. 69-77
-
-
Doyle, D.A.1
Cabral, J.M.2
Pfuetzner, R.A.3
Kuo, A.4
Gulbis, J.M.5
Cohen, S.L.6
Chait, B.T.7
MacKinnon, R.8
-
6
-
-
0035499447
-
Energetic optimization of ion conduction rate by the K selectivity filter
-
Morais-Cabral JH, Zhou Y, MacKinnon R (2001) Energetic optimization of ion conduction rate by the K selectivity filter. Nature 414: 37-42.
-
(2001)
Nature
, vol.414
, pp. 37-42
-
-
Morais-Cabral, J.H.1
Zhou, Y.2
MacKinnon, R.3
-
7
-
-
0035498860
-
+ channel
-
DOI 10.1038/35102067
-
Berneche S, Roux B (2001) Energetics of ion conduction through the K+ channel. Nature 414: 73-77. (Pubitemid 33041625)
-
(2001)
Nature
, vol.414
, Issue.6859
, pp. 73-77
-
-
Berneche, S.1
Roux, B.2
-
9
-
-
79958031754
-
Selectivity and permeation of alkali metal ions in K+-channels
-
Furini S, Domene C (2011) Selectivity and permeation of alkali metal ions in K+-channels. J Mol Biol 409: 867-878.
-
(2011)
J Mol Biol
, vol.409
, pp. 867-878
-
-
Furini, S.1
Domene, C.2
-
10
-
-
77950544751
-
Principles of conduction and hydrophobic gating in K+ channels
-
Jensen MO, Borhani DW, Lindorff-Larsen K, Maragakis P, Jogini V, et al. (2010) Principles of conduction and hydrophobic gating in K+ channels. Proc Natl Acad Sci U S A 107: 5833-5838.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 5833-5838
-
-
Jensen, M.O.1
Borhani, D.W.2
Lindorff-Larsen, K.3
Maragakis, P.4
Jogini, V.5
-
11
-
-
79956067240
-
Perspectives on: Ion Selectivity
-
Andersen OS (2011) Perspectives on : Ion Selectivity. J Gen Physiol 137: 393-395.
-
(2011)
J Gen Physiol
, vol.137
, pp. 393-395
-
-
Andersen, O.S.1
-
12
-
-
10344245541
-
On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation
-
DOI 10.1085/jgp.200409111
-
Allen TW, Andersen OS, Roux B (2004) On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation. J Gen Physiol 124: 679-690. (Pubitemid 39628135)
-
(2004)
Journal of General Physiology
, vol.124
, Issue.6
, pp. 679-690
-
-
Allen, T.W.1
Andersen, O.S.2
Roux, B.3
-
13
-
-
79956123183
-
Structural studies of ion selectivity in tetrameric cation channels
-
Alam A, Jiang Y (2011) Structural studies of ion selectivity in tetrameric cation channels. J Gen Physiol 137: 397-403.
-
(2011)
J Gen Physiol
, vol.137
, pp. 397-403
-
-
Alam, A.1
Jiang, Y.2
-
14
-
-
33645318420
-
Atomic structure of a Na+- and K+-conducting channel
-
Shi N, Ye S, Alam A, Chen L, Jiang Y (2006) Atomic structure of a Na+- and K+-conducting channel. Nature 440: 570-574.
-
(2006)
Nature
, vol.440
, pp. 570-574
-
-
Shi, N.1
Ye, S.2
Alam, A.3
Chen, L.4
Jiang, Y.5
-
15
-
-
79551660280
-
Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites
-
Derebe MG, Sauer DB, Zeng W, Alam A, Shi N, et al. (2011) Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites. Proc Natl Acad Sci U S A 108: 598-602.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 598-602
-
-
Derebe, M.G.1
Sauer, D.B.2
Zeng, W.3
Alam, A.4
Shi, N.5
-
16
-
-
79958039013
-
Examining ion channel properties using free-energy methods
-
Domene C, Furini S (2009) Examining ion channel properties using free-energy methods. Methods Enzymol 466: 155-177.
-
(2009)
Methods Enzymol
, vol.466
, pp. 155-177
-
-
Domene, C.1
Furini, S.2
-
17
-
-
7244251461
-
Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands
-
DOI 10.1038/nature02943
-
Noskov SY, Berneche S, Roux B (2004) Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 431: 830-834. (Pubitemid 39434076)
-
(2004)
Nature
, vol.431
, Issue.7010
, pp. 830-834
-
-
Noskov, S.Y.1
Berneche, S.2
Roux, B.3
-
18
-
-
33846625994
-
Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels
-
DOI 10.1085/jgp.200609633
-
Noskov SY, Roux B (2007) Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels. J Gen Physiol 129: 135-143. (Pubitemid 46184871)
-
(2007)
Journal of General Physiology
, vol.129
, Issue.2
, pp. 135-143
-
-
Noskov, S.Yu.1
Roux, B.2
-
19
-
-
79958056648
-
Design principles for K+ selectivity in membrane transport
-
Varma S, Rogers DM, Pratt LR, Rempe SB (2011) Design principles for K+ selectivity in membrane transport. J Gen Physiol 137: 479-488.
-
(2011)
J Gen Physiol
, vol.137
, pp. 479-488
-
-
Varma, S.1
Rogers, D.M.2
Pratt, L.R.3
Rempe, S.B.4
-
20
-
-
38049095537
-
K+/Na + selectivity in K channels and valinomycin: Over-coordination versus cavity-size constraints
-
Varma S, Sabo D, Rempe SB (2008) K+/Na + selectivity in K channels and valinomycin: over-coordination versus cavity-size constraints. J Mol Biol 376: 13-22.
-
(2008)
J Mol Biol
, vol.376
, pp. 13-22
-
-
Varma, S.1
Sabo, D.2
Rempe, S.B.3
-
21
-
-
20544431525
-
Ion conduction and selectivity in K(+) channels
-
Roux B (2005) Ion conduction and selectivity in K(+) channels. Annu Rev Biophys Biomol Struct 34: 153-171.
-
(2005)
Annu Rev Biophys Biomol Struct
, vol.34
, pp. 153-171
-
-
Roux, B.1
-
22
-
-
0035499892
-
+ channel-Fab complex at 2.0 A resolution
-
DOI 10.1038/35102009
-
Zhou Y, Morais-Cabral JH, Kaufman A, MacKinnon R (2001) Chemistry of ion coordination and hydration revealed by a K channel-Fab complex at 2.0 A resolution. Nature 414: 43-48. (Pubitemid 33041616)
-
(2001)
Nature
, vol.414
, Issue.6859
, pp. 43-48
-
-
Zhou, Y.1
Morais-Cabral, J.H.2
Kaufman, A.3
Mackinnon, R.4
-
24
-
-
15244351990
-
Molecular dynamics simulation approaches to K channels: Conformational flexibility and physiological function
-
DOI 10.1109/TNB.2004.842473
-
Grottesi A, Domene C, Haider S, Sansom MS (2005) Molecular dynamics simulation approaches to K channels: conformational flexibility and physiological function. IEEE Trans Nanobioscience 4: 112-120. (Pubitemid 40384652)
-
(2005)
IEEE Transactions on Nanobioscience
, vol.4
, Issue.1
, pp. 112-120
-
-
Grottesi, A.1
Domene, C.2
Haider, S.3
Sansom, M.S.P.4
-
25
-
-
0035996966
-
+ ions in a K channel selectivity filter: A simulation study
-
Shrivastava IH, Tieleman DP, Biggin PC, Sansom MS (2002) K(+) versus Na(+) ions in a K channel selectivity filter: a simulation study. Biophysical journal 83: 633-645. (Pubitemid 34803605)
-
(2002)
Biophysical Journal
, vol.83
, Issue.2
, pp. 633-645
-
-
Shrivastava, I.H.1
Tieleman, D.P.2
Biggin, P.C.3
Sansom, M.S.P.4
-
26
-
-
0036714139
-
+ channel of known structure
-
DOI 10.1085/jgp.20028614
-
Nimigean CM, Miller C (2002) Na+ block and permeation in a K+ channel of known structure. J Gen Physiol 120: 323-335. (Pubitemid 35014732)
-
(2002)
Journal of General Physiology
, vol.120
, Issue.3
, pp. 323-335
-
-
Nimigean, C.M.1
Miller, C.2
-
27
-
-
77955550391
-
Ion selectivity of the KcsA channel: A perspective from multi-ion free energy landscapes
-
Egwolf B, Roux B (2010) Ion selectivity of the KcsA channel: a perspective from multi-ion free energy landscapes. J Mol Biol 401: 831-842.
-
(2010)
J Mol Biol
, vol.401
, pp. 831-842
-
-
Egwolf, B.1
Roux, B.2
-
28
-
-
33750609826
-
Ion selectivity in potassium channels
-
DOI 10.1016/j.bpc.2006.05.033, PII S0301462206001803
-
Noskov SY, Roux B (2006) Ion selectivity in potassium channels. Biophys Chem 124: 279-291. (Pubitemid 44692364)
-
(2006)
Biophysical Chemistry
, vol.124
, Issue.3
, pp. 279-291
-
-
Noskov, S.Yu.1
Roux, B.2
-
29
-
-
81055126297
-
On the selective ion binding hypothesis for potassium channels
-
Kim I, Allen TW (2011) On the selective ion binding hypothesis for potassium channels. Proc Natl Acad Sci U S A 108: 17963-17968.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 17963-17968
-
-
Kim, I.1
Allen, T.W.2
-
30
-
-
58149213832
-
Structural analysis of ion selectivity in the NaK channel
-
Alam A, Jiang Y (2009) Structural analysis of ion selectivity in the NaK channel. Nat Struct Mol Biol 16: 35-41.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 35-41
-
-
Alam, A.1
Jiang, Y.2
-
31
-
-
4243754128
-
Nonequilibrium equality for free energy differences
-
Jarzynski C (1997) Nonequilibrium equality for free energy differences. Phys Rev Lett 78: 2690-2693.
-
(1997)
Phys Rev Lett
, vol.78
, pp. 2690-2693
-
-
Jarzynski, C.1
-
32
-
-
84859013740
-
Parallel-pulling protocol for free-energy evaluation
-
Ngo VA (2012) Parallel-pulling protocol for free-energy evaluation. Physical Review E 85: 036702.
-
(2012)
Physical Review e
, vol.85
, pp. 036702
-
-
Ngo, V.A.1
-
33
-
-
84866939634
-
Demonstration of Jarzynski's equality in open quantum systems using a stepwise pulling protocol
-
Ngo VA, Haas S (2012) Demonstration of Jarzynski's equality in open quantum systems using a stepwise pulling protocol. Phys Rev E Stat Nonlin Soft Matter Phys 86: 031127.
-
(2012)
Phys Rev e Stat Nonlin Soft Matter Phys
, vol.86
, pp. 031127
-
-
Ngo, V.A.1
Haas, S.2
-
34
-
-
0042885340
-
Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality
-
Park S, Khalili-Araghi F, Tajkhorshid E, Schulten K (2003) Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality. J Chem Phys 119: 3559-3566.
-
(2003)
J Chem Phys
, vol.119
, pp. 3559-3566
-
-
Park, S.1
Khalili-Araghi, F.2
Tajkhorshid, E.3
Schulten, K.4
-
35
-
-
4143087050
-
Calculating potentials of mean force from steered molecular dynamics simulations
-
Park S, Schulten K (2004) Calculating potentials of mean force from steered molecular dynamics simulations. J Chem Phys 120: 5946-5961.
-
(2004)
J Chem Phys
, vol.120
, pp. 5946-5961
-
-
Park, S.1
Schulten, K.2
-
36
-
-
42149194240
-
Adaptive biasing force method for scalar and vector free energy calculations
-
Darve E, Rodriguez-Gomez D, Pohorille A (2008) Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys 128: 144120.
-
(2008)
J Chem Phys
, vol.128
, pp. 144120
-
-
Darve, E.1
Rodriguez-Gomez, D.2
Pohorille, A.3
-
37
-
-
36849122972
-
High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
-
Zwanzig RW (1954) High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases. J Chem Phys 22.
-
(1954)
J Chem Phys
, vol.22
-
-
Zwanzig, R.W.1
-
38
-
-
84986519238
-
The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules. 1. The Method
-
Kumar S, Bouzia D, Swendsen RH, Kollman PA, Rosenberg JM (1992) The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules. 1. The Method. Journal of Computational Chemistry 13: 1011-1021.
-
(1992)
Journal of Computational Chemistry
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzia, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
39
-
-
0042415783
-
NAMD2: Greater Scalability for Parallel Molecular Dynamics
-
Kalé L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, et al. (1999) NAMD2: Greater Scalability for Parallel Molecular Dynamics. Journal of Computational Physics 151: 283-312.
-
(1999)
Journal of Computational Physics
, vol.151
, pp. 283-312
-
-
Kalé, L.1
Skeel, R.2
Bhandarkar, M.3
Brunner, R.4
Gursoy, A.5
-
40
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
DOI 10.1002/jcc.20289
-
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26: 1781-1802. (Pubitemid 43078511)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
42
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell Jr A, Bashford D, Bellott M, Dunbrack Jr R, Evanseck J, et al. (1998) All-Atom Empirical Potential For Molecular Modeling and Dynamics Studies of Proteins. J Phys Chem B 102: 3586-3616. (Pubitemid 128576688)
-
(1998)
Journal of Physical Chemistry B
, vol.102
, Issue.18
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher III, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
43
-
-
4444351490
-
Empirical force fields for biological macromolecules: Overview and issues
-
Mackerell AD, Jr. (2004) Empirical force fields for biological macromolecules: overview and issues. J Comput Chem 25: 1584-1604.
-
(2004)
J Comput Chem
, vol.25
, pp. 1584-1604
-
-
Mackerell Jr., A.D.1
-
44
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
Mackerell AD, Jr., Feig M, Brooks CL, 3rd (2004) Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 25: 1400-1415.
-
(2004)
J Comput Chem
, vol.25
, pp. 1400-1415
-
-
Mackerell Jr., A.D.1
Feig, M.2
Brooks III, C.L.3
-
45
-
-
33750652614
-
Brownian dynamics with hydrodynamic interactions
-
Ermak DL, MacCammon JA (1978) Brownian dynamics with hydrodynamic interactions. J Chem Phys 69: 1352-1360.
-
(1978)
J Chem Phys
, vol.69
, pp. 1352-1360
-
-
Ermak, D.L.1
MacCammon, J.A.2
-
46
-
-
71449094441
-
Mechanism of potassium-channel selectivity revealed by Na(+) and Li(+) binding sites within the KcsA pore
-
Thompson AN, Kim I, Panosian TD, Iverson TM, Allen TW, et al. (2009) Mechanism of potassium-channel selectivity revealed by Na(+) and Li(+) binding sites within the KcsA pore. Nat Struct Mol Biol 16: 1317-1324.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 1317-1324
-
-
Thompson, A.N.1
Kim, I.2
Panosian, T.D.3
Iverson, T.M.4
Allen, T.W.5
-
48
-
-
0023823843
-
Discrete Ba2 + block as a probe of ion occupancy and pore structure in the high-conductance Ca2+ -activated K+ channel
-
Neyton J, Miller C (1988) Discrete Ba2 + block as a probe of ion occupancy and pore structure in the high-conductance Ca2+ -activated K+ channel. J Gen Physiol 92: 569-586.
-
(1988)
J Gen Physiol
, vol.92
, pp. 569-586
-
-
Neyton, J.1
Miller, C.2
-
49
-
-
0023709415
-
Potassium blocks barium permeation through a calcium-activated potassium channel
-
Neyton J, Miller C (1988) Potassium blocks barium permeation through a calcium-activated potassium channel. J Gen Physiol 92: 549-567.
-
(1988)
J Gen Physiol
, vol.92
, pp. 549-567
-
-
Neyton, J.1
Miller, C.2
-
50
-
-
84862867185
-
Why continuum electrostatics theories cannot explain biological structure, polyelectrolytes or ionic strength effects in ion-protein interactions
-
Collins KD (2012) Why continuum electrostatics theories cannot explain biological structure, polyelectrolytes or ionic strength effects in ion-protein interactions. Biophys Chem 167: 43-59.
-
(2012)
Biophys Chem
, vol.167
, pp. 43-59
-
-
Collins, K.D.1
-
51
-
-
0037120735
-
Dynamic hydration numbers for biologically important ions
-
Kiriukhin MY, Collins KD (2002) Dynamic hydration numbers for biologically important ions. Biophys Chem 99: 155-168.
-
(2002)
Biophys Chem
, vol.99
, pp. 155-168
-
-
Kiriukhin, M.Y.1
Collins, K.D.2
-
52
-
-
0018117903
-
Potassium channels as multi-ion single-file pores
-
DOI 10.1085/jgp.72.4.409
-
Hille B, Schwarz W (1978) Potassium channels as multi-ion single-file pores. J Gen Physiol 72: 409-442. (Pubitemid 9002761)
-
(1978)
Journal of General Physiology
, vol.72
, Issue.4
, pp. 409-442
-
-
Hille, B.1
Schwarz, W.2
-
53
-
-
0036286651
-
Modeling diverse range of potassium channels with Brownian dynamics
-
Chung SH, Allen TW, Kuyucak S (2002) Modeling diverse range of potassium channels with Brownian dynamics. Biophysical journal 83: 263-277. (Pubitemid 34694737)
-
(2002)
Biophysical Journal
, vol.83
, Issue.1
, pp. 263-277
-
-
Chung, S.-H.1
Allen, T.W.2
Kuyucak, S.3
-
54
-
-
0034690250
-
Ion permeation mechanism of the potassium channel
-
DOI 10.1038/35009114
-
Aqvist J, Luzhkov V (2000) Ion permeation mechanism of the potassium channel. Nature 404: 881-884. (Pubitemid 30230340)
-
(2000)
Nature
, vol.404
, Issue.6780
, pp. 881-884
-
-
Aqvist, J.1
Luzhkov, V.2
-
55
-
-
77953029106
-
Molecular simulations of ion channels: A quantum chemist's perspective
-
Bucher D, Rothlisberger U (2010) Molecular simulations of ion channels: a quantum chemist's perspective. J Gen Physiol 135: 549-554.
-
(2010)
J Gen Physiol
, vol.135
, pp. 549-554
-
-
Bucher, D.1
Rothlisberger, U.2
|