Computational studies of membrane channels
Open accessAbstract
The determination of the structure of several members of the K+ channel and aquaporin family represents a unique opportunity to explain the mechanism of these biomolecular systems. With their ability to go beyond static structures, molecular dynamics simulations offer a unique route for relating functional properties to membrane channel structure. The recent progress in this area is reviewed.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In model channels such as the bacterial KcsA channel, one K+ ion crosses the channel per 10-20 ns under physiological conductances of roughly 80-100 pS.
“In model channels such as the bacterial KcsA channel one K+ ion crosses the channel per 10–20 ns under physiological conductances of roughly 80–100 pS [84], which is consistent with the frequencies of external electric stimulation mentioned above.”
From An Overview of Sub-Cellular Mechanisms Involved in the Action of TTFields (2016) · cites this paper as [84]
Cites
VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952 · see citing works
Self-citationHodgkin, A. L., & Huxley, A. F. (1952) · The Journal of Physiology · doi:10.1113/jphysiol.1952.sp004764 · Cited by 23,191 · see citing works
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp973084f · Cited by 14,270 · see citing works
Self-citationCHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Brooks, B., Bruccoleri, R., Olafson, B. D., States, D., Swaminathan, S., & Karplus, M. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040211 · Cited by 13,736 · see citing works
The Structure of the Potassium Channel: Molecular Basis of K + Conduction and Selectivity
Doyle, D., Morais-Cabral, J. H., Pfuetzner, R. A., Kuo, A., Gulbis, J. M., Cohen, S. L., Chait, B. T., & MacKinnon, R. (1998) · Science · doi:10.1126/science.280.5360.69 · Cited by 6,816 · see citing works
Nonequilibrium Equality for Free Energy Differences
Jarzynski, C. (1997) · Physical Review Letters · doi:10.1103/physrevlett.78.2690 · Cited by 5,231 · see citing works
Water conduction through the hydrophobic channel of a carbon nanotube
Hummer, G., Rasaiah, J. C., & Noworyta, J. P. (2001) · Nature · doi:10.1038/35102535 · Cited by 3,569 · see citing works
Statistical Mechanics of Fluid Mixtures
Kirkwood, J. G. (1935) · The Journal of Chemical Physics · doi:10.1063/1.1749657 · Cited by 3,454 · see citing works
High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
Zwanzig, R. (1954) · The Journal of Chemical Physics · doi:10.1063/1.1740409 · Cited by 2,923 · see citing works
Optimized Monte Carlo data analysis
Ferrenberg, A. M., & Swendsen, R. H. (1989) · Physical Review Letters · doi:10.1103/physrevlett.63.1195 · Cited by 2,613 · see citing works
NAMD2: Greater Scalability for Parallel Molecular Dynamics
Kalé, L. V., Skeel, R. D., Bhandarkar, M. A., Brunner, R., Gürsoy, A., Krawetz, N., Phillips, J., Shinozaki, A., Varadarajan, K., & Schulten, K. J. (1999) · Journal of Computational Physics · doi:10.1006/jcph.1999.6201 · Cited by 2,428 · see citing works
Self-citationFree energy calculations: Applications to chemical and biochemical phenomena
Kollman, P. A. (1993) · Chemical Reviews · doi:10.1021/cr00023a004 · Cited by 2,131 · see citing works
Chemistry of ion coordination and hydration revealed by a K+ channel–Fab complex at 2.0 Å resolution
Zhou, Y., Morais-Cabral, J. H., Kaufman, A., & MacKinnon, R. (2001) · Nature · doi:10.1038/35102009 · Cited by 2,092 · see citing works
Appearance of Water Channels in Xenopus Oocytes Expressing Red Cell CHIP28 Protein
Preston, G. M., Carroll, T. P., Guggino, W. B., & Agre, P. C. (1992) · Science · doi:10.1126/science.256.5055.385 · Cited by 2,059 · see citing works
McCammon, J., Gelin, B., & Karplus, M. (1977) · Nature · doi:10.1038/267585a0 · Cited by 1,972 · see citing works
Structural determinants of water permeation through aquaporin-1
Murata, K., Mitsuoka, K., Hirai, T., Walz, T., Agre, P. C., Heymann, J. B., Engel, A. H., & Fujiyoshi, Y. (2000) · Nature · doi:10.1038/35036519 · Cited by 1,810 · see citing works
X-ray structure of a voltage-dependent K+ channel
Jiang, Y., Lee, A., Chen, J., Ruta, V., Cadène, M., Chait, B. T., & MacKinnon, R. (2003) · Nature · doi:10.1038/nature01580 · Cited by 1,798 · see citing works
Torrie, G. M., & Valleau, J. P. (1974) · Chemical Physics Letters · doi:10.1016/0009-2614(74)80109-0 · Cited by 1,446 · see citing works
Crystal structure and mechanism of a calcium-gated potassium channel
Jiang, Y., Lee, A., Chen, J., Cadène, M., Chait, B. T., & MacKinnon, R. (2002) · Nature · doi:10.1038/417515a · Cited by 1,332 · see citing works
The open pore conformation of potassium channels
Jiang, Y., Lee, A., Chen, J., Cadène, M., Chait, B. T., & MacKinnon, R. (2002) · Nature · doi:10.1038/417523a · Cited by 1,189 · see citing works
Climatic Impact of Tropical Lowland Deforestation on Nearby Montane Cloud Forests
Lawton, R. O., Nair, U. S., Pielke, R. A., & Welch, R. M. (2001) · Science · doi:10.1126/science.1062459 · Cited by 1,169 · see citing works
Structural basis of water-specific transport through the AQP1 water channel
Sui, H., Han, B.-G., Lee, J. K., Walian, P., & Jap, B. K. (2001) · Nature · doi:10.1038/414872a · Cited by 1,166 · see citing works
The potassium permeability of a giant nerve fibre
Hodgkin, A. L., & Keynes, R. D. (1955) · The Journal of Physiology · doi:10.1113/jphysiol.1955.sp005291 · Cited by 1,104 · see citing works
Structure of a Glycerol-Conducting Channel and the Basis for Its Selectivity
Fu, D., Libson, A. M., Miercke, L. J. W., Weitzman, C., Nollert, P., Krucinski, J., & Stroud, R. M. (2000) · Science · doi:10.1126/science.290.5491.481 · Cited by 1,000 · see citing works
Free energy reconstruction from nonequilibrium single-molecule pulling experiments
Hummer, G., & Szabó, A. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.071034098 · Cited by 998 · see citing works
Calculating potentials of mean force from steered molecular dynamics simulations
Park, S., & Schulten, K. J. (2004) · The Journal of Chemical Physics · doi:10.1063/1.1651473 · Cited by 945 · see citing works
Self-citationControl of the Selectivity of the Aquaporin Water Channel Family by Global Orientational Tuning
Tajkhorshid, E., Nollert, P., Jensen, M. Ø., Miercke, L. J. W., O’Connell, J. D., Stroud, R. M., & Schulten, K. J. (2002) · Science · doi:10.1126/science.1067778 · Cited by 915 · see citing works
Self-citationWater Permeation Across Biological Membranes: Mechanism and Dynamics of Aquaporin-1 and GlpF
de Groot, B. L., & Grubmüller, H. (2001) · Science · doi:10.1126/science.1066115 · Cited by 914 · see citing works
Cellular and Molecular Biology of the Aquaporin Water Channels
Borgnia, M. J., Nielsen, S. M., Engel, A. H., & Agre, P. C. (1999) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.68.1.425 · Cited by 844 · see citing works
Energetics of ion conduction through the K+ channel
Bernèche, S., & Roux, B. (2001) · Nature · doi:10.1038/35102067 · Cited by 804 · see citing works
Self-citationCrystal Structure of the Potassium Channel KirBac1.1 in the Closed State
Kuo, A., Gulbis, J. M., Antcliff, J. F., Rahman, T., Lowe, E. D., Zimmer, J., Cuthbertson, J. M., Ashcroft, F. M., Ezaki, T., & Doyle, D. (2003) · Science · doi:10.1126/science.1085028 · Cited by 787 · see citing works
The tobacco aquaporin NtAQP1 is a membrane CO2 pore with physiological functions
Uehlein, N., Lovisolo, C., Siefritz, F., et al. (2003) · Nature · doi:10.1038/nature02027 · Cited by 643 · see citing works
The Role of Aquaporins in Root Water Uptake
Javot, H. (2002) · Annals of Botany · doi:10.1093/aob/mcf199 · Cited by 621 · see citing works
Structural Rearrangements Underlying K + -Channel Activation Gating
Perozo, E., Marien, D., Cortes, & Cuello, L. G. (1999) · Science · doi:10.1126/science.285.5424.73 · Cited by 552 · see citing works
Computational Biochemistry and Biophysics
(2001) · CRC Press eBooks · doi:10.1201/9780203903827 · Cited by 492 · see citing works
Roux, B., & MacKinnon, R. (1999) · Science · doi:10.1126/science.285.5424.100 · Cited by 439 · see citing works
Self-citationIon permeation mechanism of the potassium channel
Åqvist, J., & Luzhkov, V. B. (2000) · Nature · doi:10.1038/35009114 · Cited by 432 · see citing works
Role of a Single Aquaporin Isoform in Root Water Uptake
Javot, H., Lauvergeat, V., Santoni, V., Martin-Laurent, F. A., Güçlü, J., Vinh, J., Heyes, J. A., Franck, K. I., Schäffner, A. R., Bouchez, D., et al. (2003) · The Plant Cell · doi:10.1105/tpc.008888 · Cited by 372 · see citing works
Energetics of glycerol conduction through aquaglyceroporin GlpF
Jensen, M. Ø., Park, S., Tajkhorshid, E., & Schulten, K. J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.102649299 · Cited by 364 · see citing works
Self-citationTheory and Simulation of Water Permeation in Aquaporin-1
Zhu, F., Tajkhorshid, E., & Schulten, K. J. (2004) · Biophysical Journal · doi:10.1016/s0006-3495(04)74082-5 · Cited by 361 · see citing works
Self-citationLeMasurier, M., Heginbotham, L., & Miller, C. (2001) · The Journal of General Physiology · doi:10.1085/jgp.118.3.303 · Cited by 348 · see citing works
Blocker protection in the pore of a voltage-gated K+ channel and its structural implications
del Camino, D., Holmgren, M., Liu, Y., & Yellen, G. (2000) · Nature · doi:10.1038/35002099 · Cited by 333 · see citing works
Molecular Dynamics of the KcsA K+ Channel in a Bilayer Membrane
Bernèche, S., & Roux, B. (2000) · Biophysical Journal · doi:10.1016/s0006-3495(00)76831-7 · Cited by 331 · see citing works
Self-citationSchlenkrich, M., Brickmann, J., MacKerell, A. D., & Karplus, M. (1996) · Birkhäuser Boston eBooks · doi:10.1007/978-1-4684-8580-6_2 · Cited by 327 · see citing works
Biological membranes : a molecular perspective from computation and experiment
Merz, K. M., & Roux, B. (1996) · Cited by 314 · see citing works
Self-citationPomès, R., & Roux, B. (1996) · Biophysical Journal · doi:10.1016/s0006-3495(96)79211-1 · Cited by 302 · see citing works
Self-citationArchitecture and Selectivity in Aquaporins: 2.5 Å X-Ray Structure of Aquaporin Z
Savage, D. F., Egea, P. F., Robles‐Colmenares, Y., O’Connell, J. D., & Stroud, R. M. (2003) · PLoS Biology · doi:10.1371/journal.pbio.0000072 · Cited by 301 · see citing works
Single Streptomyces lividans K+ Channels
Heginbotham, L., LeMasurier, M., Kolmakova-Partensky, L., & Miller, C. (1999) · The Journal of General Physiology · doi:10.1085/jgp.114.4.551 · Cited by 293 · see citing works
Understanding nature's design for a nanosyringe
Lopez, C. F., Nielsen, S. O., Moore, P. B., & Klein, M. L. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400352101 · Cited by 293 · see citing works
The Mechanism of Proton Exclusion in the Aquaporin-1 Water Channel
de Groot, B. L., Frigato, T., Helms, V., & Grubmüller, H. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.08.003 · Cited by 285 · see citing works
Shrivastava, I. H., & Sansom, M. S. P. (2000) · Biophysical Journal · doi:10.1016/s0006-3495(00)76616-1 · Cited by 283 · see citing works
Molecular Architecture of Full-Length KcsA
Cortés, D. M., Cuello, L. G., & Perozo, E. (2001) · The Journal of General Physiology · doi:10.1085/jgp.117.2.165 · Cited by 244 · see citing works
A microscopic view of ion conduction through the K+ channel
Bernèche, S., & Roux, B. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1431750100 · Cited by 237 · see citing works
Self-citationAquaporins: Phylogeny, Structure, and Physiology of Water Channels
Heymann, J. B., & Engel, A. H. (1999) · Physiology · doi:10.1152/physiologyonline.1999.14.5.187 · Cited by 226 · see citing works
Borgnia, M. J., & Agre, P. C. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.051628098 · Cited by 217 · see citing works
Biological membranes. A molecular perspective from computation and experiment
Mehedintu, M. (1997) · Bioelectrochemistry and Bioenergetics · doi:10.1016/s0302-4598(97)00047-0 · Cited by 205 · see citing works
Structure and dynamics of ion transport through gramicidin A
Mackay, D. H., Berens, P. H., Wilson, K. R., et al. (1984) · Biophysical Journal · doi:10.1016/s0006-3495(84)84016-3 · Cited by 181 · see citing works
Burykin, A., & Warshel, A. (2003) · Biophysical Journal · doi:10.1016/s0006-3495(03)74786-9 · Cited by 176 · see citing works
Electrostatic Tuning of Permeation and Selectivity in Aquaporin Water Channels
Jensen, M. Ø., Tajkhorshid, E., & Schulten, K. (2003) · Biophysical Journal · doi:10.1016/s0006-3495(03)74711-0 · Cited by 172 · see citing works
Self-citationThe mechanism of proton exclusion in aquaporin channels
Ilan, B., Tajkhorshid, E., Schulten, K. J., et al. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20038 · Cited by 171 · see citing works
Self-citationIon Channels, Permeation, and Electrostatics: Insight into the Function of KcsA
Roux, B., Bernèche, S., & Im, W. (2000) · Biochemistry · doi:10.1021/bi001567v · Cited by 166 · see citing works
Self-citationMolecular Basis of Proton Blockage in Aquaporins
Chakrabarti, N., Tajkhorshid, E., Roux, B., & Pomès, R. (2004) · Structure · doi:10.1016/j.str.2003.11.017 · Cited by 164 · see citing works
Self-citationGating of MscL Studied by Steered Molecular Dynamics
Gullingsrud, J., & Schulten, K. J. (2003) · Biophysical Journal · doi:10.1016/s0006-3495(03)74637-2 · Cited by 161 · see citing works
Self-citationThe Mechanism of Glycerol Conduction in Aquaglyceroporins
Jensen, M. Ø., Tajkhorshid, E., & Schulten, K. (2001) · Structure · doi:10.1016/s0969-2126(01)00668-2 · Cited by 152 · see citing works
Self-citationA refined structure of human aquaporin‐1
de Groot, B. L., Engel, A. H., & Grubmüller, H. (2001) · FEBS Letters · doi:10.1016/s0014-5793(01)02743-0 · Cited by 141 · see citing works
Potassium and Sodium Binding to the Outer Mouth of the K+ Channel
Guidoni, L., Torre, V., & Carloni, P. (1999) · Biochemistry · doi:10.1021/bi990540c · Cited by 139 · see citing works
A Mutant KcsA K+ Channel with Altered Conduction Properties and Selectivity Filter Ion Distribution
Zhou, M., & MacKinnon, R. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.03.020 · Cited by 128 · see citing works
Voltage-Dependent Insertion of Alamethicin at Phospholipid/Water and Octane/Water Interfaces
Tieleman, D. P., Berendsen, H. J. C., & Sansom, M. S. P. (2001) · Biophysical Journal · doi:10.1016/s0006-3495(01)76018-3 · Cited by 122 · see citing works
Theoretical and computational models of ion channels
Roux, B. (2002) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(02)00307-x · Cited by 116 · see citing works
Self-citationLuzhkov, V. B., & Åqvist, J. (2001) · Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology · doi:10.1016/s0167-4838(01)00213-8 · Cited by 109 · see citing works
Rotational movement during cyclic nucleotide-gated channel opening
Johnson, J. P., & Zagotta, W. N. (2001) · Nature · doi:10.1038/35091089 · Cited by 107 · see citing works
Pohl, P., Saparov, S. M., Borgnia, M. J., et al. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.161299398 · Cited by 103 · see citing works
Mechanisms of Selectivity in Channels and Enzymes Studied with Interactive Molecular Dynamics
Grayson, P. D., Tajkhorshid, E., & Schulten, K. J. (2003) · Biophysical Journal · doi:10.1016/s0006-3495(03)74452-x · Cited by 103 · see citing works
Self-citationde Groot, B. L., Tieleman, D. P., Pohl, P., & Grubmüller, H. (2002) · Biophysical Journal · doi:10.1016/s0006-3495(02)75634-8 · Cited by 99 · see citing works
Aquaporins and disease: lessons from mice to humans
King, L. S., & Yasui, M. (2002) · Trends in Endocrinology and Metabolism · doi:10.1016/s1043-2760(02)00665-3 · Cited by 75 · see citing works
Glycerol Conductance and Physical Asymmetry of the Escherichia coli Glycerol Facilitator GlpF
Lu, D., Grayson, P., & Schulten, K. J. (2003) · Biophysical Journal · doi:10.1016/s0006-3495(03)74718-3 · Cited by 57 · see citing works
Self-citationOpen-State Models of a Potassium Channel
Biggin, P. C., & Sansom, M. S. P. (2002) · Biophysical Journal · doi:10.1016/s0006-3495(02)73951-9 · Cited by 51 · see citing works
Large Scale Simulation of Protein Mechanics and Function
Tajkhorshid, E., Aksimentiev, A., Balabin, I. A., Gao, M., Isralewitz, B., Phillips, J. C., Zhu, F., & Schulten, K. J. (2003) · Advances in protein chemistry · doi:10.1016/s0065-3233(03)66006-7 · Cited by 41 · see citing works
Self-citationCritical assessment of a proposed model of Shaker
Lainé, M., Papazian, D. M., & Roux, B. (2004) · FEBS Letters · doi:10.1016/s0014-5793(04)00273-x · Cited by 38 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
An Overview of Sub-Cellular Mechanisms Involved in the Action of TTFields
Tuszynski, J., Wenger, C., Friesen, D., & Preto, J. (2016) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph13111128 · Cited by 95 · see citing works
Quantum coherence in ion channels: resonances, transport and verification
Vaziri, A., & Plenio, M. B. (2010) · New Journal of Physics · doi:10.1088/1367-2630/12/8/085001 · Cited by 88 · see citing works
- Authors
- Roux, B., & Schulten, K.
- Affiliations
- University of Illinois Urbana-Champaign (US)
- ORCID
- Schulten, Klaus
- Venue
- Structure
- Publisher
- Elsevier BV
- Published
- 2004-08
- Volume
- 12
- Issue
- 8
- Pages
- 1343-1351
- ISSN
- 0969-2126 (ISSN-L)
- OpenAlex
- W2019922184
- Cited by
- 145
- References
- 79
- Citations by year
- 2026: 4 · 2025: 3 · 2024: 2 · 2023: 2 · 2022: 3 · 2021: 2 · 2020: 7 · 2019: 3 · 2018: 4 · 2017: 3 · 2016: 2 · 2015: 5 · 2014: 7 · 2013: 3 · 2012: 16
- FWCI
- 1.01
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 3272 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Structure (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Health Research Institutes (GM60946, NRAC MCA93S028, PHS5P41RR05969)
- National Science Foundation (NRAC MCA01S018)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ion channel regulation and function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ion Transport and Channel Regulation
- Keywords
- membrane channels, potassium channels, aquaporins, molecular dynamics simulation, channel structure-function relationship, ion transport mechanism, channel gating
- MeSH terms
- Animals, Humans, Ion Channels, Molecular Conformation, Software, Systems Theory, Aquaporins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
