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Volumn 19, Issue 2, 2009, Pages 128-137

Molecular dynamics simulations of membrane channels and transporters

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; AQUAPORIN; CARRIER PROTEIN; ION CHANNEL; MEMBRANE PROTEIN; POTASSIUM CHANNEL;

EID: 64649084606     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2009.02.011     Document Type: Review
Times cited : (187)

References (62)
  • 1
    • 49549083949 scopus 로고    scopus 로고
    • Membrane proteins: molecular dynamics simulations
    • Lindahl E., and Sansom M.S.P. Membrane proteins: molecular dynamics simulations. Curr Opin Struct Biol 18 (2008) 425-431
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 425-431
    • Lindahl, E.1    Sansom, M.S.P.2
  • 2
    • 34447325646 scopus 로고    scopus 로고
    • Water transport in aquaporins: osmotic permeability matrix analysis of molecular dynamics simulations
    • Osmotic permeability of water in aquaporins is described by a matrix that can be decomposed into contributions from each local region of the channel.
    • Hashido M., Kidera A., and Ikeguchi M. Water transport in aquaporins: osmotic permeability matrix analysis of molecular dynamics simulations. Biophys J 93 (2007) 373-385. Osmotic permeability of water in aquaporins is described by a matrix that can be decomposed into contributions from each local region of the channel.
    • (2007) Biophys J , vol.93 , pp. 373-385
    • Hashido, M.1    Kidera, A.2    Ikeguchi, M.3
  • 3
    • 42749105522 scopus 로고    scopus 로고
    • Collective diffusion model for water permeation through microscopic channels
    • Zhu F., Tajkhorshid E., and Schulten K. Collective diffusion model for water permeation through microscopic channels. Phys Rev Lett 93 (2004) 224501
    • (2004) Phys Rev Lett , vol.93 , pp. 224501
    • Zhu, F.1    Tajkhorshid, E.2    Schulten, K.3
  • 5
    • 33846021582 scopus 로고    scopus 로고
    • Charge delocalization in proton channels. I. The aquaporin channels and proton blockage
    • Mechanism of proton blockage in aquaporins is investigated by a combination of steered MD simulations and quantum chemistry calculations.
    • Chen H., Ilan B., Wu Y., Zhu F., Schulten K., and Voth G.A. Charge delocalization in proton channels. I. The aquaporin channels and proton blockage. Biophys J 92 (2007) 46-60. Mechanism of proton blockage in aquaporins is investigated by a combination of steered MD simulations and quantum chemistry calculations.
    • (2007) Biophys J , vol.92 , pp. 46-60
    • Chen, H.1    Ilan, B.2    Wu, Y.3    Zhu, F.4    Schulten, K.5    Voth, G.A.6
  • 6
    • 33847313314 scopus 로고    scopus 로고
    • Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics
    • Wang Y., Cohen J., Boron W.F., Schulten K., and Tajkhorshid E. Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics. J Struct Biol 157 (2007) 534-544
    • (2007) J Struct Biol , vol.157 , pp. 534-544
    • Wang, Y.1    Cohen, J.2    Boron, W.F.3    Schulten, K.4    Tajkhorshid, E.5
  • 7
    • 39549085136 scopus 로고    scopus 로고
    • Mechanism of selectivity in aquaporins and aquaglyceroporins
    • Hub J., and de Groot B. Mechanism of selectivity in aquaporins and aquaglyceroporins. Proc Natl Acad Sci U S A 105 (2008) 1198-1203
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 1198-1203
    • Hub, J.1    de Groot, B.2
  • 8
    • 38849088221 scopus 로고    scopus 로고
    • Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF
    • Henin J., Tajkhorshid E., Schulten K., and Chipot C. Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Biophys J 94 (2008) 832-839
    • (2008) Biophys J , vol.94 , pp. 832-839
    • Henin, J.1    Tajkhorshid, E.2    Schulten, K.3    Chipot, C.4
  • 9
    • 55749105149 scopus 로고    scopus 로고
    • Dynamic control of slow water transport by aquaporin 0: implications for hydration and junction stability in the eye lens
    • Jensen M., Dror R., Xu H., Borhani D., Arkin I., Eastwood M., and Shaw D. Dynamic control of slow water transport by aquaporin 0: implications for hydration and junction stability in the eye lens. Proc Natl Acad Sci U S A 105 (2008) 14430-14435
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 14430-14435
    • Jensen, M.1    Dror, R.2    Xu, H.3    Borhani, D.4    Arkin, I.5    Eastwood, M.6    Shaw, D.7
  • 10
    • 33846625994 scopus 로고    scopus 로고
    • Importance of hydration and dynamic on the selectivity of the KcsA and NaK channels
    • Noskov S., and Roux B. Importance of hydration and dynamic on the selectivity of the KcsA and NaK channels. J Gen Physiol 129 (2007) 135-143
    • (2007) J Gen Physiol , vol.129 , pp. 135-143
    • Noskov, S.1    Roux, B.2
  • 12
    • 35848958366 scopus 로고    scopus 로고
    • Molecular driving forces determining potassium channel slow inactivation
    • A combination of experiment and simulation is used to identify the inactivated state of the potassium channel, KcsA.
    • Cordero-Morales J.F., Jogini V., Lewis A., Vasquez V., Cortes D.M., Roux B., and Perozo E. Molecular driving forces determining potassium channel slow inactivation. Nat Struct Mol Biol 14 (2007) 1062-1069. A combination of experiment and simulation is used to identify the inactivated state of the potassium channel, KcsA.
    • (2007) Nat Struct Mol Biol , vol.14 , pp. 1062-1069
    • Cordero-Morales, J.F.1    Jogini, V.2    Lewis, A.3    Vasquez, V.4    Cortes, D.M.5    Roux, B.6    Perozo, E.7
  • 13
    • 47749110306 scopus 로고    scopus 로고
    • Conformational changes and gating at the selectivity filter of potassium channels
    • The free energy of ion conduction through the potassium channel is calculated along a pathway, in which the conformation of the selectivity filter changes according to the lowest free energy path obtained in metadynamics simulations.
    • Domene C., Klein M.L., Branduardi D., Gervasio F.K., and Parrinello M. Conformational changes and gating at the selectivity filter of potassium channels. J Am Chem Soc 130 (2008) 9474-9480. The free energy of ion conduction through the potassium channel is calculated along a pathway, in which the conformation of the selectivity filter changes according to the lowest free energy path obtained in metadynamics simulations.
    • (2008) J Am Chem Soc , vol.130 , pp. 9474-9480
    • Domene, C.1    Klein, M.L.2    Branduardi, D.3    Gervasio, F.K.4    Parrinello, M.5
  • 14
    • 33646135082 scopus 로고    scopus 로고
    • Environment of the gating charge in the Kv1.2 Shaker potassium channel
    • Treptow W., and Tarek M. Environment of the gating charge in the Kv1.2 Shaker potassium channel. Biophys J 90 (2006) L64-L66
    • (2006) Biophys J , vol.90
    • Treptow, W.1    Tarek, M.2
  • 15
    • 33846785439 scopus 로고    scopus 로고
    • How does a voltage sensor interact with a lipid bilayer? Simulations of a potassium channel domain
    • Sands Z.A., and Sansom M.S. How does a voltage sensor interact with a lipid bilayer? Simulations of a potassium channel domain. Structure 15 (2007) 235-244
    • (2007) Structure , vol.15 , pp. 235-244
    • Sands, Z.A.1    Sansom, M.S.2
  • 16
    • 34547628129 scopus 로고    scopus 로고
    • + channel in a membrane environment
    • + channel in a membrane environment. Biophys J 93 (2007) 3070-3082
    • (2007) Biophys J , vol.93 , pp. 3070-3082
    • Jogini, V.1    Roux, B.2
  • 17
    • 50349088433 scopus 로고    scopus 로고
    • Molecular dynamics simulation of Kv channel voltage sensor helix in a lipid membrane with applied voltage
    • Extensive simulations of the voltage-sensor domain revealed the initial steps of potassium channel gating. The environment of the gating charge is characterized from electrostatic calculations.
    • Nishizawa M., and Nishizawa K. Molecular dynamics simulation of Kv channel voltage sensor helix in a lipid membrane with applied voltage. Biophys J 95 (2008) 1729-1744. Extensive simulations of the voltage-sensor domain revealed the initial steps of potassium channel gating. The environment of the gating charge is characterized from electrostatic calculations.
    • (2008) Biophys J , vol.95 , pp. 1729-1744
    • Nishizawa, M.1    Nishizawa, K.2
  • 18
    • 33847258823 scopus 로고    scopus 로고
    • Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations
    • Bond P.J., and Sansom M. Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations. Proc Natl Acad Sci U S A 104 (2007) 2631-2636
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 2631-2636
    • Bond, P.J.1    Sansom, M.2
  • 19
    • 33746828240 scopus 로고    scopus 로고
    • A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL
    • A finite element methodology is used to model the gating transition of M. tuberculosis and Escherichia coli MscL under equi-biaxial tension and axisymmetric bending. Modeling predicts full opening of MscL under equi-biaxial tension with structural transitions that are consistent with previous experimental and theoretical models. This technique provides a continuum description with a natural connection to specific all-atom models.
    • Tang Y., Cao G., Chen X., Yoo J., Yethiraj A., and Cui Q. A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL. Biophys J 91 (2006) 1248-1263. A finite element methodology is used to model the gating transition of M. tuberculosis and Escherichia coli MscL under equi-biaxial tension and axisymmetric bending. Modeling predicts full opening of MscL under equi-biaxial tension with structural transitions that are consistent with previous experimental and theoretical models. This technique provides a continuum description with a natural connection to specific all-atom models.
    • (2006) Biophys J , vol.91 , pp. 1248-1263
    • Tang, Y.1    Cao, G.2    Chen, X.3    Yoo, J.4    Yethiraj, A.5    Cui, Q.6
  • 21
    • 34249651256 scopus 로고    scopus 로고
    • Cooperative gating and spatial organization of membrane proteins through elastic interactions
    • A generic continuum mechanics model is used to study how interactions between neighboring channels may affect MscL gating. The model predicts cooperative gating and an effect in average separation between two proteins due to their conformational changes.
    • Ursell T., Huang K.C., Peterson E., and Phillips R. Cooperative gating and spatial organization of membrane proteins through elastic interactions. PLoS Comput Biol 3 (2007) 803-812. A generic continuum mechanics model is used to study how interactions between neighboring channels may affect MscL gating. The model predicts cooperative gating and an effect in average separation between two proteins due to their conformational changes.
    • (2007) PLoS Comput Biol , vol.3 , pp. 803-812
    • Ursell, T.1    Huang, K.C.2    Peterson, E.3    Phillips, R.4
  • 22
    • 33846828514 scopus 로고    scopus 로고
    • Ion conduction through MscS as determined by electrophysiology and simulation
    • Sotomayor M., Vasquez V., Perozo E., and Schulten K. Ion conduction through MscS as determined by electrophysiology and simulation. Biophys J 92 (2007) 886-902
    • (2007) Biophys J , vol.92 , pp. 886-902
    • Sotomayor, M.1    Vasquez, V.2    Perozo, E.3    Schulten, K.4
  • 23
    • 36849026098 scopus 로고    scopus 로고
    • Straightening and sequential buckling of the pore-lining helices define the gating cycle of MscS
    • Akitake B., Anishkin A., and Sukharev S. Straightening and sequential buckling of the pore-lining helices define the gating cycle of MscS. Nat Struct Mol Biol 14 (2007) 1141-1149
    • (2007) Nat Struct Mol Biol , vol.14 , pp. 1141-1149
    • Akitake, B.1    Anishkin, A.2    Sukharev, S.3
  • 24
    • 38949147131 scopus 로고    scopus 로고
    • Characterization of the resting MscS: modeling and analysis of the closed bacterial mechanosensitive channel of small conductance
    • Anishkin A., Akitake B., and Sukharev S. Characterization of the resting MscS: modeling and analysis of the closed bacterial mechanosensitive channel of small conductance. Biophys J 94 (2008) 1252-1266
    • (2008) Biophys J , vol.94 , pp. 1252-1266
    • Anishkin, A.1    Akitake, B.2    Sukharev, S.3
  • 25
    • 48749122220 scopus 로고    scopus 로고
    • Mechanosensitive channel MscS in the open state: modeling of the transition, explicit simulations, and experimental measurements of conductance
    • Models of MscS in open and closed conformations are presented [23,24], characterized by MD simulations, and partially validated through patch-clamp experiments and mutagenesis.
    • Anishkin A., Kamaraju K., and Sukharev S. Mechanosensitive channel MscS in the open state: modeling of the transition, explicit simulations, and experimental measurements of conductance. J Gen Physiol 132 (2008) 67-83. Models of MscS in open and closed conformations are presented [23,24], characterized by MD simulations, and partially validated through patch-clamp experiments and mutagenesis.
    • (2008) J Gen Physiol , vol.132 , pp. 67-83
    • Anishkin, A.1    Kamaraju, K.2    Sukharev, S.3
  • 26
    • 41149173530 scopus 로고    scopus 로고
    • Three dimensional architecture of membrane-embedded MscS in the closed conformation
    • Vasquez V., Sotomayor M., Cortes D.M., Roux B., Schulten K., and Perozo E. Three dimensional architecture of membrane-embedded MscS in the closed conformation. J Mol Biol 378 (2008) 55-70
    • (2008) J Mol Biol , vol.378 , pp. 55-70
    • Vasquez, V.1    Sotomayor, M.2    Cortes, D.M.3    Roux, B.4    Schulten, K.5    Perozo, E.6
  • 27
    • 50649109171 scopus 로고    scopus 로고
    • A structural mechanism for MscS gating in lipid bilayers
    • Electron paramagnetic resonance spectroscopy data are used to drive MD simulations and obtain an experimentally determined open model of MscS. Standard MD simulations are then used to thoroughly characterize open and closed [22,26] conformations of MscS.
    • Vasquez V., Sotomayor M., Cordero-Morales J., Schulten K., and Perozo E. A structural mechanism for MscS gating in lipid bilayers. Science 321 (2008) 1210-1214. Electron paramagnetic resonance spectroscopy data are used to drive MD simulations and obtain an experimentally determined open model of MscS. Standard MD simulations are then used to thoroughly characterize open and closed [22,26] conformations of MscS.
    • (2008) Science , vol.321 , pp. 1210-1214
    • Vasquez, V.1    Sotomayor, M.2    Cordero-Morales, J.3    Schulten, K.4    Perozo, E.5
  • 29
    • 34848895197 scopus 로고    scopus 로고
    • Structural determinants of lateral gate opening in the protein translocon
    • Gumbart J., and Schulten K. Structural determinants of lateral gate opening in the protein translocon. Biochemistry 46 (2007) 11147-11157
    • (2007) Biochemistry , vol.46 , pp. 11147-11157
    • Gumbart, J.1    Schulten, K.2
  • 30
    • 59649110315 scopus 로고    scopus 로고
    • The roles of pore ring and plug in the SecY protein-conducting channel
    • Gumbart J., and Schulten K. The roles of pore ring and plug in the SecY protein-conducting channel. J Gen Physiol 132 (2008) 709-719
    • (2008) J Gen Physiol , vol.132 , pp. 709-719
    • Gumbart, J.1    Schulten, K.2
  • 31
    • 55749104248 scopus 로고    scopus 로고
    • Embedded cholesterol in the nicotinic acetylcholine receptor
    • Simulations showed that binding of cholesterol is essential for maintaining the stability of the EM structure of nAchR. Such instability was not identified in previous (short time scale) simulations of the same structure.
    • Brannigan G., Henin J., Law R., Eckenhoff R., and Klein M.L. Embedded cholesterol in the nicotinic acetylcholine receptor. Proc Natl Acad Sci U S A 105 (2008) 14418-14423. Simulations showed that binding of cholesterol is essential for maintaining the stability of the EM structure of nAchR. Such instability was not identified in previous (short time scale) simulations of the same structure.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 14418-14423
    • Brannigan, G.1    Henin, J.2    Law, R.3    Eckenhoff, R.4    Klein, M.L.5
  • 32
    • 34447131659 scopus 로고    scopus 로고
    • Barriers to ion translocation in cationic and anionic receptors from the cys-loop family
    • Ivanov I., Cheng X., Sine S.M., and McCammon J.A. Barriers to ion translocation in cationic and anionic receptors from the cys-loop family. J Am Chem Soc 129 (2007) 8217-8224
    • (2007) J Am Chem Soc , vol.129 , pp. 8217-8224
    • Ivanov, I.1    Cheng, X.2    Sine, S.M.3    McCammon, J.A.4
  • 33
    • 58149332703 scopus 로고    scopus 로고
    • + binding sites in acid sensing ion channel-1
    • + binding sites in acid sensing ion channel-1. Biophys J 95 (2008) 5153-5164
    • (2008) Biophys J , vol.95 , pp. 5153-5164
    • Shaikh, S.A.1    Tajkhorshid, E.2
  • 34
    • 33748776270 scopus 로고    scopus 로고
    • The dynamics of the MgATP-driven closure of MalK, the energy-transducing subunit of the maltose ABC transporter
    • Oloo E.O., Fung E.Y., and Tieleman D.P. The dynamics of the MgATP-driven closure of MalK, the energy-transducing subunit of the maltose ABC transporter. J Biol Chem 281 (2006) 28397-28407
    • (2006) J Biol Chem , vol.281 , pp. 28397-28407
    • Oloo, E.O.1    Fung, E.Y.2    Tieleman, D.P.3
  • 35
    • 34547943910 scopus 로고    scopus 로고
    • Nucleotide-dependent allostery within the ABC transporter ATP-binding cassette
    • Jones P.M., and George A.M. Nucleotide-dependent allostery within the ABC transporter ATP-binding cassette. J Biol Chem 282 (2007) 22793-22803
    • (2007) J Biol Chem , vol.282 , pp. 22793-22803
    • Jones, P.M.1    George, A.M.2
  • 36
    • 66149139241 scopus 로고    scopus 로고
    • Opening of the ADP-bound active site in the ABC transporter ATPase dimer: evidence for a constant contact, alternating sites model for the catalytic cycle
    • Jones P.M., and George A.M. Opening of the ADP-bound active site in the ABC transporter ATPase dimer: evidence for a constant contact, alternating sites model for the catalytic cycle. Proteins: Struct, Func, Bioinf 75 (2008) 387-396
    • (2008) Proteins: Struct, Func, Bioinf , vol.75 , pp. 387-396
    • Jones, P.M.1    George, A.M.2
  • 37
    • 58149359858 scopus 로고    scopus 로고
    • Dimer opening of the nucleotide binding domains of ABC transporters after ATP hydrolysis
    • Wen P.C., and Tajkhorshid E. Dimer opening of the nucleotide binding domains of ABC transporters after ATP hydrolysis. Biophys J 95 (2008) 5100-5110
    • (2008) Biophys J , vol.95 , pp. 5100-5110
    • Wen, P.C.1    Tajkhorshid, E.2
  • 38
    • 46749137537 scopus 로고    scopus 로고
    • ΔF508 mutation increases conformational flexibility of CFTR protein
    • Wieczorek G., and Zielenkiewicz P. ΔF508 mutation increases conformational flexibility of CFTR protein. J Cyst Fibros 7 (2008) 295-300
    • (2008) J Cyst Fibros , vol.7 , pp. 295-300
    • Wieczorek, G.1    Zielenkiewicz, P.2
  • 39
    • 33947284958 scopus 로고    scopus 로고
    • Dynamics and function in a bacterial ABC transporter: simulation studies of the BtuCDF system and its components
    • Ivetac A., Campbell J.D., and Sansom M.S. Dynamics and function in a bacterial ABC transporter: simulation studies of the BtuCDF system and its components. Biochemistry 46 (2007) 2767-2778
    • (2007) Biochemistry , vol.46 , pp. 2767-2778
    • Ivetac, A.1    Campbell, J.D.2    Sansom, M.S.3
  • 40
    • 34147168584 scopus 로고    scopus 로고
    • Simulation of the coupling between nucleotide binding and transmembrane domains in the ATP binding cassette transporter BtuCD
    • This paper describes two simulation methods (perturbed anisotropic network model and essential dynamics sampling) to facilitate large conformational changes of a transporter in designed directions and to interpret its mode of motion. Using knowledge of its structural component as a guide, the motion of the complete protein assembly can be successfully annotated with both methods.
    • Sonne J., Kandt C., Peters G.H., Hansen F.Y., Jansen M.Ø., and Tieleman D.P. Simulation of the coupling between nucleotide binding and transmembrane domains in the ATP binding cassette transporter BtuCD. Biophys J 92 (2007) 2727-2734. This paper describes two simulation methods (perturbed anisotropic network model and essential dynamics sampling) to facilitate large conformational changes of a transporter in designed directions and to interpret its mode of motion. Using knowledge of its structural component as a guide, the motion of the complete protein assembly can be successfully annotated with both methods.
    • (2007) Biophys J , vol.92 , pp. 2727-2734
    • Sonne, J.1    Kandt, C.2    Peters, G.H.3    Hansen, F.Y.4    Jansen, M.Ø.5    Tieleman, D.P.6
  • 41
    • 41049089116 scopus 로고    scopus 로고
    • Molecular dynamics simulations and membrane protein structure quality
    • Ivetac A., and Sansom M.S. Molecular dynamics simulations and membrane protein structure quality. Eur Biophys J 37 (2008) 403-409
    • (2008) Eur Biophys J , vol.37 , pp. 403-409
    • Ivetac, A.1    Sansom, M.S.2
  • 43
    • 33845380397 scopus 로고    scopus 로고
    • Sugar binding and protein conformational changes in lactose permease
    • Yin Y., Jensen MØ, Tajkhorshid E., and Schulten K. Sugar binding and protein conformational changes in lactose permease. Biophys J 91 (2006) 3972-3985
    • (2006) Biophys J , vol.91 , pp. 3972-3985
    • Yin, Y.1    Jensen MØ2    Tajkhorshid, E.3    Schulten, K.4
  • 44
    • 34447253999 scopus 로고    scopus 로고
    • Sugar transport across lactose permease probed by steered molecular dynamics
    • Jensen MØ, Yin Y., Tajkhorshid E., and Schulten K. Sugar transport across lactose permease probed by steered molecular dynamics. Biophys J 93 (2007) 92-102
    • (2007) Biophys J , vol.93 , pp. 92-102
    • Jensen MØ1    Yin, Y.2    Tajkhorshid, E.3    Schulten, K.4
  • 45
    • 34447256364 scopus 로고    scopus 로고
    • Conformational change in an MFS protein: MD simulations of LacY
    • Holyoake J., and Sansom M.S.P. Conformational change in an MFS protein: MD simulations of LacY. Structure 15 (2007) 873-884
    • (2007) Structure , vol.15 , pp. 873-884
    • Holyoake, J.1    Sansom, M.S.P.2
  • 46
    • 33947132573 scopus 로고    scopus 로고
    • Sugar binding in lactose permease: anomeric state of a disaccharide influences binding structure
    • Klauda J.B., and Brooks B.R. Sugar binding in lactose permease: anomeric state of a disaccharide influences binding structure. J Mol Biol 367 (2007) 1523-1534
    • (2007) J Mol Biol , vol.367 , pp. 1523-1534
    • Klauda, J.B.1    Brooks, B.R.2
  • 48
    • 47749083479 scopus 로고    scopus 로고
    • An intracellular interaction network regulates conformational transitions in the dopamine transporter
    • Kniazeff J., Shi L., Loland C.J., Javitch J.A., Weinstein H., and Gether U. An intracellular interaction network regulates conformational transitions in the dopamine transporter. J Biol Chem 283 (2008) 17691-17701
    • (2008) J Biol Chem , vol.283 , pp. 17691-17701
    • Kniazeff, J.1    Shi, L.2    Loland, C.J.3    Javitch, J.A.4    Weinstein, H.5    Gether, U.6
  • 49
    • 36549031819 scopus 로고    scopus 로고
    • How dopamine transporter interacts with dopamine: insights from molecular modeling and simulation
    • Huang X., and Zhan C.G. How dopamine transporter interacts with dopamine: insights from molecular modeling and simulation. Biophys J 93 (2007) 3627-3639
    • (2007) Biophys J , vol.93 , pp. 3627-3639
    • Huang, X.1    Zhan, C.G.2
  • 50
    • 41449093586 scopus 로고    scopus 로고
    • Substrate binding and formation of an occluded state in the leucine transporter
    • Celik L., Schiott B., and Tajkhorshid E. Substrate binding and formation of an occluded state in the leucine transporter. Biophys J 94 (2008) 1600-1612
    • (2008) Biophys J , vol.94 , pp. 1600-1612
    • Celik, L.1    Schiott, B.2    Tajkhorshid, E.3
  • 51
    • 57649119782 scopus 로고    scopus 로고
    • Time-resolved mechanism of extracellular gate opening and substrate binding in a glutamate transporter
    • Shrivastava I.H., Jiang J., Amara S.G., and Bahar I. Time-resolved mechanism of extracellular gate opening and substrate binding in a glutamate transporter. J Biol Chem 283 (2008) 28680-28690
    • (2008) J Biol Chem , vol.283 , pp. 28680-28690
    • Shrivastava, I.H.1    Jiang, J.2    Amara, S.G.3    Bahar, I.4
  • 52
    • 51649088013 scopus 로고    scopus 로고
    • Dynamics of the extracellular gate and ion-substrate coupling in the glutamate transporter
    • Huang Z., and Tajkhorshid E. Dynamics of the extracellular gate and ion-substrate coupling in the glutamate transporter. Biophys J 95 (2008) 2292-2300
    • (2008) Biophys J , vol.95 , pp. 2292-2300
    • Huang, Z.1    Tajkhorshid, E.2
  • 53
    • 44949086583 scopus 로고    scopus 로고
    • + and substrate is triggered by substrate in a second binding site
    • Simulations combined with experiments reveal the existence of a secondary substrate binding site in the leucine transporter LeuT. Binding of leucine to the secondary binding site triggers release from the primary one, while antidepressants, known to bind to the secondary site, are suggested to prevent release.
    • + and substrate is triggered by substrate in a second binding site. Mol Cell 30 (2008) 667-677. Simulations combined with experiments reveal the existence of a secondary substrate binding site in the leucine transporter LeuT. Binding of leucine to the secondary binding site triggers release from the primary one, while antidepressants, known to bind to the secondary site, are suggested to prevent release.
    • (2008) Mol Cell , vol.30 , pp. 667-677
    • Shi, L.1    Quick, M.2    Zhao, Y.3    Weinstein, H.4    Javitch, J.A.5
  • 54
    • 40649098564 scopus 로고    scopus 로고
    • + binding sites with two different mechanisms
    • + binding sites with two different mechanisms. J Mol Biol 377 (2008) 804-818
    • (2008) J Mol Biol , vol.377 , pp. 804-818
    • Noskov, S.Y.1    Roux, B.2
  • 55
    • 34250331233 scopus 로고    scopus 로고
    • The influence of protonation states on the dynamics of the NhaA antiporter from Escherichia coli
    • Olkhova E., Padan E., and Michel H. The influence of protonation states on the dynamics of the NhaA antiporter from Escherichia coli. Biophys J 92 (2007) 3784-3791
    • (2007) Biophys J , vol.92 , pp. 3784-3791
    • Olkhova, E.1    Padan, E.2    Michel, H.3
  • 57
    • 34447339675 scopus 로고    scopus 로고
    • Mechanics of force propagation in TonB-dependent outer membrane transport
    • Gumbart J., Wiener M.C., and Tajkhorshid E. Mechanics of force propagation in TonB-dependent outer membrane transport. Biophys J 93 (2007) 496-504
    • (2007) Biophys J , vol.93 , pp. 496-504
    • Gumbart, J.1    Wiener, M.C.2    Tajkhorshid, E.3
  • 58
    • 47749085530 scopus 로고    scopus 로고
    • Electrostatic funneling of substrate in mitochondrial inner membrane carriers
    • The first report in which spontaneous ligand binding to a protein was captured in 0.1 μs simulations and the unknown binding pocket along with initial protein conformational changes triggered by the substrate were identified. The study characterizes electrostatic forces as a common mechanism of substrate recruitment in all mitochondrial carriers.
    • Wang Y., and Tajkhorshid E. Electrostatic funneling of substrate in mitochondrial inner membrane carriers. Proc Natl Acad Sci U S A 105 (2008) 9598-9603. The first report in which spontaneous ligand binding to a protein was captured in 0.1 μs simulations and the unknown binding pocket along with initial protein conformational changes triggered by the substrate were identified. The study characterizes electrostatic forces as a common mechanism of substrate recruitment in all mitochondrial carriers.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 9598-9603
    • Wang, Y.1    Tajkhorshid, E.2
  • 59
    • 52449099841 scopus 로고    scopus 로고
    • Binding of ADP in the mitochondrial ADP/ATP carrier is driven by an electrostatic funnel
    • Dehez F., Pebay-Peyroula E., and Chipot C. Binding of ADP in the mitochondrial ADP/ATP carrier is driven by an electrostatic funnel. J Am Chem Soc 130 (2008) 12725-12733
    • (2008) J Am Chem Soc , vol.130 , pp. 12725-12733
    • Dehez, F.1    Pebay-Peyroula, E.2    Chipot, C.3
  • 60
    • 56849094008 scopus 로고    scopus 로고
    • Conformational dynamics of the mitochondrial ADP/ATP carrier: a simulation study
    • Johnston J.M., Khalid S., and Sansom M.S.P. Conformational dynamics of the mitochondrial ADP/ATP carrier: a simulation study. Mol Membr Biol 25 (2008) 506-517
    • (2008) Mol Membr Biol , vol.25 , pp. 506-517
    • Johnston, J.M.1    Khalid, S.2    Sansom, M.S.P.3
  • 61
    • 77950865843 scopus 로고    scopus 로고
    • Many-body polarization effects and the membrane dipole potential
    • Harder E., MacKerell A.D., and Roux B. Many-body polarization effects and the membrane dipole potential. J Am Chem Soc 131 (2009) 2760-2761
    • (2009) J Am Chem Soc , vol.131 , pp. 2760-2761
    • Harder, E.1    MacKerell, A.D.2    Roux, B.3
  • 62
    • 43849093505 scopus 로고    scopus 로고
    • Ten-microsecond MD simulation of a fast-folding WW domain
    • Freddolino P.L., Liu F., Gruebele M., and Schulten K. Ten-microsecond MD simulation of a fast-folding WW domain. Biophys J 94 (2008) L75-L77
    • (2008) Biophys J , vol.94
    • Freddolino, P.L.1    Liu, F.2    Gruebele, M.3    Schulten, K.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.