-
1
-
-
49549083949
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
+ 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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
28
-
-
50649125767
-
The structure of an open form of an E. coli mechanosensitive channel at 3.45 Å resolution
-
Wang W., Black S.S., Edwards M.D., Miller S., Morrison E.L., Bartlett W., Dong C., Naismith J.H., and Booth I.R. The structure of an open form of an E. coli mechanosensitive channel at 3.45 Å resolution. Science 321 (2008) 1179-1183
-
(2008)
Science
, vol.321
, pp. 1179-1183
-
-
Wang, W.1
Black, S.S.2
Edwards, M.D.3
Miller, S.4
Morrison, E.L.5
Bartlett, W.6
Dong, C.7
Naismith, J.H.8
Booth, I.R.9
-
29
-
-
34848895197
-
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
-
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
-
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
-
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
-
+ 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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
42
-
-
48749106109
-
+/sugar symport
-
+/sugar symport. Science 321 (2008) 810-814
-
(2008)
Science
, vol.321
, pp. 810-814
-
-
Faham, S.1
Watanabe, A.2
Besserer, G.M.3
Cascio, D.4
Specht, A.5
Hirayama, B.A.6
Wright, E.M.7
Abramson, J.8
-
43
-
-
33845380397
-
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
-
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
-
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
-
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
-
47
-
-
41949130566
-
Salt-bridge dynamics control substrate-induced conformational change in the membrane transporter GlpT
-
Law C.J., Almqvist J., Bernstein A., Goetz R.M., Huang Y., Soudant C., Laaksonen A., Hovmöller S., and Wang D.N. Salt-bridge dynamics control substrate-induced conformational change in the membrane transporter GlpT. J Mol Biol 378 (2008) 828-839
-
(2008)
J Mol Biol
, vol.378
, pp. 828-839
-
-
Law, C.J.1
Almqvist, J.2
Bernstein, A.3
Goetz, R.M.4
Huang, Y.5
Soudant, C.6
Laaksonen, A.7
Hovmöller, S.8
Wang, D.N.9
-
48
-
-
47749083479
-
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
-
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
-
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
-
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
-
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
-
+ 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
-
+ 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
-
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
-
56
-
-
34547902820
-
+ antiporting
-
+ antiporter NhaA.
-
+ antiporter NhaA.
-
(2007)
Science
, vol.317
, pp. 799-802
-
-
Arkin, I.T.1
Xu, H.2
Jensen, M.3
Arbely, E.4
Bennett, E.R.5
Bowers, K.J.6
Chow, E.7
Dror, R.O.8
Eastwood, M.P.9
Flitman-Tene, R.10
-
57
-
-
34447339675
-
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
-
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
-
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
-
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
-
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
|