-
3
-
-
84856225222
-
X-ray structures of LeuT in substrate-free outward-open and apo inward-open states
-
H. Krishnamurthy, and E. Gouaux X-ray structures of LeuT in substrate-free outward-open and apo inward-open states Nature 481 2012 469 474
-
(2012)
Nature
, vol.481
, pp. 469-474
-
-
Krishnamurthy, H.1
Gouaux, E.2
-
4
-
-
84881405804
-
Sodium-coupled Secondary Transporters: Insights from Structure-based Computations
-
B. Roux, Word Scientific Publishing Co. Pte. Ltd. Singapore
-
E. Zomot, and A. Bakan I. Bahar Sodium-coupled Secondary Transporters: Insights from Structure-based Computations B. Roux, Molecular Machines 2011 Word Scientific Publishing Co. Pte. Ltd. Singapore 199 229
-
(2011)
Molecular Machines
, pp. 199-229
-
-
Zomot, E.1
Bakan, A.2
Bahar, I.3
-
5
-
-
66249098083
-
Unlocking the molecular secrets of sodium-coupled transporters
-
H. Krishnamurthy, C.L. Piscitelli, and E. Gouaux Unlocking the molecular secrets of sodium-coupled transporters Nature 459 2009 347 355
-
(2009)
Nature
, vol.459
, pp. 347-355
-
-
Krishnamurthy, H.1
Piscitelli, C.L.2
Gouaux, E.3
-
6
-
-
84872781515
-
Structural biology. (Pseudo-)symmetrical transport
-
L.R. Forrest Structural biology. (Pseudo-)symmetrical transport Science 339 2013 399 401
-
(2013)
Science
, vol.339
, pp. 399-401
-
-
Forrest, L.R.1
-
7
-
-
48349140230
-
Mechanism for alternating access in neurotransmitter transporters
-
L.R. Forrest, and Y.W. Zhang G. Rudnick Mechanism for alternating access in neurotransmitter transporters Proc. Natl. Acad. Sci. USA 105 2008 10338 10343
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 10338-10343
-
-
Forrest, L.R.1
Zhang, Y.W.2
Rudnick, G.3
-
8
-
-
84873845174
-
Visualizing functional motions of membrane transporters with molecular dynamics simulations
-
S.A. Shaikh, and J. Li E. Tajkhorshid Visualizing functional motions of membrane transporters with molecular dynamics simulations Biochemistry 52 2013 569 587
-
(2013)
Biochemistry
, vol.52
, pp. 569-587
-
-
Shaikh, S.A.1
Li, J.2
Tajkhorshid, E.3
-
9
-
-
77952481518
-
The sodium/galactose symporter crystal structure is a dynamic, not so occluded state
-
E. Zomot, and I. Bahar The sodium/galactose symporter crystal structure is a dynamic, not so occluded state Mol. Biosyst. 6 2010 1040 1046
-
(2010)
Mol. Biosyst.
, vol.6
, pp. 1040-1046
-
-
Zomot, E.1
Bahar, I.2
-
10
-
-
58149311441
-
Molecular mechanism of substrate specificity in the bacterial neutral amino acid transporter LeuT
-
S.Y. Noskov Molecular mechanism of substrate specificity in the bacterial neutral amino acid transporter LeuT Proteins 73 2008 851 863
-
(2008)
Proteins
, vol.73
, pp. 851-863
-
-
Noskov, S.Y.1
-
12
-
-
44949086583
-
+ and substrate is triggered by substrate in a second binding site
-
+ and substrate is triggered by substrate in a second binding site Mol. Cell 30 2008 667 677
-
(2008)
Mol. Cell
, vol.30
, pp. 667-677
-
-
Shi, L.1
Quick, M.2
Javitch, J.A.3
-
14
-
-
84868108835
-
Investigation of the sodium-binding sites in the sodium-coupled betaine transporter BetP
-
K. Khafizov, and C. Perez L.R. Forrest Investigation of the sodium-binding sites in the sodium-coupled betaine transporter BetP Proc. Natl. Acad. Sci. USA 109 2012 E3035 E3044
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
-
-
Khafizov, K.1
Perez, C.2
Forrest, L.R.3
-
15
-
-
41449093586
-
Substrate binding and formation of an occluded state in the leucine transporter
-
L. Celik, B. Schiøtt, and E. Tajkhorshid 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
Schiøtt, B.2
Tajkhorshid, E.3
-
16
-
-
79952811744
-
The role of local hydration and hydrogen-bonding dynamics in ion and solute release from ion-coupled secondary transporters
-
C. Zhao, and S.Y. Noskov The role of local hydration and hydrogen-bonding dynamics in ion and solute release from ion-coupled secondary transporters Biochemistry 50 2011 1848 1856
-
(2011)
Biochemistry
, vol.50
, pp. 1848-1856
-
-
Zhao, C.1
Noskov, S.Y.2
-
17
-
-
84865754444
-
Ion-controlled conformational dynamics in the outward-open transition from an occluded state of LeuT
-
C. Zhao, and S. Stolzenberg L. Shi Ion-controlled conformational dynamics in the outward-open transition from an occluded state of LeuT Biophys. J. 103 2012 878 888
-
(2012)
Biophys. J.
, vol.103
, pp. 878-888
-
-
Zhao, C.1
Stolzenberg, S.2
Shi, L.3
-
19
-
-
84866376631
-
A conformational switch in a partially unwound helix selectively determines the pathway for substrate release from the carnitine/γ- butyrobetaine antiporter CaiT
-
E. Zomot, and I. Bahar A conformational switch in a partially unwound helix selectively determines the pathway for substrate release from the carnitine/γ-butyrobetaine antiporter CaiT J. Biol. Chem. 287 2012 31823 31832
-
(2012)
J. Biol. Chem.
, vol.287
, pp. 31823-31832
-
-
Zomot, E.1
Bahar, I.2
-
21
-
-
79957625386
-
Protonation of glutamate 208 induces the release of agmatine in an outward-facing conformation of an arginine/agmatine antiporter
-
E. Zomot, and I. Bahar Protonation of glutamate 208 induces the release of agmatine in an outward-facing conformation of an arginine/agmatine antiporter J. Biol. Chem. 286 2011 19693 19701
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 19693-19701
-
-
Zomot, E.1
Bahar, I.2
-
22
-
-
81255164752
-
Simulations of the alternating access mechanism of the sodium symporter Mhp1
-
J.L. Adelman, and A.L. Dale M. Grabe Simulations of the alternating access mechanism of the sodium symporter Mhp1 Biophys. J. 101 2011 2399 2407
-
(2011)
Biophys. J.
, vol.101
, pp. 2399-2407
-
-
Adelman, J.L.1
Dale, A.L.2
Grabe, M.3
-
23
-
-
84863476382
-
LeuT conformational sampling utilizing accelerated molecular dynamics and principal component analysis
-
J.R. Thomas, and P.C. Gedeon J.D. Madura LeuT conformational sampling utilizing accelerated molecular dynamics and principal component analysis Biophys. J. 103 2012 L1 L3
-
(2012)
Biophys. J.
, vol.103
-
-
Thomas, J.R.1
Gedeon, P.C.2
Madura, J.D.3
-
24
-
-
0014029736
-
Simple allosteric model for membrane pumps
-
O. Jardetzky Simple allosteric model for membrane pumps Nature 211 1966 969 970
-
(1966)
Nature
, vol.211
, pp. 969-970
-
-
Jardetzky, O.1
-
25
-
-
58149233796
-
A competitive inhibitor traps LeuT in an open-to-out conformation
-
S.K. Singh, and C.L. Piscitelli E. Gouaux A competitive inhibitor traps LeuT in an open-to-out conformation Science 322 2008 1655 1661
-
(2008)
Science
, vol.322
, pp. 1655-1661
-
-
Singh, S.K.1
Piscitelli, C.L.2
Gouaux, E.3
-
26
-
-
65249169367
-
Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation
-
M. Quick, and A.M. Winther J.A. Javitch Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation Proc. Natl. Acad. Sci. USA 106 2009 5563 5568
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 5563-5568
-
-
Quick, M.1
Winther, A.M.2
Javitch, J.A.3
-
27
-
-
78650817193
-
Neurotransmitter/sodium symporter orthologue LeuT has a single high-affinity substrate site
-
C.L. Piscitelli, H. Krishnamurthy, and E. Gouaux Neurotransmitter/sodium symporter orthologue LeuT has a single high-affinity substrate site Nature 468 2010 1129 1132
-
(2010)
Nature
, vol.468
, pp. 1129-1132
-
-
Piscitelli, C.L.1
Krishnamurthy, H.2
Gouaux, E.3
-
28
-
-
84856709995
-
Experimental conditions can obscure the second high-affinity site in LeuT
-
M. Quick, and L. Shi J.A. Javitch Experimental conditions can obscure the second high-affinity site in LeuT Nat. Struct. Mol. Biol. 19 2012 207 211
-
(2012)
Nat. Struct. Mol. Biol.
, vol.19
, pp. 207-211
-
-
Quick, M.1
Shi, L.2
Javitch, J.A.3
-
29
-
-
84862790971
-
Structures of LeuT in bicelles define conformation and substrate binding in a membrane-like context
-
H. Wang, J. Elferich, and E. Gouaux Structures of LeuT in bicelles define conformation and substrate binding in a membrane-like context Nat. Struct. Mol. Biol. 19 2012 212 219
-
(2012)
Nat. Struct. Mol. Biol.
, vol.19
, pp. 212-219
-
-
Wang, H.1
Elferich, J.2
Gouaux, E.3
-
30
-
-
84865730840
-
Substrate binds in the S1 site of the F253A mutant of LeuT, a neurotransmitter sodium symporter homologue
-
H. Wang, and E. Gouaux Substrate binds in the S1 site of the F253A mutant of LeuT, a neurotransmitter sodium symporter homologue EMBO Rep. 13 2012 861 866
-
(2012)
EMBO Rep.
, vol.13
, pp. 861-866
-
-
Wang, H.1
Gouaux, E.2
-
31
-
-
79957935490
-
+-coupled neurotransmitter transporter homologue
-
+-coupled neurotransmitter transporter homologue Nature 474 2011 109 113
-
(2011)
Nature
, vol.474
, pp. 109-113
-
-
Zhao, Y.1
Terry, D.S.2
Javitch, J.A.3
-
33
-
-
44849091207
-
Sodium-coupled neurotransmitter transporters
-
B.I. Kanner, and E. Zomot Sodium-coupled neurotransmitter transporters Chem. Rev. 108 2008 1654 1668
-
(2008)
Chem. Rev.
, vol.108
, pp. 1654-1668
-
-
Kanner, B.I.1
Zomot, E.2
-
34
-
-
0346882663
-
ModLoop: Automated modeling of loops in protein structures
-
A. Fiser, and A. Sali ModLoop: automated modeling of loops in protein structures Bioinformatics 19 2003 2500 2501
-
(2003)
Bioinformatics
, vol.19
, pp. 2500-2501
-
-
Fiser, A.1
Sali, A.2
-
36
-
-
3142716857
-
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
-
D. Hamelberg, J. Mongan, and J.A. McCammon Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules J. Chem. Phys. 120 2004 11919 11929
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 11919-11929
-
-
Hamelberg, D.1
Mongan, J.2
McCammon, J.A.3
-
37
-
-
29744459271
-
Exploring the free-energy landscape of a short peptide using an average force
-
C. Chipot, and J. Hénin Exploring the free-energy landscape of a short peptide using an average force J. Chem. Phys. 123 2005 244906
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 244906
-
-
Chipot, C.1
Hénin, J.2
-
39
-
-
33750407288
-
Anisotropic network model: Systematic evaluation and a new web interface
-
E. Eyal, L.W. Yang, and I. Bahar Anisotropic network model: systematic evaluation and a new web interface Bioinformatics 22 2006 2619 2627
-
(2006)
Bioinformatics
, vol.22
, pp. 2619-2627
-
-
Eyal, E.1
Yang, L.W.2
Bahar, I.3
-
40
-
-
79957788878
-
ProDy: Protein dynamics inferred from theory and experiments
-
A. Bakan, L.M. Meireles, and I. Bahar ProDy: protein dynamics inferred from theory and experiments Bioinformatics 27 2011 1575 1577
-
(2011)
Bioinformatics
, vol.27
, pp. 1575-1577
-
-
Bakan, A.1
Meireles, L.M.2
Bahar, I.3
-
41
-
-
77949634796
-
Normal mode analysis of biomolecular structures: Functional mechanisms of membrane proteins
-
I. Bahar, and T.R. Lezon I.H. Shrivastava Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins Chem. Rev. 110 2010 1463 1497
-
(2010)
Chem. Rev.
, vol.110
, pp. 1463-1497
-
-
Bahar, I.1
Lezon, T.R.2
Shrivastava, I.H.3
-
42
-
-
77952938726
-
Global dynamics of proteins: Bridging between structure and function
-
I. Bahar, and T.R. Lezon E. Eyal Global dynamics of proteins: bridging between structure and function Annu Rev Biophys 39 2010 23 42
-
(2010)
Annu Rev Biophys
, vol.39
, pp. 23-42
-
-
Bahar, I.1
Lezon, T.R.2
Eyal, E.3
-
43
-
-
34547809547
-
A unified formulation of the constant-temperature molecular-dynamics methods
-
S. Nosé A unified formulation of the constant-temperature molecular-dynamics methods J. Chem. Phys. 81 1984 511 519
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 511-519
-
-
Nosé, S.1
-
44
-
-
0001538909
-
Canonical dynamics: Equilibrium phase-space distributions
-
W.G. Hoover Canonical dynamics: equilibrium phase-space distributions Phys. Rev. A 31 1985 1695 1697
-
(1985)
Phys. Rev. A
, vol.31
, pp. 1695-1697
-
-
Hoover, W.G.1
-
45
-
-
33846823909
-
Particle mesh Ewald - An N.Log(N) method for Ewald sums in large systems
-
T. Darden, D. York, and L. Pedersen Particle mesh Ewald - an N.Log(N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
46
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
A.D. MacKerell, and D. Bashford M. Karplus All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Karplus, M.3
-
47
-
-
77953377650
-
Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types
-
J.B. Klauda, and R.M. Venable R.W. Pastor Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types J. Phys. Chem. B 114 2010 7830 7843
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 7830-7843
-
-
Klauda, J.B.1
Venable, R.M.2
Pastor, R.W.3
-
49
-
-
0029560322
-
Hinge-bending motion in citrate synthase arising from normal mode calculations
-
O. Marques, and Y.H. Sanejouand Hinge-bending motion in citrate synthase arising from normal mode calculations Proteins 23 1995 557 560
-
(1995)
Proteins
, vol.23
, pp. 557-560
-
-
Marques, O.1
Sanejouand, Y.H.2
|