메뉴 건너뛰기




Volumn 73, Issue 4, 2008, Pages 851-863

Molecular mechanism of substrate specificity in the bacterial neutral amino acid transporter LeuT

Author keywords

Free energy simulations; NSS transporters; Substrate specificity

Indexed keywords

ALANINE; AMINO ACID TRANSPORTER; AMPHOLYTE; GLYCINE; LEUCINE; LEUT PROTEIN; NEUROTRANSMITTER TRANSPORTER; UNCLASSIFIED DRUG; WATER; AMINO ACID; LIGAND;

EID: 58149311441     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22108     Document Type: Article
Times cited : (34)

References (61)
  • 3
    • 0003398292 scopus 로고    scopus 로고
    • Neurotransmitter transporters: Structure, functions, and regulations
    • Reith RA, editor. Totowa, NJ: Humana Press
    • Rudnick G. Neurotransmitter transporters: structure, functions, and regulations. In: Reith RA, editor. Mechanisms of biogenic amine neurotransmitter transporters. Totowa, NJ: Humana Press; 2002.
    • (2002) Mechanisms of Biogenic Amine Neurotransmitter Transporters
    • Rudnick, G.1
  • 4
    • 2542464048 scopus 로고    scopus 로고
    • Transporter structure and mechanism
    • DeFelice L. Transporter structure and mechanism. Trends Neurosci 2004;27:352-359.
    • (2004) Trends Neurosci , vol.27 , pp. 352-359
    • DeFelice, L.1
  • 5
    • 0015044844 scopus 로고
    • Role of transmitter uptake mechanism in synaptic transmission
    • Iversen LL. Role of transmitter uptake mechanism in synaptic transmission. Br J Pharmacol 1971;41:571-577.
    • (1971) Br J Pharmacol , vol.41 , pp. 571-577
    • Iversen, L.L.1
  • 7
    • 20444428381 scopus 로고    scopus 로고
    • How did the neurotransmitter cross the bilayer? A closer view
    • DOI 10.1016/j.conb.2005.05.009, PII S0959438805000747
    • Sonders MS, Quick M, Javitch JA. How did the neurotransmitter cross the bilayer? A closer view. Curr Opin Neurobiol 2005;15:296-304. (Pubitemid 40806441)
    • (2005) Current Opinion in Neurobiology , vol.15 , Issue.3 SPEC. ISS. , pp. 296-304
    • Sonders, M.S.1    Quick, M.2    Javitch, J.A.3
  • 8
    • 35148815052 scopus 로고    scopus 로고
    • Mechanism of chloride interaction with neurotransmitter:sodium symporters
    • DOI 10.1038/nature06133, PII NATURE06133
    • Zomot E, Bendahan A, Quick M, Zhao Y, Javitch JA, Kanner B. Mechanism of chloride interaction with neurotransmitter sodium symporters. Nature 2007;449:726-730. (Pubitemid 47552085)
    • (2007) Nature , vol.449 , Issue.7163 , pp. 726-730
    • Zomot, E.1    Bendahan, A.2    Quick, M.3    Zhao, Y.4    Javitch, J.A.5    Kanner, B.I.6
  • 9
    • 33846505059 scopus 로고    scopus 로고
    • Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter
    • DOI 10.1038/nature05455, PII NATURE05455
    • Boudker O, Ryan RM, Yernool D, Shimamoto K, Gouaux E. Coupling substrate and ion binding to extracellular gate of a sodiumdependent aspartate transporter. Nature 2007;445:387-393. (Pubitemid 46160902)
    • (2007) Nature , vol.445 , Issue.7126 , pp. 387-393
    • Boudker, O.1    Ryan, R.M.2    Yernool, D.3    Shimamoto, K.4    Gouaux, E.5
  • 10
    • 0038266898 scopus 로고    scopus 로고
    • Membrane-inserted conformation of transmembrane domain 4 of divalent-metal transporter
    • DOI 10.1042/BJ20030075
    • Li H, Li F, Sun H, Qian ZM. Membrane-inserted conformation of transmembrane domain 4 of divalent-metal transporter. Biochem J 2003;372:757-766. (Pubitemid 36760389)
    • (2003) Biochemical Journal , vol.372 , Issue.3 , pp. 757-766
    • Li, H.1    Li, F.2    Sun, H.3    Qian, Z.M.4
  • 11
    • 33744948233 scopus 로고    scopus 로고
    • 136) in transmembrane domain 2 of the serotonin transporter is required for the conformational switch in the transport cycle
    • DOI 10.1074/jbc.M511382200
    • Korkhov VM, Holy M, Freissmuth M, Sitte HH. The conserved glutamate (Glu136) in TM2 of the serotonin transporter is required for the conformational switch in the transport cycle. J Biol Chem 2006;281:13439-13448. (Pubitemid 43855256)
    • (2006) Journal of Biological Chemistry , vol.281 , Issue.19 , pp. 13439-13448
    • Korkhov, V.M.1    Holy, M.2    Freissmuth, M.3    Sitte, H.H.4
  • 12
    • 33751194447 scopus 로고    scopus 로고
    • + symporters (NSS) aids in the use of the LeuT structure to probe NSS structure and function
    • + symporters (NSS) aids in the use of the LeuT structure to probe NSS structure and function. Mol Pharmacol 2006;70:1630-1642.
    • (2006) Mol Pharmacol , vol.70 , pp. 1630-1642
    • Beuming, T.1    Shi, L.2    Javitch, J.A.3    Weinstein, H.A.4
  • 13
    • 34247648737 scopus 로고    scopus 로고
    • The uncoupled chloride conductance of a bacterial glutamate transporter homolog
    • DOI 10.1038/nsmb1230, PII NSMB1230
    • Ryan RM, Mindell JA. The uncoupled chloride conductance of a bacterial glutamate transporter homolog. Natl Struct Mol Biol 2007; 14:365-371. (Pubitemid 46685880)
    • (2007) Nature Structural and Molecular Biology , vol.14 , Issue.5 , pp. 365-371
    • Ryan, R.M.1    Mindell, J.A.2
  • 14
    • 34548178234 scopus 로고    scopus 로고
    • Antidepressant binding site in a bacterial homologue of neurotransmitter transporters
    • DOI 10.1038/nature06038, PII NATURE06038
    • Singh SK, Yamashita A, Gouaux E. Antidepressant binding site in a bacterial homologue of neurotransmitter transporters. Nature 2007;448:952-956. (Pubitemid 47312772)
    • (2007) Nature , vol.448 , Issue.7156 , pp. 952-956
    • Singh, S.K.1    Yamashita, A.2    Gouaux, E.3
  • 15
    • 33749532284 scopus 로고    scopus 로고
    • Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials
    • DOI 10.1529/biophysj.106.084301
    • Wang JY, Deng YQ, Roux B. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys J 2006;91:2798-2814. (Pubitemid 44526470)
    • (2006) Biophysical Journal , vol.91 , Issue.8 , pp. 2798-2814
    • Wang, J.1    Deng, Y.2    Roux, B.3
  • 16
    • 33749238080 scopus 로고    scopus 로고
    • Calculation of standard binding free energies: Aromatic molecules in the T4 lysozyme L99A mutant
    • Deng YQ, Roux B. Calculation of standard binding free energies: aromatic molecules in the T4 lysozyme L99A mutant. J Chem Theor Comp 2006;2:1255-1273.
    • (2006) J Chem Theor Comp , vol.2 , pp. 1255-1273
    • Deng, Y.Q.1    Roux, B.2
  • 17
    • 0042787283 scopus 로고    scopus 로고
    • The role of bonded terms in free energy simulations: Theoretical analysis
    • Boresch S, Karplus M. The role of bonded terms in free energy simulations: theoretical analysis. J Phys Chem A 2000;103:103-118.
    • (2000) J Phys Chem A , vol.103 , pp. 103-118
    • Boresch, S.1    Karplus, M.2
  • 18
    • 0141682863 scopus 로고    scopus 로고
    • Absolute binding free energies: A quantitative approach for their calculation
    • Boresch S, Tettinger F, Leitgeb M, Karplus M. Absolute binding free energies: a quantitative approach for their calculation. J Phys Chem B 2003;107:9535-9551.
    • (2003) J Phys Chem B , vol.107 , pp. 9535-9551
    • Boresch, S.1    Tettinger, F.2    Leitgeb, M.3    Karplus, M.4
  • 19
    • 7544232432 scopus 로고    scopus 로고
    • Hydration of amino acid side chains: Non-polar and electrostatic contributions calculated from staged molecular dynamics free energy simulations with explicit water molecules
    • Deng Y, Roux B. Hydration of amino acid side chains: non-polar and electrostatic contributions calculated from staged molecular dynamics free energy simulations with explicit water molecules. J Phys Chem B 2004;108:16567-16576.
    • (2004) J Phys Chem B , vol.108 , pp. 16567-16576
    • Deng, Y.1    Roux, B.2
  • 20
    • 85005687495 scopus 로고
    • The free energy of xenon binding to myoglobin from molecular dynamics simulation
    • Hermans J, Shankar S. The free energy of xenon binding to myoglobin from molecular dynamics simulation. Isr J Chem 1986;27: 225-227.
    • (1986) Isr J Chem , vol.27 , pp. 225-227
    • Hermans, J.1    Shankar, S.2
  • 21
    • 0030887944 scopus 로고    scopus 로고
    • Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme
    • DOI 10.1021/ja963568+, PII S0002786396035688
    • Hermans J, Wang L. Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme. J Am Chem Soc 1997;119:2707-2714. (Pubitemid 27189565)
    • (1997) Journal of the American Chemical Society , vol.119 , Issue.11 , pp. 2707-2714
    • Hermans, J.1    Wang, L.2
  • 22
    • 0027160197 scopus 로고
    • Backbone-dependent rotamer library for proteins. Application to side-chain prediction
    • DOI 10.1006/jmbi.1993.1170
    • Dunbrack RL, Karplus M. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J Mol Biol 1993; 230:543. (Pubitemid 23161363)
    • (1993) Journal of Molecular Biology , vol.230 , Issue.2 , pp. 543-574
    • Dunbrack Jr., R.L.1    Karplus, M.2
  • 23
    • 7244251461 scopus 로고    scopus 로고
    • 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. Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 2004;431:830-834. (Pubitemid 39434076)
    • (2004) Nature , vol.431 , Issue.7010 , pp. 830-834
    • Noskov, S.Y.1    Berneche, S.2    Roux, B.3
  • 28
    • 33846625994 scopus 로고    scopus 로고
    • Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels
    • DOI 10.1085/jgp.200609633
    • Noskov SY, Roux B. Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels. J Gen Physiol 2007;129: 135-143. (Pubitemid 46184871)
    • (2007) Journal of General Physiology , vol.129 , Issue.2 , pp. 135-143
    • Noskov, S.Y.1    Roux, B.2
  • 29
    • 40649098564 scopus 로고    scopus 로고
    • + selectivity in LeuT: Two binding sites. Two mechanisms
    • + selectivity in LeuT: two binding sites. Two mechanisms. J Mol Biol 2008;377:804-817.
    • (2008) J Mol Biol , vol.377 , pp. 804-817
    • Noskov, S.Y.1    Roux, B.2
  • 30
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equation of motions of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert J, Ciccotti G, Berendsen H. Numerical integration of the cartesian equation of motions of a system with constraints: molecular dynamics of n-alkanes. J Comp Chem 1977;23:327-341.
    • (1977) J Comp Chem , vol.23 , pp. 327-341
    • Ryckaert, J.1    Ciccotti, G.2    Berendsen, H.3
  • 32
    • 0035249196 scopus 로고    scopus 로고
    • Generalized solvent boundary potential for computer simulations
    • DOI 10.1063/1.1336570
    • Im W, Bernèche S, Roux B. Generalized solvent boundary potentials for computer simulations. J Chem Phys 2001;114:2924-2937. (Pubitemid 32253408)
    • (2001) Journal of Chemical Physics , vol.114 , Issue.7 , pp. 2924-2937
    • Im, W.1    Berneche, S.2    Roux, B.3
  • 33
    • 0010159070 scopus 로고
    • Optimized cluster expansion for classical fluids. II. Theory of molecular liquids
    • Chandler D, Andersen HC. Optimized cluster expansion for classical fluids. II. Theory of molecular liquids. J Chem Phys 1972;57: 1930-1937.
    • (1972) J Chem Phys , vol.57 , pp. 1930-1937
    • Chandler, D.1    Andersen, H.C.2
  • 34
    • 33947405744 scopus 로고    scopus 로고
    • Solvation free energy of amino acids and side-chain analogues
    • DOI 10.1021/jp0620163
    • Chang J, Lenhoff AM, Sandler SI. Solvation free energy of amino acids and side-chain analogues. J Phys Chem B 2007;111:2098-2106. (Pubitemid 46456207)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.8 , pp. 2098-2106
    • Chang, J.1    Lenhoff, A.M.2    Sandler, S.I.3
  • 35
    • 7044249333 scopus 로고    scopus 로고
    • Grand canonical Monte Carlo simulation of water in protein environments
    • Woo H, Dinner A, Roux B. Grand canonical Monte Carlo simulation of water in protein environments. J Chem Phys 2004;121: 6392-6400.
    • (2004) J Chem Phys , vol.121 , pp. 6392-6400
    • Woo, H.1    Dinner, A.2    Roux, B.3
  • 37
    • 36049017659 scopus 로고    scopus 로고
    • Confine-and-release method: Obtaining correct binding free energies in the presence of protein conformational change
    • Mobley DL, Chodera JD, Dill KA. Confine-and-release method: obtaining correct binding free energies in the presence of protein conformational change. J Chem Theor Comp 2007;3:1231-1235.
    • (2007) J Chem Theor Comp , vol.3 , pp. 1231-1235
    • Mobley, D.L.1    Chodera, J.D.2    Dill, K.A.3
  • 38
    • 34347228685 scopus 로고    scopus 로고
    • Molecular basis for substrate discrimination by glycine transporters
    • DOI 10.1074/jbc.M609158200
    • Vandenberg RJ, Shaddick K, Ju PC. Molecular basis for substrate discrimination by glycine transporters. J Biol Chem 2007;282: 14447-14453. (Pubitemid 47100462)
    • (2007) Journal of Biological Chemistry , vol.282 , Issue.19 , pp. 14447-14453
    • Vandenberg, R.J.1    Shaddick, K.2    Ju, P.3
  • 39
    • 0034900495 scopus 로고    scopus 로고
    • Free energy decomposition of protein-protein interactions
    • Noskov SY, Lim C. Free energy decomposition of protein-protein interactions. Biophys J 2001;81:737-750. (Pubitemid 32721449)
    • (2001) Biophysical Journal , vol.81 , Issue.2 , pp. 737-750
    • Noskov, S.Y.1    Lim, C.2
  • 40
    • 0031058541 scopus 로고    scopus 로고
    • The statistical-thermodynamic basis for computation of binding affinities: A critical review
    • Gilson MK, Given JA, Bush BL, McCammon JA. The statisticalthermodynamic basis for computation of binding affinities: a critical review. Biophys J 1997;72:1047-1069. (Pubitemid 27113632)
    • (1997) Biophysical Journal , vol.72 , Issue.3 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 42
    • 41449093586 scopus 로고    scopus 로고
    • Substrate binding and formation of an occluded state in the leucine transporter
    • Celik L, Schiott B, Tajkhorshid E. Substrate binding and formation of an occluded state in the leucine transporter. Biophys J 2008; 94:1600-1612.
    • (2008) Biophys J , vol.94 , pp. 1600-1612
    • Celik, L.1    Schiott, B.2    Tajkhorshid, E.3
  • 43
    • 33746839659 scopus 로고    scopus 로고
    • Identification of a lithium interaction site in the GABA transporter GAT-1
    • Zhou Y, Zomot E, Kanner BI. Identification of a lithium interaction site in the GABA transporter GAT-1. J Biol Chem 2006;281:22092-22099.
    • (2006) J Biol Chem , vol.281 , pp. 22092-22099
    • Zhou, Y.1    Zomot, E.2    Kanner, B.I.3
  • 48
    • 0041353145 scopus 로고    scopus 로고
    • Structure and mechanism of the lactose permease of Escherichia coli
    • DOI 10.1126/science.1088196
    • Abramson J, Smirnova I, Kasho V, Verner G, Kaback H, Iwata S. Structure and mechanism of the lactose permease of Escherichia coli. Science 2003;301:610-615. (Pubitemid 36927939)
    • (2003) Science , vol.301 , Issue.5633 , pp. 610-615
    • Abramson, J.1    Smirnova, I.2    Kasho, V.3    Verner, G.4    Kaback, H.R.5    Iwata, S.6
  • 49
    • 0242332305 scopus 로고    scopus 로고
    • Glycerol Conductance and Physical Asymmetry of the Escherichia coli Glycerol Facilitator GlpF
    • Lu D, Grayson P, Tajkhorshid E, Schulten K. Glycerol conductance and physical asymmetry of the Escherichia coli glycerol facilitator GlpF. Biophys J 2003;85:2977-2987. (Pubitemid 37351013)
    • (2003) Biophysical Journal , vol.85 , Issue.5 , pp. 2977-2987
    • Lu, D.1    Grayson, P.2    Schulten, K.3
  • 51
    • 0034690250 scopus 로고    scopus 로고
    • Ion permeation mechanism of the potassium channel
    • DOI 10.1038/35009114
    • Åqvist J, Luzhkov V. Ion permeation mechanism of the potassium channel. Nature 2000;404:881-884. (Pubitemid 30230340)
    • (2000) Nature , vol.404 , Issue.6780 , pp. 881-884
    • Aqvist, J.1    Luzhkov, V.2
  • 52
    • 0035855251 scopus 로고    scopus 로고
    • + selectivity of the KcsA potassium channel from microscopic free energy perturbation calculations
    • + selectivity of the KcsA potassium channel from microscopic free energy perturbation calculations. Biochim Biophys Acta 2001;1548:194-202.
    • (2001) Biochim Biophys Acta , vol.1548 , pp. 194-202
    • Luzhkov, V.B.1    Åqvist, J.2
  • 53
    • 33750616752 scopus 로고
    • Ionic selectivity of proteins: Lessons from molecular dynamics simualtions on valinomycin
    • Gaber BP, Easwaran KRK, editors. Adenine Press
    • Eisenman G, Alvarez O. Ionic selectivity of proteins: lessons from molecular dynamics simualtions on valinomycin. In: Gaber BP, Easwaran KRK, editors. Biomembrane structure and functions: the state of the art. Adenine Press; 1992. pp 321-351.
    • (1992) Biomembrane Structure and Functions: The State of the Art , pp. 321-351
    • Eisenman, G.1    Alvarez, O.2
  • 55
    • 3042736867 scopus 로고    scopus 로고
    • On the theory of noncovalent binding
    • Mihailescu M, Gilson M. On the theory of noncovalent binding. Biophys J 2004;87:23-36.
    • (2004) Biophys J , vol.87 , pp. 23-36
    • Mihailescu, M.1    Gilson, M.2
  • 56
    • 3142652094 scopus 로고    scopus 로고
    • Theoretical and computational models of biological ion channels
    • Roux B, Allen TW, Bernèche S, Im W. Theoretical and computational models of biological ion channels. Quart Rev Biophys 2004; 37:15-103.
    • (2004) Quart Rev Biophys , vol.37 , pp. 15-103
    • Roux, B.1    Allen, T.W.2    Bernèche, S.3    Im, W.4
  • 57
    • 0037134267 scopus 로고    scopus 로고
    • Control of the selectivity of the aquaporin water channel family by global orientational tuning
    • DOI 10.1126/science.1067778
    • Tajkhorshid E, Nollert P, Jensen MO, Miercke LJ, O'Connell J, Stroud RM, Schulten K. Control of the selectivity of the aquaporin water channel family by global orientational tuning. Science 2002; 296:525-530. (Pubitemid 34413590)
    • (2002) Science , vol.296 , Issue.5567 , pp. 525-530
    • Tajkhorshid, E.1    Nollert, P.2    Jensen, M.O.3    Miercke, L.J.W.4    O'Connell, J.5    Stroud, R.M.6    Schulten, K.7
  • 58
    • 0036389892 scopus 로고    scopus 로고
    • Ion permeation and selectivity of OmpF porin: A theoretical study based on molecular dynamics. Brownian dynamics, and continuum electrodiffusion theory
    • Im W, Roux B. Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics. Brownian dynamics, and continuum electrodiffusion theory. J Mol Biol 2002;322: 851-869.
    • (2002) J Mol Biol , vol.322 , pp. 851-869
    • Im, W.1    Roux, B.2
  • 59
    • 0036301334 scopus 로고    scopus 로고
    • Ions and counterions in a biological channel: A molecular dynamics simulation of ompf porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution
    • DOI 10.1016/S0022-2836(02)00380-7
    • Im W, Roux B. Ions and counterions in a biological channel: a molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution. J Mol Biol 2002;319:1177-1197. (Pubitemid 34729427)
    • (2002) Journal of Molecular Biology , vol.319 , Issue.5 , pp. 1177-1197
    • Im, W.1    Roux, B.2
  • 60
    • 33947139278 scopus 로고    scopus 로고
    • Setting up and running molecular dynamics simulations of membrane proteins
    • DOI 10.1016/j.ymeth.2006.08.006, PII S1046202306001873
    • Kandt C, Ash WL, Tieleman DP. Setting up and running molecular dynamics simulations of membrane proteins. Methods 2007;41:475-488. (Pubitemid 46400527)
    • (2007) Methods , vol.41 , Issue.4 , pp. 475-488
    • Kandt, C.1    Ash, W.L.2    Peter Tieleman, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.