메뉴 건너뛰기




Volumn 108, Issue 10, 2011, Pages 3970-3975

Periplasmic vestibule plays an important role for solute recruitment, selectivity, and gating in the Rh/Amt/MEP superfamily

Author keywords

Ammonia channel; Membrane proteins; Molecular dynamic simulations

Indexed keywords

AMMONIA; AMMONIUM TRANSPORTER B; CARBON DIOXIDE; CARBONYL DERIVATIVE; PERMEASE; PHENYL GROUP; UNCLASSIFIED DRUG;

EID: 79952762852     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1007240108     Document Type: Article
Times cited : (19)

References (52)
  • 1
    • 33845318547 scopus 로고    scopus 로고
    • The Amt/MEP/Rh family: Structure of AmtB and the mechanism of ammonia gas conduction
    • DOI 10.1152/physiol.00051.2005
    • Khademi S, Stroud RM (2006) The Amt/MEP/Rh family: Structure of AmtB and the mechanism of ammonia gas conduction. Physiology 21:419-429. (Pubitemid 44879251)
    • (2006) Physiology , vol.21 , Issue.6 , pp. 419-429
    • Khademi, S.1    Stroud, R.M.2
  • 2
    • 0027980905 scopus 로고
    • Cloning and expression of the MEP1 gene encoding an ammonium transporter in Saccharomyces cerevisiae
    • Marini AM, Vissers S, Urrestarazu A, Andre B (1994) Cloning and expression of the MEP1 gene encoding an ammonium transporter in Saccharomyces cerevisiae. EMBO J 13:3456-3463. (Pubitemid 24246181)
    • (1994) EMBO Journal , vol.13 , Issue.15 , pp. 3456-3463
    • Marini, A.-M.1    Vissers, S.2    Urrestarazu, A.3    Andre, B.4
  • 6
    • 0033757434 scopus 로고    scopus 로고
    • The human Rhesus-associated RhAG protein and a kidney homologue promote ammonium transport in yeast
    • Marini AM, et al. (2000) The human Rhesus-associated RhAG protein and a kidney homologue promote ammonium transport in yeast. Nat Genet 26:341-344.
    • (2000) Nat Genet , vol.26 , pp. 341-344
    • Marini, A.M.1
  • 7
    • 0034682768 scopus 로고    scopus 로고
    • Characterization of human RhCG and mouse Rhcg as novel non-erythroid Rh glycoprotein homologues predominantly expressed in kidney and testis
    • Liu Z, et al. (2000) Characterization of human RhCG and mouse Rhcg as novel non-erythroid Rh glycoprotein homologues predominantly expressed in kidney and testis. J Biol Chem 275:25641-25651.
    • (2000) J Biol Chem , vol.275 , pp. 25641-25651
    • Liu, Z.1
  • 8
    • 0035847047 scopus 로고    scopus 로고
    • Rh type B glycoprotein is a new member of the Rh superfamily and a putative ammonia transporter in mammals
    • DOI 10.1074/jbc.M007528200
    • Liu Z, Peng J, Mo R, Hui C, Huang CH (2001) Rh type B glycoprotein is a new member of the Rh superfamily and a putative ammonia transporter in mammals. J Biol Chem 276:1424-1433. (Pubitemid 32096574)
    • (2001) Journal of Biological Chemistry , vol.276 , Issue.2 , pp. 1424-1433
    • Liu, Z.1    Peng, J.2    Mo, R.3    Hui, C.-C.4    Huang, C.-H.5
  • 9
    • 56749100371 scopus 로고    scopus 로고
    • A role for Rhesus factor Rhcg in renal ammonium excretion and male fertility
    • Biver S, et al. (2008) A role for Rhesus factor Rhcg in renal ammonium excretion and male fertility. Nature 456:339-343.
    • (2008) Nature , vol.456 , pp. 339-343
    • Biver, S.1
  • 12
    • 77749251881 scopus 로고    scopus 로고
    • Functional reconstitution into liposomes of purified human RhCG ammonia channel
    • Mouro-Chanteloup I, et al. (2010) Functional reconstitution into liposomes of purified human RhCG ammonia channel. PLoS One 5:e8921.
    • (2010) PLoS One , vol.5
    • Mouro-Chanteloup, I.1
  • 13
    • 62149124787 scopus 로고    scopus 로고
    • Concentration-dependent effects on intracellular and surface pH of exposing Xenopus oocytes to solutions containing NH3/NH4(+)
    • Musa-Aziz R, Jiang L, Chen LM, Behar KL, Boron WF (2009) Concentration-dependent effects on intracellular and surface pH of exposing Xenopus oocytes to solutions containing NH3/NH4(+). J Membr Biol 228:15-31.
    • (2009) J Membr Biol , vol.228 , pp. 15-31
    • Musa-Aziz, R.1    Jiang, L.2    Chen, L.M.3    Behar, K.L.4    Boron, W.F.5
  • 15
    • 33646029103 scopus 로고    scopus 로고
    • Ion transport versus gas conduction: Function of AMT/Rh-type proteins
    • Ludewig U (2006) Ion transport versus gas conduction: Function of AMT/Rh-type proteins. Transfus Clin Biol 13:111-116.
    • (2006) Transfus Clin Biol , vol.13 , pp. 111-116
    • Ludewig, U.1
  • 20
    • 37649023285 scopus 로고    scopus 로고
    • The 1.3-A resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3 transport by Rhesus family proteins
    • Lupo D, et al. (2007) The 1.3-A resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3 transport by Rhesus family proteins. Proc Natl Acad Sci USA 104:19303-19308.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 19303-19308
    • Lupo, D.1
  • 22
    • 77953097228 scopus 로고    scopus 로고
    • Function of human Rh based on structure of RhCG at 2.1 A
    • Gruswitz F, et al. (2010) Function of human Rh based on structure of RhCG at 2.1 A. Proc Natl Acad Sci USA 107:9638-9643.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 9638-9643
    • Gruswitz, F.1
  • 23
    • 0036606751 scopus 로고    scopus 로고
    • Purification of the Escherichia coli ammonium transporter AmtB reveals a trimeric stoichiometry
    • DOI 10.1042/BJ20011761
    • Blakey D, et al. (2002) Purification of the Escherichia coliammonium transporter AmtB reveals a trimeric stoichiometry. Biochem J 364:527-535. (Pubitemid 34620813)
    • (2002) Biochemical Journal , vol.364 , Issue.2 , pp. 527-535
    • Blakey, D.1    Leech, A.2    Thomas, G.H.3    Coutts, G.4    Findlay, K.5    Merrick, M.6
  • 26
    • 33748495575 scopus 로고    scopus 로고
    • Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB
    • DOI 10.1021/bi0610799
    • Luzhkov VB, Almlof M, Nervall M, Aqvist J (2006) Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB. Biochemistry 45:10807-10814. (Pubitemid 44360150)
    • (2006) Biochemistry , vol.45 , Issue.36 , pp. 10807-10814
    • Luzhkov, V.B.1    Almlof, M.2    Nervall, M.3    Aqvist, J.4
  • 27
    • 34548167328 scopus 로고    scopus 로고
    • Modulation of the protein environment in the hydrophilic pore of the ammonia transporter protein AmtB upon GlnK protein binding
    • Ishikita H (2007) Modulation of the protein environment in the hydrophilic pore of the ammonia transporter protein AmtB upon GlnK protein binding. FEBS Lett 581:4293-4297.
    • (2007) FEBS Lett , vol.581 , pp. 4293-4297
    • Ishikita, H.1
  • 29
    • 34247648064 scopus 로고    scopus 로고
    • A stable water chain in the hydrophobic pore of the AmtB ammonium transporter
    • Lamoureux G, Klein ML, Berneche S (2007) A stable water chain in the hydrophobic pore of the AmtB ammonium transporter. Biophys J 92:L82-84.
    • (2007) Biophys J , vol.92
    • Lamoureux, G.1    Klein, M.L.2    Berneche, S.3
  • 30
    • 33846796146 scopus 로고    scopus 로고
    • Protonation states of ammonia/ammonium in the hydrophobic pore of ammonia transporter protein AmtB
    • DOI 10.1021/ja066208n
    • Ishikita H, Knapp EW (2007) Protonation states of ammonia/ammonium in the hydrophobic pore of ammonia transporter protein AmtB. J Am Chem Soc 129:1210-1215. (Pubitemid 46208591)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.5 , pp. 1210-1215
    • Ishikita, H.1    Knapp, E.-W.2
  • 31
    • 34250313708 scopus 로고    scopus 로고
    • On the equivalence point for ammonium (de)protonation during its transport through the AmtB channel
    • Bostick DL, Brooks CL, 3rd (2007) On the equivalence point for ammonium (de)protonation during its transport through the AmtB channel. Biophys J 92:L103-105.
    • (2007) Biophys J , vol.92
    • Bostick, D.L.1    Brooks III, C.L.2
  • 32
    • 33847311716 scopus 로고    scopus 로고
    • Deprotonation by dehydration: The origin of ammonium sensing in the AmtB channel
    • Bostick DL, Brooks CL, 3rd (2007) Deprotonation by dehydration: The origin of ammonium sensing in the AmtB channel. PLoS Comput Biol 3:e22.
    • (2007) PLoS Comput Biol , vol.3
    • Bostick, D.L.1    Brooks III, C.L.2
  • 33
    • 33845461593 scopus 로고    scopus 로고
    • Ammonium recruitment and ammonia transport by E. coli ammonia channel AmtB
    • DOI 10.1529/biophysj.106.089714
    • Nygaard TP, Rovira C, Peters GH, Jensen MO (2006) Ammonium recruitment and ammonia transport by E. coliammonia channel AmtB. Biophys J 91:4401-4412. (Pubitemid 44904227)
    • (2006) Biophysical Journal , vol.91 , Issue.12 , pp. 4401-4412
    • Nygaard, T.P.1    Rovira, C.2    Peters, G.H.3    Jensen, M.O.4
  • 34
    • 33748098179 scopus 로고    scopus 로고
    • Molecular dynamics simulations on the Escherichia coli ammonia channel protein AmtB: Mechanism of ammonia/ammonium transport
    • DOI 10.1021/ja0631549
    • Lin Y, Cao Z, Mo Y (2006) Molecular dynamics simulations on the Escherichia coli ammonia channel protein AmtB: Mechanism of ammonia/ammonium transport. J Am Chem Soc 128:10876-10884. (Pubitemid 44304267)
    • (2006) Journal of the American Chemical Society , vol.128 , Issue.33 , pp. 10876-10884
    • Lin, Y.1    Cao, Z.2    Mo, Y.3
  • 35
    • 32544443795 scopus 로고    scopus 로고
    • Molecular determinants for binding of ammonium ion in the ammonia transporter AmtB - A quantum chemical analysis
    • DOI 10.1021/jp054261c
    • Liu Y, Hu X (2006) Molecular determinants for binding of ammonium ion in the ammonia transporter AmtB-A quantum chemical analysis. J Phys Chem A 110:1375-1381. (Pubitemid 43235704)
    • (2006) Journal of Physical Chemistry A , vol.110 , Issue.4 , pp. 1375-1381
    • Liu, Y.1    Hu, X.2
  • 36
    • 1542275558 scopus 로고    scopus 로고
    • Ammonium sensing in Escherichia coli: Role of the ammonium transporter Amtb and AmtB-GlnK complex formation
    • DOI 10.1074/jbc.M312399200
    • Javelle A, Severi E, Thornton J, Merrick M (2004) Ammonium sensing in Escherichia coli. Role of the ammonium transporter AmtB and AmtB-GlnK complex formation. J Biol Chem 279:8530-8538. (Pubitemid 38295906)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.10 , pp. 8530-8538
    • Javelle, A.1    Severi, E.2    Thornton, J.3    Merrick, M.4
  • 37
    • 33847313314 scopus 로고    scopus 로고
    • Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics
    • DOI 10.1016/j.jsb.2006.11.008, PII S1047847706003789, Advanced in Molecular Dynamics Simulations
    • Wang Y, Cohen J, Boron WF, Schulten K, Tajkhorshid E (2007) Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics. J Struct Biol 157:534-544. (Pubitemid 46321519)
    • (2007) Journal of Structural Biology , vol.157 , Issue.3 , pp. 534-544
    • Wang, Y.1    Cohen, J.2    Boron, W.F.3    Schulten, K.4    Tajkhorshid, E.5
  • 38
    • 65249185794 scopus 로고    scopus 로고
    • Functional role of Asp160 and the deprotonation mechanism of ammonium in the Escherichia coli ammonia channel protein AmtB
    • Lin Y, Cao Z, Mo Y (2009) Functional role of Asp160 and the deprotonation mechanism of ammonium in the Escherichia coli ammonia channel protein AmtB. J Phys Chem B 113:4922-4929.
    • (2009) J Phys Chem B , vol.113 , pp. 4922-4929
    • Lin, Y.1    Cao, Z.2    Mo, Y.3
  • 39
    • 70349260169 scopus 로고    scopus 로고
    • Functional analysis of human RhCG: Comparison with E. coli ammonium transporter reveals similarities in the pore and differences in the vestibule
    • Zidi-Yahiaoui N, et al. (2009) Functional analysis of human RhCG: Comparison with E. coli ammonium transporter reveals similarities in the pore and differences in the vestibule. Am J Physiol-Cell Ph 297:C537-547.
    • (2009) Am J Physiol-Cell Ph , vol.297
    • Zidi-Yahiaoui, N.1
  • 44
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of proteins
    • MacKerell AD, Jr, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616.
    • (1998) J Phys Chem B , vol.102 , pp. 3586-3616
    • MacKerell Jr., A.D.1
  • 45
    • 0002062192 scopus 로고    scopus 로고
    • An empirical potential energy function for phospholipids: Criteria for parameter optimization and applications
    • eds KM Merz and B Roux (Birkhauser, Boston)
    • Schlenkrich M, et al. (1996) An empirical potential energy function for phospholipids: Criteria for parameter optimization and applications. Biological Membranes: A Molecular Perspective from Computation and Experiment, eds KM Merz and B Roux (Birkhauser, Boston), pp 31-81.
    • (1996) Biological Membranes: A Molecular Perspective from Computation and Experiment , pp. 31-81
    • Schlenkrich, M.1
  • 46
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics simulation the Langevin piston method
    • Feller SE, Zhang YH, Pastor RW, Brooks BR (1995) Constant pressure molecular dynamics simulation the Langevin piston method. J Chem Phys 103:4613-4621.
    • (1995) J Chem Phys , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.H.2    Pastor, R.W.3    Brooks, B.R.4
  • 47
    • 33645961739 scopus 로고
    • A smooth particle mesh Ewald method
    • Essmann U, et al. (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577-8593.
    • (1995) J Chem Phys , vol.103 , pp. 8577-8593
    • Essmann, U.1
  • 48
    • 84986497803 scopus 로고
    • Multidimensional free-energy calculations using the weighted histogram analysis method
    • Kumar S, Rosenberg J, Bouzida D, Swendsen R, Kollman P (1995) Multidimensional free-energy calculations using the weighted histogram analysis method. J Comput Chem 16:1339-1350.
    • (1995) J Comput Chem , vol.16 , pp. 1339-1350
    • Kumar, S.1    Rosenberg, J.2    Bouzida, D.3    Swendsen, R.4    Kollman, P.5
  • 49
    • 0029633155 scopus 로고
    • The calculation of the potential of mean force using computer simulations
    • Roux B (1995) The calculation of the potential of mean force using computer simulations. Comput Phys Commun 91:275-282.
    • (1995) Comput Phys Commun , vol.91 , pp. 275-282
    • Roux, B.1
  • 50
    • 0035312645 scopus 로고    scopus 로고
    • Steered molecular dynamics and mechanical functions of proteins
    • DOI 10.1016/S0959-440X(00)00194-9
    • Isralewitz B, Gao M, Schulten K (2001) Steered molecular dynamics and mechanical functions of proteins. Curr Opin Struct Biol 11:224-230. (Pubitemid 32289426)
    • (2001) Current Opinion in Structural Biology , vol.11 , Issue.2 , pp. 224-230
    • Isralewitz, B.1    Gao, M.2    Schulten, K.3
  • 52
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium equality for free energy differences
    • Jarzynski C (1997) Nonequilibrium equality for free energy differences. Phys Rev Lett 78:2690-2693.
    • (1997) Phys Rev Lett , vol.78 , pp. 2690-2693
    • Jarzynski, C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.