메뉴 건너뛰기




Volumn 61, Issue 3-4, 2015, Pages 249-260

Structure refinement and membrane positioning of selectively labeled OmpX in phospholipid nanodiscs

Author keywords

Membrane proteins; NOESY back calculation; Non uniform sampling; RDCs; Selective labeling; Structure

Indexed keywords

AMINO ACID; ESCHERICHIA COLI PROTEIN; HYDROLASE; LIPID BILAYER; MICELLE; NITROGEN; OMPX PROTEIN, E COLI; OUTER MEMBRANE PROTEIN; PHOSPHOLIPID;

EID: 84938503088     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-014-9883-6     Document Type: Article
Times cited : (45)

References (42)
  • 1
    • 0025346254 scopus 로고
    • Transmembrane protein structure: Spin labeling of bacteriorhodopsin mutants
    • 1990Sci.248.1088A
    • Altenbach C, Marti T, Khorana HG, Hubbell WL (1990) Transmembrane protein structure: spin labeling of bacteriorhodopsin mutants. Science 248:1088-1092
    • (1990) Science , vol.248 , pp. 1088-1092
    • Altenbach, C.1    Marti, T.2    Khorana, H.G.3    Hubbell, W.L.4
  • 2
    • 58149463865 scopus 로고    scopus 로고
    • An efficient protocol for the complete incorporation of methyl-protonated alanine in perdeuterated protein
    • Ayala I, Sounier R, Use N, Gans P, Boisbouvier J (2009) An efficient protocol for the complete incorporation of methyl-protonated alanine in perdeuterated protein. J Biomol NMR 43:111-119. doi: 10.1007/s10858-008-9294-7
    • (2009) J Biomol NMR , vol.43 , pp. 111-119
    • Ayala, I.1    Sounier, R.2    Use, N.3    Gans, P.4    Boisbouvier, J.5
  • 3
    • 0034625121 scopus 로고    scopus 로고
    • Utilization of site-directed spin labeling and high-resolution heteronuclear nuclear magnetic resonance for global fold determination of large proteins with limited nuclear overhauser effect data
    • Battiste JL, Wagner G (2000) Utilization of site-directed spin labeling and high-resolution heteronuclear nuclear magnetic resonance for global fold determination of large proteins with limited nuclear overhauser effect data. Biochemistry 39:5355-5365
    • (2000) Biochemistry , vol.39 , pp. 5355-5365
    • Battiste, J.L.1    Wagner, G.2
  • 4
    • 84876163719 scopus 로고    scopus 로고
    • DNA nanotubes for NMR structure determination of membrane proteins
    • Bellot G, McClintock MA, Chou JJ, Shih WM (2013) DNA nanotubes for NMR structure determination of membrane proteins. Nat Protoc 8:755-770. doi: 10.1038/nprot.2013.037
    • (2013) Nat Protoc , vol.8 , pp. 755-770
    • Bellot, G.1    McClintock, M.A.2    Chou, J.J.3    Shih, W.M.4
  • 5
    • 4243089402 scopus 로고    scopus 로고
    • Persistent contrast enhancement by sterically stabilized paramagnetic liposomes in murine melanoma
    • Bertini I et al (2004) Persistent contrast enhancement by sterically stabilized paramagnetic liposomes in murine melanoma. Magn Reson Med 52:669-672. doi: 10.1002/mrm.20189
    • (2004) Magn Reson Med , vol.52 , pp. 669-672
    • Bertini, I.1
  • 6
    • 84904157781 scopus 로고    scopus 로고
    • Measuring membrane protein bond orientations in nanodiscs via residual dipolar couplings
    • Bibow S, Carneiro MG, Sabo TM, Schwiegk C, Becker S, Riek R, Lee D (2014) Measuring membrane protein bond orientations in nanodiscs via residual dipolar couplings. Protein Sci 23:851-856. doi: 10.1002/pro.2482
    • (2014) Protein Sci , vol.23 , pp. 851-856
    • Bibow, S.1    Carneiro, M.G.2    Sabo, T.M.3    Schwiegk, C.4    Becker, S.5    Riek, R.6    Lee, D.7
  • 7
    • 84855677622 scopus 로고    scopus 로고
    • FLAMEnGO: A fuzzy logic approach for methyl group assignment using NOESY and paramagnetic relaxation enhancement data
    • Chao FA, Shi L, Masterson LR, Veglia G (2012) FLAMEnGO: a fuzzy logic approach for methyl group assignment using NOESY and paramagnetic relaxation enhancement data. J Magn Reson 214:103-110. doi: 10.1016/j.jmr.2011.10.008
    • (2012) J Magn Reson , vol.214 , pp. 103-110
    • Chao, F.A.1    Shi, L.2    Masterson, L.R.3    Veglia, G.4
  • 9
    • 1642382983 scopus 로고    scopus 로고
    • Directed self-assembly of monodisperse phospholipid bilayer nanodiscs with controlled size
    • Denisov IG, Grinkova YV, Lazarides AA, Sligar SG (2004) Directed self-assembly of monodisperse phospholipid bilayer nanodiscs with controlled size. J Am Chem Soc 126:3477-3487. doi: 10.1021/ja0393574
    • (2004) J Am Chem Soc , vol.126 , pp. 3477-3487
    • Denisov, I.G.1    Grinkova, Y.V.2    Lazarides, A.A.3    Sligar, S.G.4
  • 10
    • 0032694547 scopus 로고    scopus 로고
    • An efficient strategy for assignment of cross-peaks in 3D heteronuclear NOESY experiments
    • Diercks T, Coles M, Kessler H (1999) An efficient strategy for assignment of cross-peaks in 3D heteronuclear NOESY experiments. J Biomol NMR 15:177-180. doi: 10.1023/A:1008367912535
    • (1999) J Biomol NMR , vol.15 , pp. 177-180
    • Diercks, T.1    Coles, M.2    Kessler, H.3
  • 11
    • 34249856814 scopus 로고    scopus 로고
    • DNA-nanotube-induced alignment of membrane proteins for NMR structure determination
    • Douglas SM, Chou JJ, Shih WM (2007) DNA-nanotube-induced alignment of membrane proteins for NMR structure determination. Proc Natl Acad Sci USA 104:6644-6648. doi: 10.1073/pnas.0700930104
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 6644-6648
    • Douglas, S.M.1    Chou, J.J.2    Shih, W.M.3
  • 12
    • 0242485159 scopus 로고    scopus 로고
    • Lipid-binding studies of human apolipoprotein A-I and its terminally truncated mutants
    • Fang Y, Gursky O, Atkinson D (2003) Lipid-binding studies of human apolipoprotein A-I and its terminally truncated mutants. Biochemistry 42:13260-13268. doi: 10.1021/bi0354031
    • (2003) Biochemistry , vol.42 , pp. 13260-13268
    • Fang, Y.1    Gursky, O.2    Atkinson, D.3
  • 13
    • 77949363063 scopus 로고    scopus 로고
    • Stereospecific isotopic labeling of methyl groups for NMR spectroscopic studies of high-molecular-weight proteins
    • Gans P et al (2010) Stereospecific isotopic labeling of methyl groups for NMR spectroscopic studies of high-molecular-weight proteins. Angew Chem 49:1958-1962. doi: 10.1002/anie.200905660
    • (2010) Angew Chem , vol.49 , pp. 1958-1962
    • Gans, P.1
  • 14
    • 69349103941 scopus 로고    scopus 로고
    • Integral membrane proteins in nanodiscs can be studied by solution NMR spectroscopy
    • Gluck JM, Wittlich M, Feuerstein S, Hoffmann S, Willbold D, Koenig BW (2009) Integral membrane proteins in nanodiscs can be studied by solution NMR spectroscopy. J Am Chem Soc 131:12060-12061. doi: 10.1021/ja904897p
    • (2009) J Am Chem Soc , vol.131 , pp. 12060-12061
    • Gluck, J.M.1    Wittlich, M.2    Feuerstein, S.3    Hoffmann, S.4    Willbold, D.5    Koenig, B.W.6
  • 15
    • 0032898682 scopus 로고    scopus 로고
    • A robust and cost-effective method for the production of Val, Leu, Ile (delta 1) methyl-protonated 15N-, 13C-, 2H-labeled proteins
    • Goto NK, Gardner KH, Mueller GA, Willis RC, Kay LE (1999) A robust and cost-effective method for the production of Val, Leu, Ile (delta 1) methyl-protonated 15N-, 13C-, 2H-labeled proteins. J Biomol NMR 13:369-374
    • (1999) J Biomol NMR , vol.13 , pp. 369-374
    • Goto, N.K.1    Gardner, K.H.2    Mueller, G.A.3    Willis, R.C.4    Kay, L.E.5
  • 16
    • 84873400562 scopus 로고    scopus 로고
    • Optimized phospholipid bilayer nanodiscs facilitate high-resolution structure determination of membrane proteins
    • Hagn F, Etzkorn M, Raschle T, Wagner G (2013) Optimized phospholipid bilayer nanodiscs facilitate high-resolution structure determination of membrane proteins. J Am Chem Soc 135:1919-1925. doi: 10.1021/ja310901f
    • (2013) J Am Chem Soc , vol.135 , pp. 1919-1925
    • Hagn, F.1    Etzkorn, M.2    Raschle, T.3    Wagner, G.4
  • 17
    • 0036308102 scopus 로고    scopus 로고
    • Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA
    • Herrmann T, Guntert P, Wuthrich K (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209-227
    • (2002) J Mol Biol , vol.319 , pp. 209-227
    • Herrmann, T.1    Guntert, P.2    Wuthrich, K.3
  • 18
    • 0036700404 scopus 로고    scopus 로고
    • Side chain NMR assignments in the membrane protein OmpX reconstituted in DHPC micelles
    • Hilty C, Fernandez C, Wider G, Wuthrich K (2002) Side chain NMR assignments in the membrane protein OmpX reconstituted in DHPC micelles. J Biomol NMR 23:289-301
    • (2002) J Biomol NMR , vol.23 , pp. 289-301
    • Hilty, C.1    Fernandez, C.2    Wider, G.3    Wuthrich, K.4
  • 19
    • 0142149113 scopus 로고    scopus 로고
    • Stereospecific assignments of the isopropyl methyl groups of the membrane protein OmpX in DHPC micelles
    • Hilty C, Wider G, Fernandez C, Wuthrich K (2003) Stereospecific assignments of the isopropyl methyl groups of the membrane protein OmpX in DHPC micelles. J Biomol NMR 27:377-382
    • (2003) J Biomol NMR , vol.27 , pp. 377-382
    • Hilty, C.1    Wider, G.2    Fernandez, C.3    Wuthrich, K.4
  • 20
    • 77950835733 scopus 로고    scopus 로고
    • Poisson-gap sampling and forward maximum entropy reconstruction for enhancing the resolution and sensitivity of protein NMR data
    • Hyberts SG, Takeuchi K, Wagner G (2010) Poisson-gap sampling and forward maximum entropy reconstruction for enhancing the resolution and sensitivity of protein NMR data. J Am Chem Soc 132:2145-2147. doi: 10.1021/ja908004w
    • (2010) J Am Chem Soc , vol.132 , pp. 2145-2147
    • Hyberts, S.G.1    Takeuchi, K.2    Wagner, G.3
  • 21
    • 84863114255 scopus 로고    scopus 로고
    • Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional poisson gap scheduling
    • Hyberts SG, Milbradt AG, Wagner AB, Arthanari H, Wagner G (2012) Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional poisson gap scheduling. J Biomol NMR 52:315-327. doi: 10.1007/s10858-012-9611-z
    • (2012) J Biomol NMR , vol.52 , pp. 315-327
    • Hyberts, S.G.1    Milbradt, A.G.2    Wagner, A.B.3    Arthanari, H.4    Wagner, G.5
  • 22
    • 0017828622 scopus 로고
    • Replacement of endogenous cholesteryl esters of low density lipoprotein with exogenous cholesteryl linoleate Reconstitution of a biologically active lipoprotein particle
    • Krieger M, Brown MS, Faust JR, Goldstein JL (1978) Replacement of endogenous cholesteryl esters of low density lipoprotein with exogenous cholesteryl linoleate Reconstitution of a biologically active lipoprotein particle. J Biol Chem 253:4093-4101
    • (1978) J Biol Chem , vol.253 , pp. 4093-4101
    • Krieger, M.1    Brown, M.S.2    Faust, J.R.3    Goldstein, J.L.4
  • 23
  • 24
    • 0037316363 scopus 로고    scopus 로고
    • ARIA: Automated NOE assignment and NMR structure calculation
    • Linge JP, Habeck M, Rieping W, Nilges M (2003) ARIA: automated NOE assignment and NMR structure calculation. Bioinformatics 19:315-316
    • (2003) Bioinformatics , vol.19 , pp. 315-316
    • Linge, J.P.1    Habeck, M.2    Rieping, W.3    Nilges, M.4
  • 25
    • 33644861214 scopus 로고    scopus 로고
    • OPM: Orientations of proteins in membranes database
    • Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006) OPM: orientations of proteins in membranes database. Bioinformatics 22:623-625. doi: 10.1093/bioinformatics/btk023
    • (2006) Bioinformatics , vol.22 , pp. 623-625
    • Lomize, M.A.1    Lomize, A.L.2    Pogozheva, I.D.3    Mosberg, H.I.4
  • 26
    • 0008075262 scopus 로고    scopus 로고
    • Atomistic models and force fields
    • O.M. Becker A.D.J. MacKerell B. Roux M. Watanabe (eds) Marcel Dekker Inc New York
    • MacKerell ADJ (2001) Atomistic models and force fields. In: Becker OM, MacKerell ADJ, Roux B, Watanabe M (eds) Computational biochemistry and biophysics. Marcel Dekker Inc, New York, pp 7-38
    • (2001) Computational Biochemistry and Biophysics , pp. 7-38
    • Mackerell, A.D.J.1
  • 27
    • 84874849890 scopus 로고    scopus 로고
    • Membrane-dependent modulation of the mTOR activator Rheb: NMR observations of a GTPase tethered to a lipid-bilayer nanodisc
    • Mazhab-Jafari MT et al (2013) Membrane-dependent modulation of the mTOR activator Rheb: nMR observations of a GTPase tethered to a lipid-bilayer nanodisc. J Am Chem Soc 135:3367-3370. doi: 10.1021/ja312508w
    • (2013) J Am Chem Soc , vol.135 , pp. 3367-3370
    • Mazhab-Jafari, M.T.1
  • 28
    • 33847639732 scopus 로고    scopus 로고
    • Applications of phospholipid bilayer nanodiscs in the study of membranes and membrane proteins
    • Nath A, Atkins WM, Sligar SG (2007) Applications of phospholipid bilayer nanodiscs in the study of membranes and membrane proteins. Biochemistry 46:2059-2069. doi: 10.1021/bi602371n
    • (2007) Biochemistry , vol.46 , pp. 2059-2069
    • Nath, A.1    Atkins, W.M.2    Sligar, S.G.3
  • 29
    • 79954429599 scopus 로고    scopus 로고
    • A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins
    • Plevin MJ, Hamelin O, Boisbouvier J, Gans P (2011) A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins. J Biomol NMR 49:61-67. doi: 10.1007/s10858-010-9463-3
    • (2011) J Biomol NMR , vol.49 , pp. 61-67
    • Plevin, M.J.1    Hamelin, O.2    Boisbouvier, J.3    Gans, P.4
  • 30
    • 71749095971 scopus 로고    scopus 로고
    • Structural and functional characterization of the integral membrane protein VDAC-1 in lipid bilayer nanodiscs
    • Raschle T, Hiller S, Yu TY, Rice AJ, Walz T, Wagner G (2009) Structural and functional characterization of the integral membrane protein VDAC-1 in lipid bilayer nanodiscs. J Am Chem Soc 131:17777-17779. doi: 10.1021/ja907918r
    • (2009) J Am Chem Soc , vol.131 , pp. 17777-17779
    • Raschle, T.1    Hiller, S.2    Yu, T.Y.3    Rice, A.J.4    Walz, T.5    Wagner, G.6
  • 31
  • 32
    • 68349093958 scopus 로고    scopus 로고
    • TALOS+: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts
    • Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213-223. doi: 10.1007/s10858-009-9333-z
    • (2009) J Biomol NMR , vol.44 , pp. 213-223
    • Shen, Y.1    Delaglio, F.2    Cornilescu, G.3    Bax, A.4
  • 33
    • 77952565432 scopus 로고    scopus 로고
    • Lipid-protein nanodiscs as reference medium in detergent screening for high-resolution NMR studies of integral membrane proteins
    • Shenkarev ZO et al (2010) Lipid-protein nanodiscs as reference medium in detergent screening for high-resolution NMR studies of integral membrane proteins. J Am Chem Soc 132:5628-5629. doi: 10.1021/ja9097498
    • (2010) J Am Chem Soc , vol.132 , pp. 5628-5629
    • Shenkarev, Z.O.1
  • 34
    • 84899619887 scopus 로고    scopus 로고
    • Solution-NMR characterization of outer-membrane protein A from E. Coli in lipid bilayer nanodiscs and detergent micelles
    • Susac L, Horst R, Wuthrich K (2014) Solution-NMR characterization of outer-membrane protein A from E. coli in lipid bilayer nanodiscs and detergent micelles. Chem Bio Chem 15:995-1000. doi: 10.1002/cbic.201300729
    • (2014) Chem Bio Chem , vol.15 , pp. 995-1000
    • Susac, L.1    Horst, R.2    Wuthrich, K.3
  • 35
    • 14144254537 scopus 로고    scopus 로고
    • Solution NMR-derived global fold of a monomeric 82-kDa enzyme
    • Tugarinov V, Choy WY, Orekhov VY, Kay LE (2005) Solution NMR-derived global fold of a monomeric 82-kDa enzyme. Proc Natl Acad Sci USA 102:622-627. doi: 10.1073/pnas.0407792102
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 622-627
    • Tugarinov, V.1    Choy, W.Y.2    Orekhov, V.Y.3    Kay, L.E.4
  • 36
    • 34547687784 scopus 로고    scopus 로고
    • Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy
    • Tugarinov V, Kanelis V, Kay LE (2006) Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy. Nat Protoc 1:749-754. doi: 10.1038/nprot.2006.101
    • (2006) Nat Protoc , vol.1 , pp. 749-754
    • Tugarinov, V.1    Kanelis, V.2    Kay, L.E.3
  • 37
    • 80755190088 scopus 로고    scopus 로고
    • Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl-methyl nuclear Overhauser enhancement spectroscopy
    • Venditti V, Fawzi NL, Clore GM (2011) Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl-methyl nuclear Overhauser enhancement spectroscopy. J Biomol NMR 51:319-328. doi: 10.1007/s10858-011-9559-4
    • (2011) J Biomol NMR , vol.51 , pp. 319-328
    • Venditti, V.1    Fawzi, N.L.2    Clore, G.M.3
  • 38
    • 0033570111 scopus 로고    scopus 로고
    • The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence
    • Vogt J, Schulz GE (1999) The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence. Structure 7:1301-1309
    • (1999) Structure , vol.7 , pp. 1301-1309
    • Vogt, J.1    Schulz, G.E.2
  • 39
    • 67650495515 scopus 로고    scopus 로고
    • Automated assignment in selectively methyl-labeled proteins
    • Xu Y et al (2009) Automated assignment in selectively methyl-labeled proteins. J Am Chem Soc 131:9480-9481. doi: 10.1021/ja9020233
    • (2009) J Am Chem Soc , vol.131 , pp. 9480-9481
    • Xu, Y.1
  • 40
    • 84859777973 scopus 로고    scopus 로고
    • Solution NMR spectroscopic characterization of human VDAC-2 in detergent micelles and lipid bilayer nanodiscs
    • Yu TY, Raschle T, Hiller S, Wagner G (2012) Solution NMR spectroscopic characterization of human VDAC-2 in detergent micelles and lipid bilayer nanodiscs. Biochim Biophys Acta 1818:1562-1569. doi: 10.1016/j.bbamem.2011.11.012
    • (2012) Biochim Biophys Acta , vol.1818 , pp. 1562-1569
    • Yu, T.Y.1    Raschle, T.2    Hiller, S.3    Wagner, G.4
  • 41
    • 0031616834 scopus 로고    scopus 로고
    • A NOESY-HSQC simulation program spirit
    • Zhu L, Dyson HJ, Wright PE (1998) A NOESY-HSQC simulation program spirit. J Biomol NMR 11:17-29
    • (1998) J Biomol NMR , vol.11 , pp. 17-29
    • Zhu, L.1    Dyson, H.J.2    Wright, P.E.3
  • 42
    • 42149130389 scopus 로고    scopus 로고
    • NMR: Prediction of molecular alignment from structure using the PALES software
    • Zweckstetter M (2008) NMR: prediction of molecular alignment from structure using the PALES software. Nat Protoc 3:679-690. doi: 10.1038/nprot.2008.36
    • (2008) Nat Protoc , vol.3 , pp. 679-690
    • Zweckstetter, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.