메뉴 건너뛰기




Volumn 57, Issue 1, 2013, Pages 65-72

Resonance assignment for a particularly challenging protein based on systematic unlabeling of amino acids to complement incomplete NMR data sets

Author keywords

Aprataxin; Resonance assignment; Reverse labeling; Selective isotope labeling; Unlabeling

Indexed keywords

AMINO ACID; APRATAXIN; MEMBRANE PROTEIN; UNCLASSIFIED DRUG;

EID: 84883554623     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-013-9768-0     Document Type: Article
Times cited : (25)

References (40)
  • 1
    • 33749821755 scopus 로고    scopus 로고
    • The neurodegenerative disease protein aprataxin resolves abortive DNA ligation intermediates
    • 2006Natur.443.713A 10.1038/nature05164
    • Ahel I, Rass U, El-Khamisy SF, Katyal S, Clements PM, McKinnon PJ, Caldecott KW, West SC (2006) The neurodegenerative disease protein aprataxin resolves abortive DNA ligation intermediates. Nature 443(7112):713-716
    • (2006) Nature , vol.443 , Issue.7112 , pp. 713-716
    • Ahel, I.1    Rass, U.2    El-Khamisy, S.F.3    Katyal, S.4    Clements, P.M.5    McKinnon, P.J.6    Caldecott, K.W.7    West, S.C.8
  • 2
    • 84877875388 scopus 로고    scopus 로고
    • Combination of 15N reverse labeling and afterglow spectroscopy for assigning membrane protein spectra by magic-angle-spinning solid-state NMR: Application to the multidrug resistance protein EmrE
    • 10.1007/s10858-013-9724-z
    • Banigan JR, Gayen A, Traaseth NJ (2013) Combination of 15N reverse labeling and afterglow spectroscopy for assigning membrane protein spectra by magic-angle-spinning solid-state NMR: application to the multidrug resistance protein EmrE. J Biomol NMR 55(4):391-399
    • (2013) J Biomol NMR , vol.55 , Issue.4 , pp. 391-399
    • Banigan, J.R.1    Gayen, A.2    Traaseth, N.J.3
  • 3
    • 0030639926 scopus 로고    scopus 로고
    • HN(COCA)NH and HN(COCA)NH experiments for 1H-15N backbone assignments in 13C/15N-labeled proteins
    • 10.1023/A:1018679819693
    • Bracken C, Palmer AG, Cavanagh J (1997) (H)N(COCA)NH and HN(COCA)NH experiments for 1H-15N backbone assignments in 13C/15N-labeled proteins. J Biomol NMR 9(1):94-100
    • (1997) J Biomol NMR , vol.9 , Issue.1 , pp. 94-100
    • Bracken, C.1    Palmer, A.G.2    Cavanagh, J.3
  • 4
    • 77957758820 scopus 로고    scopus 로고
    • Radial sampling for fast NMR: Concepts and practices over three decades
    • 10.1016/j.pnmrs.2010.07.001
    • Coggins BE, Venters RA, Zhou P (2010) Radial sampling for fast NMR: concepts and practices over three decades. Prog Nucl Magn Reson Spectrosc 57(4):381-419
    • (2010) Prog Nucl Magn Reson Spectrosc , vol.57 , Issue.4 , pp. 381-419
    • Coggins, B.E.1    Venters, R.A.2    Zhou, P.3
  • 7
    • 67650082785 scopus 로고    scopus 로고
    • Recent advances in solution NMR: Fast methods and heteronuclear direct detection
    • 10.1002/cphc.200900133
    • Felli IC, Brutscher B (2009) Recent advances in solution NMR: fast methods and heteronuclear direct detection. ChemPhysChem 10(9-10):1356-1368
    • (2009) ChemPhysChem , vol.10 , Issue.9-10 , pp. 1356-1368
    • Felli, I.C.1    Brutscher, B.2
  • 8
    • 24644462659 scopus 로고    scopus 로고
    • Magic-angle spinning solid-state NMR spectroscopy of the β1 immunoglobulin binding domain of protein G (GB1): 15N and 13C chemical shift assignments and conformational analysis
    • 10.1021/ja044497e
    • Franks WT, Zhou DH, Wylie BJ, Money BG, Graesser DT, Frericks HL, Sahota G, Rienstra CM (2005) Magic-angle spinning solid-state NMR spectroscopy of the β1 immunoglobulin binding domain of protein G (GB1): 15N and 13C chemical shift assignments and conformational analysis. J Am Chem Soc 127(35):12,291-12,305
    • (2005) J Am Chem Soc , vol.127 , Issue.35 , pp. 12
    • Franks, W.T.1    Zhou, D.H.2    Wylie, B.J.3    Money, B.G.4    Graesser, D.T.5    Frericks, H.L.6    Sahota, G.7    Rienstra, C.M.8
  • 9
    • 9444245493 scopus 로고
    • Correlating backbone amide and side chain resonances in larger proteins by multiple relayed triple resonance NMR
    • 10.1021/ja00042a003
    • Grzesiek S, Bax A (1992) Correlating backbone amide and side chain resonances in larger proteins by multiple relayed triple resonance NMR. J Am Chem Soc 114(16):6291-6293
    • (1992) J Am Chem Soc , vol.114 , Issue.16 , pp. 6291-6293
    • Grzesiek, S.1    Bax, A.2
  • 11
    • 80054858598 scopus 로고    scopus 로고
    • A simplified recipe for assigning amide NMR signals using combinatorial 14N amino acid inverse-labeling
    • 10.1007/s10969-011-9116-0
    • Hiroaki H, Umetsu Y, Nabeshima Yi, Hoshi M, Kohda D (2011) A simplified recipe for assigning amide NMR signals using combinatorial 14N amino acid inverse-labeling. J Struct Funct Genomics 12(3):167-174
    • (2011) J Struct Funct Genomics , vol.12 , Issue.3 , pp. 167-174
    • Hiroaki, H.1    Umetsu, Y.2    Nabeshima, Y.3    Hoshi, M.4    Kohda, D.5
  • 12
    • 0004755466 scopus 로고
    • Homonuclear decoupling and peak elimination in Fourier transform nuclear magnetic resonance
    • 10.1021/ja00783a068
    • Jesson JP, Meakin P, Kneissel G (1973) Homonuclear decoupling and peak elimination in Fourier transform nuclear magnetic resonance. J Am Chem Soc 95(2):618-620
    • (1973) J Am Chem Soc , vol.95 , Issue.2 , pp. 618-620
    • Jesson, J.P.1    Meakin, P.2    Kneissel, G.3
  • 13
    • 0033136436 scopus 로고    scopus 로고
    • Application of amino acid type-specific 1H- and 14N-labeling in a 2H-, 15N-labeled background to a 47 kDa homodimer: Potential for NMR structure determination of large proteins
    • 10.1023/A:1008351606073
    • Kelly MJ, Krieger C, Ball LJ, Yu Y, Richter G, Schmieder P, Bacher A, Oschkinat H (1999) Application of amino acid type-specific 1H- and 14N-labeling in a 2H-, 15N-labeled background to a 47 kDa homodimer: potential for NMR structure determination of large proteins. J Biomol NMR 14(1):79-83
    • (1999) J Biomol NMR , vol.14 , Issue.1 , pp. 79-83
    • Kelly, M.J.1    Krieger, C.2    Ball, L.J.3    Yu, Y.4    Richter, G.5    Schmieder, P.6    Bacher, A.7    Oschkinat, H.8
  • 14
    • 79951554115 scopus 로고    scopus 로고
    • Amino acid selective unlabeling for sequence specific resonance assignments in proteins
    • 10.1007/s10858-010-9459-z
    • Krishnarjuna B, Jaipuria G, Thakur A, D'Silva P, Atreya HS (2011) Amino acid selective unlabeling for sequence specific resonance assignments in proteins. J Biomol NMR 49(1):39-51
    • (2011) J Biomol NMR , vol.49 , Issue.1 , pp. 39-51
    • Krishnarjuna, B.1    Jaipuria, G.2    Thakur, A.3    D'Silva, P.4    Atreya, H.S.5
  • 15
    • 77950297481 scopus 로고    scopus 로고
    • BEST-HNN and 2D-(HN)NH experiments for rapid backbone assignment in proteins
    • 2010JMagR.204.111K 10.1016/j.jmr.2010.02.013
    • Kumar D, Paul S, Hosur RV (2010) BEST-HNN and 2D-(HN)NH experiments for rapid backbone assignment in proteins. J Magn Reson 204(1):111-117
    • (2010) J Magn Reson , vol.204 , Issue.1 , pp. 111-117
    • Kumar, D.1    Paul, S.2    Hosur, R.V.3
  • 16
    • 2442687868 scopus 로고    scopus 로고
    • Projection-reconstruction technique for speeding up multidimensional NMR spectroscopy
    • 10.1021/ja049432q
    • Kupče E, Freeman R (2004) Projection-reconstruction technique for speeding up multidimensional NMR spectroscopy. J Am Chem Soc 126(20):6429-6440
    • (2004) J Am Chem Soc , vol.126 , Issue.20 , pp. 6429-6440
    • Kupče, E.1    Freeman, R.2
  • 17
    • 34250159870 scopus 로고    scopus 로고
    • A set of BEST triple-resonance experiments for time-optimized protein resonance assignment
    • 2007JMagR.187.163L 10.1016/j.jmr.2007.04.002
    • Lescop E, Schanda P, Brutscher B (2007) A set of BEST triple-resonance experiments for time-optimized protein resonance assignment. J Magn Reson 187(1):163-169
    • (2007) J Magn Reson , vol.187 , Issue.1 , pp. 163-169
    • Lescop, E.1    Schanda, P.2    Brutscher, B.3
  • 18
    • 77955920290 scopus 로고    scopus 로고
    • Combining methods for speeding up multi-dimensional acquisition. Sparse sampling and fast pulsing methods for unfolded proteins
    • 2010JMagR.206.81M 10.1016/j.jmr.2010.06.007
    • Marion D (2010) Combining methods for speeding up multi-dimensional acquisition. Sparse sampling and fast pulsing methods for unfolded proteins. J Magn Reson 206(1):81-87
    • (2010) J Magn Reson , vol.206 , Issue.1 , pp. 81-87
    • Marion, D.1
  • 20
    • 0029338320 scopus 로고
    • Improved sensitivity of HSQC spectra of exchanging protons at short interscan delays using a new fast HSQC (FHSQC) detection scheme that avoids water saturation
    • 10.1006/jmrb.1995.1109
    • Mori S, Abeygunawardana C, Johnson MO, Vanzijl PCM (1995) Improved sensitivity of HSQC spectra of exchanging protons at short interscan delays using a new fast HSQC (FHSQC) detection scheme that avoids water saturation. J Magn Reson 108(1):94-98
    • (1995) J Magn Reson , vol.108 , Issue.1 , pp. 94-98
    • Mori, S.1    Abeygunawardana, C.2    Johnson, M.O.3    Vanzijl, P.C.M.4
  • 21
    • 4644245976 scopus 로고    scopus 로고
    • A novel way of amino acid-specific assignment in 1H- 15N HSQC spectra with a wheat germ cell-free protein synthesis system
    • 10.1023/B:JNMR.0000042956.65678.b8
    • Morita EH, Shimizu M, Ogasawara T, Endo Y, Tanaka R, Kohno T (2004) A novel way of amino acid-specific assignment in 1H- 15N HSQC spectra with a wheat germ cell-free protein synthesis system. J Biomol NMR 30(1):37-45
    • (2004) J Biomol NMR , vol.30 , Issue.1 , pp. 37-45
    • Morita, E.H.1    Shimizu, M.2    Ogasawara, T.3    Endo, Y.4    Tanaka, R.5    Kohno, T.6
  • 22
    • 0024836418 scopus 로고
    • Expression and nitrogen-15 labeling of proteins for proton and nitrogen-15 nuclear magnetic resonance
    • 10.1016/0076-6879(89)77005-1
    • Muchmore DC, McIntosh LP, Russell CB, Anderson DE, Dahlquist FW (1989) Expression and nitrogen-15 labeling of proteins for proton and nitrogen-15 nuclear magnetic resonance. Methods Enzymol 177:44-73
    • (1989) Methods Enzymol , vol.177 , pp. 44-73
    • Muchmore, D.C.1    McIntosh, L.P.2    Russell, C.B.3    Anderson, D.E.4    Dahlquist, F.W.5
  • 23
    • 84862012327 scopus 로고    scopus 로고
    • One-step amino acid selective isotope labeling of proteins in prototrophic Escherichia coli strains
    • 10.1016/j.ab.2012.04.019
    • O'Grady C, Rempel BL, Sokaribo A, Nokhrin S, Dmitriev OY (2012) One-step amino acid selective isotope labeling of proteins in prototrophic Escherichia coli strains. Anal Biochem 426(2):126-128
    • (2012) Anal Biochem , vol.426 , Issue.2 , pp. 126-128
    • O'Grady, C.1    Rempel, B.L.2    Sokaribo, A.3    Nokhrin, S.4    Dmitriev, O.Y.5
  • 24
    • 1942489643 scopus 로고    scopus 로고
    • A combinatorial selective labeling method for the assignment of backbone amide NMR resonances
    • 10.1021/ja039601r
    • Parker MJ, Aulton-Jones M, Hounslow AM, Craven CJ (2004) A combinatorial selective labeling method for the assignment of backbone amide NMR resonances. J Am Chem Soc 126(16):5020-5021
    • (2004) J Am Chem Soc , vol.126 , Issue.16 , pp. 5020-5021
    • Parker, M.J.1    Aulton-Jones, M.2    Hounslow, A.M.3    Craven, C.J.4
  • 25
    • 80055076003 scopus 로고    scopus 로고
    • Signal enhancement for the sensitivity-limited solid state NMR experiments using a continuous, non-uniform acquisition scheme
    • 2011JMagR.213.171Q 10.1016/j.jmr.2011.08.028
    • Qiang W (2011) Signal enhancement for the sensitivity-limited solid state NMR experiments using a continuous, non-uniform acquisition scheme. J Magn Reson 213(1):171-175
    • (2011) J Magn Reson , vol.213 , Issue.1 , pp. 171-175
    • Qiang, W.1
  • 26
    • 84858330492 scopus 로고    scopus 로고
    • Selective isotopic unlabeling of proteins using metabolic precursors: Application to NMR assignment of intrinsically disordered proteins
    • 10.1002/cbic.201100678
    • Rasia RM, Brutscher B, Plevin MJ (2012) Selective isotopic unlabeling of proteins using metabolic precursors: application to NMR assignment of intrinsically disordered proteins. ChemBioChem 13(5):732-739
    • (2012) ChemBioChem , vol.13 , Issue.5 , pp. 732-739
    • Rasia, R.M.1    Brutscher, B.2    Plevin, M.J.3
  • 27
    • 34248215322 scopus 로고    scopus 로고
    • Actions of aprataxin in multiple DNA repair pathways
    • 10.1074/jbc.M611489200
    • Rass U, Ahel I, West SC (2007) Actions of aprataxin in multiple DNA repair pathways. J Biol Chem 282(13):9469-9474
    • (2007) J Biol Chem , vol.282 , Issue.13 , pp. 9469-9474
    • Rass, U.1    Ahel, I.2    West, S.C.3
  • 28
    • 57749110749 scopus 로고    scopus 로고
    • Molecular mechanism of DNA deadenylation by the neurological disease protein aprataxin
    • 994-34,001
    • Rass U, Ahel I, West SC (2008) Molecular mechanism of DNA deadenylation by the neurological disease protein aprataxin. J Biol Chem 283(49):33,994-34,001
    • (2008) J Biol Chem , vol.283 , Issue.49 , pp. 33
    • Rass, U.1    Ahel, I.2    West, S.C.3
  • 29
    • 0035744056 scopus 로고    scopus 로고
    • MUSIC, selective pulses, and tuned delays: Amino acid type-selective 1H-15N correlations, II
    • 2001JMagR.148.61S 10.1006/jmre.2000.2222
    • Schubert M (2001) MUSIC, selective pulses, and tuned delays: amino acid type-selective 1H-15N correlations, II. J Magn Reson 148(1):61-72
    • (2001) J Magn Reson , vol.148 , Issue.1 , pp. 61-72
    • Schubert, M.1
  • 30
    • 0002086987 scopus 로고    scopus 로고
    • MUSIC in triple-resonance experiments: Amino acid type-selective (1)H-(15)N correlations
    • 1999JMagR.141.34S 10.1006/jmre.1999.1881
    • Schubert M, Smalla M, Schmieder P, Oschkinat H (1999) MUSIC in triple-resonance experiments: amino acid type-selective (1)H-(15)N correlations. J Magn Reson 141(1):34-43
    • (1999) J Magn Reson , vol.141 , Issue.1 , pp. 34-43
    • Schubert, M.1    Smalla, M.2    Schmieder, P.3    Oschkinat, H.4
  • 31
    • 0028504129 scopus 로고
    • Assignment of amino acid type in 1H-15N correlation spectra by labeling with 14N-amino acids
    • 10.1006/jmrb.1994.1106
    • Shortle D (1994) Assignment of amino acid type in 1H-15N correlation spectra by labeling with 14N-amino acids. J Magn Reson 105(1):88-90
    • (1994) J Magn Reson , vol.105 , Issue.1 , pp. 88-90
    • Shortle, D.1
  • 32
    • 0038386883 scopus 로고    scopus 로고
    • Amino-acid-type selective isotope labeling of proteins expressed in Baculovirus-infected insect cells useful for NMR studies
    • 10.1023/A:1024013111478
    • Strauss A, Bitsch F, Cutting B, Fendrich G, Graff P, Liebetanz J, Zurini M, Jahnke W (2003) Amino-acid-type selective isotope labeling of proteins expressed in Baculovirus-infected insect cells useful for NMR studies. J Biomol NMR 26(4):367-372
    • (2003) J Biomol NMR , vol.26 , Issue.4 , pp. 367-372
    • Strauss, A.1    Bitsch, F.2    Cutting, B.3    Fendrich, G.4    Graff, P.5    Liebetanz, J.6    Zurini, M.7    Jahnke, W.8
  • 33
    • 0023042283 scopus 로고
    • Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes
    • 10.1016/0022-2836(86)90385-2
    • Studier F, Moffatt B (1986) Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol 189(1):113-130
    • (1986) J Mol Biol , vol.189 , Issue.1 , pp. 113-130
    • Studier, F.1    Moffatt, B.2
  • 34
    • 80051665061 scopus 로고    scopus 로고
    • Suppression of isotope scrambling in cell-free protein synthesis by broadband inhibition of PLP enymes for selective 15N-labelling and production of perdeuterated proteins in H2O
    • 10.1007/s10858-011-9477-5
    • Su XC, Loh CT, Qi R, Otting G (2011) Suppression of isotope scrambling in cell-free protein synthesis by broadband inhibition of PLP enymes for selective 15N-labelling and production of perdeuterated proteins in H2O. J Biomol NMR 50(1):35-42
    • (2011) J Biomol NMR , vol.50 , Issue.1 , pp. 35-42
    • Su, X.C.1    Loh, C.T.2    Qi, R.3    Otting, G.4
  • 35
    • 34247896323 scopus 로고    scopus 로고
    • 1-13C amino acid selective labeling in a 2H15N background for NMR studies of large proteins
    • 10.1007/s10858-007-9152-z
    • Takeuchi K, Ng E, Malia TJ, Wagner G (2007) 1-13C amino acid selective labeling in a 2H15N background for NMR studies of large proteins. J Biomol NMR 38(1):89-98
    • (2007) J Biomol NMR , vol.38 , Issue.1 , pp. 89-98
    • Takeuchi, K.1    Ng, E.2    Malia, T.J.3    Wagner, G.4
  • 36
    • 59749083498 scopus 로고    scopus 로고
    • Amino acid-selective isotope labeling of proteins for nuclear magnetic resonance study: Proteins secreted by Brevibacillus choshinensis
    • 10.1016/j.ab.2008.12.027
    • Tanio M, Tanaka R, Tanaka T, Kohno T (2009) Amino acid-selective isotope labeling of proteins for nuclear magnetic resonance study: proteins secreted by Brevibacillus choshinensis. Anal Biochem 386(2):156-160
    • (2009) Anal Biochem , vol.386 , Issue.2 , pp. 156-160
    • Tanio, M.1    Tanaka, R.2    Tanaka, T.3    Kohno, T.4
  • 39
    • 0030239071 scopus 로고    scopus 로고
    • Genetic tools for selective labeling of proteins with alpha-15N-amino acids
    • 10.1007/BF00211164
    • Waugh D (1996) Genetic tools for selective labeling of proteins with alpha-15N-amino acids. J Biomol NMR 8(2):184-192
    • (1996) J Biomol NMR , vol.8 , Issue.2 , pp. 184-192
    • Waugh, D.1
  • 40
    • 43949167657 scopus 로고
    • HNCACB, a high-sensitivity 3D NMR experiment to correlate amide-proton and nitrogen resonances with the alpha-and beta-carbon resonances in proteins
    • 10.1006/jmrb.1993.1033
    • Wittekind M, Mueller L (1993) HNCACB, a high-sensitivity 3D NMR experiment to correlate amide-proton and nitrogen resonances with the alpha-and beta-carbon resonances in proteins. J Magn Reson 101(2):201-205
    • (1993) J Magn Reson , vol.101 , Issue.2 , pp. 201-205
    • Wittekind, M.1    Mueller, L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.