AMPK Methods and Protocols

(Rick Simeone) #1
-xSW 10416.667 -zSW 2351.499 \
-xOBS 800.133 -zOBS 81.086 \
-xCAR 4.703 -zCAR 119.000 \
-xLAB HN -zLAB 15N \
-ndim 3 -aq2D States \
| nmrPipe -fn TP \
| nmrPipe -fn ZTP \
| nmrPipe -fn TP -hyper \
| pipe2xyz -x -out ./fid/test_%03d.fid -verb -ov


  1. For estimation of errors of the nonlinear fits of CPMG relaxa-
    tion dispersion data,see[5, 12].


References



  1. Koay A, Rimmer KA, Mertens HD et al (2007)
    Oligosaccharide recognition and binding to
    the carbohydrate binding module of
    AMP-activated protein kinase. FEBS Lett
    581:5055–5059

  2. Koay A, Woodcroft B, Petrie EJ et al (2010)
    AMPK beta subunits display isoform specific
    affinities for carbohydrates. FEBS Lett
    584:3499–3503

  3. Mobbs JI, Koay A, Di Paolo A et al (2015)
    Determinants of oligosaccharide specificity of
    the carbohydrate-binding modules of
    AMP-activated protein kinase. Biochem J
    468:245–257

  4. Navratilova I, Papalia GA, Rich RL et al (2007)
    Thermodynamic benchmark study using Bia-
    core technology. Anal Biochem 364:67–77

  5. Demers JP, Mittermaier A (2009) Binding
    mechanism of an SH3 domain studied by
    NMR and ITC. J Am Chem Soc
    131:4355–4367

  6. Velazquez-Campoy A, Ohtaka H, Nezami A
    et al. (2004) Isothermal titration calorimetry.
    Curr Protoc Cell Biol. Chapter 17:Unit 17 18

  7. Kleckner IR, Foster MP (2011) An introduc-
    tion to NMR-based approaches for measuring
    protein dynamics. Biochim Biophys Acta
    1814:942–968

  8. Henzler-Wildman K, Kern D (2007) Dynamic
    personalities of proteins. Nature 450:964–972

  9. Vafabakhsh R, Levitz J, Isacoff EY (2015)
    Conformational dynamics of a class C G-
    protein-coupled receptor. Nature
    524:497–501

  10. Farrow NA, Zhang O, Forman-Kay JD et al
    (1994) A heteronuclear correlation experiment
    for simultaneous determination of 15N longi-
    tudinal decay and chemical exchange rates of


systems in slow equilibrium. J Biomol NMR
4:727–734


  1. Loria JP, Rance M, Palmer AG (1999) A
    relaxation-compensated carr-purcell-mei-
    boom-gill sequence for characterizing chemical
    exchange by NMR spectroscopy. J Am Chem
    Soc 121:2331–2332

  2. Korzhnev DM, Salvatella X, Vendruscolo M
    et al (2004) Low-populated folding intermedi-
    ates of Fyn SH3 characterized by relaxation
    dispersion NMR. Nature 430:586–590

  3. Meneses E, Mittermaier A (2014) Electrostatic
    interactions in the binding pathway of a tran-
    sient protein complex studied by NMR and
    isothermal titration calorimetry. J Biol Chem
    289:27911–27923

  4. Bieri M, Mobbs JI, Koay A et al (2012)
    AMP-activated protein kinase beta-subunit
    requires internal motion for optimal carbohy-
    drate binding. Biophys J 102:305–314

  5. Gill SC, Von Hippel PH (1989) Calculation of
    protein extinction coefficients from amino acid
    sequence data. Anal Biochem 182:319–326

  6. Delaglio F, Grzesiek S, Vuister GWet al (1995)
    NMRPipe: a multidimensional spectral proces-
    sing system based on UNIX pipes. J Biomol
    NMR 6:277–293

  7. Sugase K, Lansing JC, Dyson HJ et al (2007)
    Tailoring relaxation dispersion experiments for
    fast-associating protein complexes. J Am Chem
    Soc 129:13406–13407

  8. Cai M, Huang Y, Sakaguchi K et al (1998) An
    efficient and cost-effective isotope labeling pro-
    tocol for proteins expressed in Escherichia
    Coli. J Biomol NMR 11:97–102

  9. Marley J, Lu M, Bracken C (2001) A method
    for efficient isotopic labeling of recombinant
    proteins. J Biomol NMR 20:71–75


98 Paul R. Gooley et al.

Free download pdf