AMPK Methods and Protocols

(Rick Simeone) #1

  1. Macro-seeding is a common crystallographic technique used to
    improve crystal size. Transfer a crystal into a fresh drop con-
    taining protein/compounds and reservoir solution. Reduce
    the concentration of the precipitant (PEG 3350) in the reser-
    voir solution until no new crystals form (typically between 3%
    and 5% PEG 3350), but high enough that crystal growth can
    be observed over 7–10 days.

  2. Depending on the chemistry of the compounds binding to the
    γ-subunit, the RIM may or may not interact. In the case of C2,
    we would recommend using the AMPKα1/α2 RIM chimera
    for crystallization trials. The advantage of using the AMP/C2
    combined approach withα 2 β 1 γ1 is the binding of the two
    molecules can be directly compared within the one crystal
    structure.


Acknowledgments


These authors are supported by grants from the National Health
and Medical Research Council, the Australian Research Council,
the Victorian Government Operational Infrastructure Support
Scheme, and the Jack Brockhoff Foundation (JBF-4206, 2016),
and C.G.L. is an E.H. Flack Research fellow. B.E.K. and J.S.O. are
NHMRC and ARC Research fellows, respectively.

References



  1. Zhou G, Myers R, Li Y, Chen Y, Shen X,
    Fenyk-Melody J, Wu M, Ventre J, Doebber T,
    Fujii N, Musi N, Hirshman MF, Goodyear LJ,
    Moller DE (2001) Role of AMP-activated pro-
    tein kinase in mechanism of metformin action.
    J Clin Invest 108(8):1167–1174.https://doi.
    org/10.1172/JCI13505

  2. Cool B, Zinker B, Chiou W, Kifle L, Cao N,
    Perham M, Dickinson R, Adler A, Gagne G,
    Iyengar R, Zhao G, Marsh K, Kym P, Jung P,
    Camp HS, Frevert E (2006) Identification and
    characterization of a small molecule AMPK
    activator that treats key components of type
    2 diabetes and the metabolic syndrome. Cell
    Metab 3(6):403–416. https://doi.org/10.
    1016/j.cmet.2006.05.005

  3. Polekhina G, Gupta A, van Denderen BJ, Feil
    SC, Kemp BE, Stapleton D, Parker MW
    (2005) Structural basis for glycogen recogni-
    tion by AMP-activated protein kinase. Struc-
    ture 13(10):1453–1462.https://doi.org/10.
    1016/j.str.2005.07.008

  4. Nayak V, Zhao K, Wyce A, Schwartz MF, Lo
    WS, Berger SL, Marmorstein R (2006)


Structure and dimerization of the kinase
domain from yeast Snf1, a member of the
Snf1/AMPK protein family. Structure 14
(3):477–485. https://doi.org/10.1016/j.str.
2005.12.008


  1. Townley R, Shapiro L (2007) Crystal struc-
    tures of the adenylate sensor from fission yeast
    AMP-activated protein kinase. Science 315
    (5819):1726–1729. https://doi.org/10.
    1126/science.1137503

  2. Xiao B, Sanders MJ, Carmena D, Bright NJ,
    Haire LF, Underwood E, Patel BR, Heath RB,
    Walker PA, Hallen S, Giordanetto F, Martin
    SR, Carling D, Gamblin SJ (2013) Structural
    basis of AMPK regulation by small molecule
    activators. Nat Commun 4:3017.https://doi.
    org/10.1038/ncomms4017

  3. Li X, Wang L, Zhou XE, Ke J, de Waal PW,
    Gu X, Tan MHE, Wang D, Wu D, Xu HE,
    Melcher K (2015) Structural basis of AMPK
    regulation by adenine nucleotides and glyco-
    gen. Cell Res 25(3):398.https://doi.org/10.
    1038/cr.2015.27


26 Christopher G. Langendorf et al.

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