In situ observation of protein phosphorylation by high-resolution NMR spectroscopy

Although the biological significance of protein phosphorylation in cellular signaling is widely appreciated, methods to directly detect these post-translational modifications in situ are lacking. Here we introduce the application of high-resolution NMR spectroscopy for observing de novo protein phosphorylation in vitro and in Xenopus laevis egg extracts and whole live oocyte cells. We found that the stepwise modification of adjacent casein kinase 2 (CK2) substrate sites within the viral SV40 large T antigen regulatory region proceeded in a defined order and through intermediate substrate release. This kinase mechanism contrasts with a more intuitive mode of CK2 action in which the kinase would remain substrate bound to perform both modification reactions without intermediate substrate release. For cellular signaling pathways, the transient availability of partially modified CK2 substrates could exert important switch-like regulatory functions.

[1]  R. Ellis,et al.  Macromolecular crowding: an important but neglected aspect of the intracellular environment. , 2001, Current opinion in structural biology.

[2]  W. Lim,et al.  Docking interactions in protein kinase and phosphatase networks. , 2006, Current opinion in structural biology.

[3]  Brendan K Faherty,et al.  Optimization and Use of Peptide Mass Measurement Accuracy in Shotgun Proteomics*S , 2006, Molecular & Cellular Proteomics.

[4]  Gerhard Wagner,et al.  Quantitative NMR analysis of the protein G B1 domain in Xenopus laevis egg extracts and intact oocytes , 2006, Proceedings of the National Academy of Sciences.

[5]  James E. Ferrell,et al.  Mechanistic Studies of the Dual Phosphorylation of Mitogen-activated Protein Kinase* , 1997, The Journal of Biological Chemistry.

[6]  W. Lim,et al.  Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. , 2006, Annual review of biochemistry.

[7]  A. Stern,et al.  Accelerated acquisition of high resolution triple-resonance spectra using non-uniform sampling and maximum entropy reconstruction. , 2004, Journal of magnetic resonance.

[8]  L. Pinna,et al.  One‐thousand‐and‐one substrates of protein kinase CK2? , 2003, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[9]  P. Vaglio,et al.  A multifunctional network of basic residues confers unique properties to protein kinase CK2 , 2004, Molecular and Cellular Biochemistry.

[10]  J E Ferrell,et al.  Xenopus oocyte maturation: new lessons from a good egg. , 1999, BioEssays : news and reviews in molecular, cellular and developmental biology.

[11]  S. Taylor,et al.  Domain movements in protein kinases. , 1994, Current opinion in structural biology.

[12]  T. Pawson,et al.  Signaling through scaffold, anchoring, and adaptor proteins. , 1997, Science.

[13]  Charles D Schwieters,et al.  The Xplor-NIH NMR molecular structure determination package. , 2003, Journal of magnetic resonance.

[14]  Jeffrey C. Hoch,et al.  Fast Assignment of 15N-HSQC Peaks using High-Resolution 3D HNcocaNH Experiments with Non-Uniform Sampling , 2005, Journal of biomolecular NMR.

[15]  James E. Ferrell,et al.  Mechanisms of specificity in protein phosphorylation , 2007, Nature Reviews Molecular Cell Biology.

[16]  A. Minton,et al.  The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media* , 2001, The Journal of Biological Chemistry.

[17]  K. Saxena,et al.  NMR analysis of a Tau phosphorylation pattern. , 2006, Journal of the American Chemical Society.

[18]  K. Lumb,et al.  Random-coil chemical shifts of phosphorylated amino acids , 1999, Journal of biomolecular NMR.

[19]  J. Maller,et al.  Dephosphorylation and activation of Xenopusp34cdc2 protein kinase during the cell cycle , 1989, Nature.

[20]  D. Beach,et al.  p34cdc2-mediated phosphorylation at T124 inhibits nuclear import of SV- 40 T antigen proteins , 1991, The Journal of cell biology.

[21]  R. Peters,et al.  The rate of nuclear cytoplasmic protein transport is determined by the casein kinase II site flanking the nuclear localization sequence of the SV40 T‐antigen. , 1991, The EMBO journal.

[22]  A. Murray,et al.  Cell cycle extracts. , 1991, Methods in cell biology.

[23]  C. Xiao,et al.  The Protein Kinase CK2 Site (Ser111/112) Enhances Recognition of the Simian Virus 40 Large T-antigen Nuclear Localization Sequence by Importin* , 1997, The Journal of Biological Chemistry.

[24]  L. Cesaro,et al.  Tyrosine Versus Serine/Threonine Phosphorylation by Protein Kinase Casein Kinase-2 , 1999, The Journal of Biological Chemistry.

[25]  C. Allende,et al.  Expression of the subunits of protein kinase CK2 during oogenesis in Xenopus laevis. , 1995, European journal of biochemistry.

[26]  Steven P Gygi,et al.  A probability-based approach for high-throughput protein phosphorylation analysis and site localization , 2006, Nature Biotechnology.

[27]  Gerhard Wagner,et al.  A solubility-enhancement tag (SET) for NMR studies of poorly behaving proteins , 2001, Journal of biomolecular NMR.

[28]  J. Yates,et al.  Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. , 1995, Analytical chemistry.

[29]  E. Salih Phosphoproteomics by mass spectrometry and classical protein chemistry approaches. , 2005, Mass spectrometry reviews.

[30]  Christian Griesinger,et al.  Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients , 1999 .

[31]  E. Krebs,et al.  Substrate specificity determinants for casein kinase II as deduced from studies with synthetic peptides. , 1987, The Journal of biological chemistry.

[32]  L. Pinna,et al.  Structural features underlying the unusual mode of calmodulin phosphorylation by protein kinase CK2: A study with synthetic calmodulin fragments. , 1999, Biochemical and biophysical research communications.

[33]  O. Issinger,et al.  Evolved to be active: sulfate ions define substrate recognition sites of CK2alpha and emphasise its exceptional role within the CMGC family of eukaryotic protein kinases. , 2007, Journal of molecular biology.

[34]  G. Wagner,et al.  Unambiguous Assignment of NMR Protein Backbone Signals with a Time-shared Triple-resonance Experiment , 2005, Journal of biomolecular NMR.