Natalie Ahn

Natalie G. AHN

Professor of Distinction

Office: JSCBB B314
Office Phone: 303 492 4799
Lab: JSCBB B355
Lab Phone: 303 492 7794 / 303 735 4915
Fax:303 492 2439
Group Website:
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Molecular Biophysics Program
Neuroscience Program

Ph.D.: University of California, Berkeley, 1985
Postdoctoral Fellow: University of Washington, Seattle

Awards: Howard Hughes Medical Institute InvestigatorSearle Scholar, 1993-1996Merck Fellow, 1988-1991

Proteomics and Signal Transduction

Our goal is to discover new mechanisms underlying the regulation and function of cell signaling. A major aim is to develop and apply new methods for protein profiling by mass spectrometry with biochemical and cellular approaches to investigate cellular responses to signaling pathways. A second aim is to examine internal motions in protein kinases, demonstrating coupling between protein dynamics and catalytic function.

We investigate cancer progression by investigating signaling pathways that are activated in melanoma and influence cancer progression and cell behavior (Fig. 1). Current studies include projects which focus on signaling through Wnt5A and B-Raf. Past work has examined signaling through RhoA GTPases, whose activation correlates with metastatic melanoma.

Wnt5A signaling

Wnt5A, which normally controls embryonic body axis formation, is elevated in high-grade melanomas and promotes cell invasion. We discovered a novel protein-organelle complex, which directs lifting and retraction of tail-end plasma membrane during directional cell movement. The complex, named the “Wnt5a receptor-actin-myosin-polarity (WRAMP) structure" involves the MCAM/CD146/MUC18 cell adhesion receptor, which polarizes intracellularly, dynamically recruiting actin and myosin-II to the cell posterior where it triggers membrane retraction and moves cells forward (Fig. 1). Whereas cell polarity studies often focus on events at the cell leading edge, the WRAMP structure shows that signaling at the rear is equally important for directional cell movement.

We identified components of the WRAMP structure by organelle proteomics, and discovered subunits of vesicle coatomer-I (COP-I), which are localized to and required for WRAMP structure formation. We found that endoplasmic reticulum (ER) is recruited to the WRAMP structure and cortical plasma membrane, followed by cytosolic calcium mobilization. Thus, recruitment of cortical ER produces a rear-directed calcium gradient, allowing actomyosin contraction and focal adhesion disassembly, events needed for tail-end membrane lifting and retraction. This reveals a new concept for cell polarity, in which cell movement is controlled by polarized endosomal trafficking and cortical ER recruitment.

Fig. 1. The WRAMP structure modulates cell polarity and directional movement
Fig. 1. The WRAMP structure modulates cell polarity and directional movement. In response to Wnt5A, MCAM and other receptors are internalized by dynamin-dependent endocytosis. MCAM localizes to MVBs and intralumenal vesicles via trafficking mechanisms involving RhoB and Rab4. The WRAMP structure has at least three overlapping zones. MCAM, F-actin and IQGAP1 assemble in zone 1. These proteins dynamically translocate to the periphery, moving through zone 2 and arriving at the tip of the trailing edge (zone 3). Distinct events within each zone combine to link organelle trafficking to membrane contractility.

B-Raf signaling

B-Raf is mutated in ~50% of melanomas, enhancing cell transformation, invasion and metastasis. We developed a large-scale strategy for phosphoprotein profiling, using negative precursor ion mass spectrometry, first described by Steven Carr (Broad Institute, MIT) and Roland Annan (GlaxoSmithKline), to selectively detect and quantify phosphopeptides based on their fragmentation signature following release of PO3– (Fig. 2). The method bypasses the need for metabolic cell labeling with stable isotope-labelled amino acids, and for phosphopeptide enrichment using affinity resins, which do not recognize all peptide chemistries.

Phosphoprotein targets that we identified included FAM129B/MINERVA, a protein with unknown function. We demonstrated that FAM129B functions in promoting 3D-invasion via phosphorylation by MAPK/ERK, localizes to the WRAMP structure and is required for its assembly. Current studies are aimed at investigating mechanisms important for cancer therapies targeting B-Raf/MKK/ERK signaling, comparing PLX4032/vemurafenib, an inhibitor of B-Raf-V600E which is approved for treating advanced melanomas, and the MKK1/2 inhibitor, AZD6244/selumetinib, which elicits poor responses in patients despite impressive pre-clinical success. We are keen to learn what determines the efficacy of different kinase inhibitors which target the B-Raf/MKK/ERK pathway.

Fig. 2. Phosphopeptide identification by -79 Da precursor ion scanning.

Fig. 2. Phosphopeptide identification by -79 Da precursor ion scanning. Proteins in lysates are proteolyzed and analyzed in parallel by negative mode and positive mode mass spectrometry. (A) Phosphopeptides are revealed by their -79 Da signal intensities, plotting HPLC retention (x-axis) vs precursor ion m/z (y-axis). Each -79 Da signal triggers polarity switching and selective phosphopeptide sequencing by MS/MS in positive mode. (B) All peptides, detected by positive LC-MS/MS of the same sample. Thus, precursor ion scanning enables selective phosphopeptide identification in complex mixtures.

Proteomics Technologies

Many studies in our lab implement large-scale proteomics by multidimensional LC-MS/MS, where proteins in complex mixtures are proteolyzed in solution, and peptides are separated by multi-dimensional liquid chromatography and sequenced by MS/MS. Currently, we are able to identify 8,000 proteins in a single 2D-LC-MS/MS run. Limitations remain in validating peptide sequences, inferring protein identity from peptide information, quantifying protein abundances, and phosphorylation site mapping. We are developing new experimental and computational strategies to address these problems. A key goal is to improve the accuracy and sensitivity of peptide assignments, using kinetic modeling of gas phase fragmentation to evaluate chemical plausibility of MS/MS spectra, and a "peptide-centric" database to reduce ambiguities in protein identification.

Protein Kinase Dynamics

We use hydrogen-exchange mass spectrometry (HX-MS) to reveal internal protein motions in kinases, where exchange predominantly occurs through low energy fluctuations in structure, allowing transient solvent exposure of backbone amides. Our goal is to address how protein dynamics regulates catalytic activity in protein kinases and other enzymes. The MAP kinase, ERK2, provides an ideal system, because its dynamics are clearly linked to activity, and active vs inactive forms of wild-type enzyme can be directly compared.

Our studies of ERK2 have revealed that kinase activation enhances HX at the linker between N- and C-terminal domains, which we ascribe to increased backbone flexibility. We showed that active (2P) vs inactive (0P) forms of ERK2 differ in their HX protection patterns upon nucleotide binding, reflecting closed vs open conformations, respectively (Fig. 3). Thus, ERK2 is constrained from domain closure before phosphorylation, and part of the activation mechanism involves releasing these constraints to form a competent catalytic site.

Current work integrates HX-MS and NMR studies of ERK2 with site-directed mutagenesis to identify relevant residues linking enzyme dynamics and catalytic turnover. We envision that motions of some residues influence catalysis, while others regulate linker flexibility through side-chain and backbone interconnectivities linked to the phosphorylation sites. A fascinating finding is that ERK1, which is closely related in sequence and structure to ERK2, differs significantly in its regulation of domain closure by phosphorylation. These differences are being exploited to identify mechanisms conveying motional information from the phosphorylation site to the linker region in ERK2. Eventually, targeting mechanisms which control protein dynamics may be exploitable for the design of inhibitors with selectivities that are difficult to achieve with ATP analogues.

ahn_f3

 

Fig. 3. Activation of ERK2 releases constraints to domain closure. (A) HX-MS measures changes in conformational mobility, which increases (red) or decreases (green) upon ERK2 activation by phosphorylation. Of particular importance is the linker region, containing the pivot point for domain closure (arrow). HX evidence compared to X-ray and EPR data argues that activation changes the linker flexibility, not structure. (B) Constraints to interdomain closure in 0P-ERK2 are overcome in 2P-ERK2. HX-MS shows that both 0P-ERK2 and 2P-ERK2 show comparable steric protection by Mg+2-AMP-PNP within the N-terminal domain and hinge, but 2P-ERK2 shows stronger protection in the C-terminus, indicating a closed domain conformation.

Selected Publications

Couts, K.L., Anderson, E.M., Gross, M.M., Sullivan, K. and Ahn, N.G. (2012) Oncogenic B-Raf signaling in melanoma cells controls a network of microRNAs with combinatorial functions. Oncogene, In press.

Wang, D., Zhang, Z., O’Loughlin, E., Lee, T., Houel, S., O’Carroll, D., Tarakhovsky, A., Ahn, N.G. and Yi, R. (2012) Quantitative functions of Argonaute proteins in mammalian development.  Genes Dev., In press.

Luo, Y., Ellis, L.Z., Dallaglio, K.,  Takeda, M., Robinson, W.A., Robinson, S., Lewis, K.D., McCarter, M.D., Gonzalez, R., Norris, D.A., Roop, D.R., Ahn, N.G. and Fujita, M. (2012) Side population cells from human melanoma tumors reveal diverse mechanisms of chemoresistance. J. Invest. Dermatol., In press.

 

Yen, C.Y., Houel, S., Ahn, N.G., and Old, W.M. (2011) Spectrum-to-spectrum searching using a proteome-wide spectral library. Mol. Cell. Proteomics In press, 10, M111.007666.

 

Oyeyemi, O.A., Sours, K.M., Lee, T., Kohen, A., Resing, K.A., Ahn, N.G. and Klinman, J.P. (2011) Comparative hydrogen-deuterium exchange for a mesophilic vs thermophilic dihydrofolate reductase at 25 °C: Identification of a single active site region with enhanced flexibility in the mesophilic protein. Biochemistry 50, 8251-8260.

Meyer-Arendt, K., Old, W.M., Houel, S., Renganathan, K., Eichelberger, B., Resing, K.A., and Ahn, N.G. (2011) IsoformResolver: A peptide-centric algorithm for protein inference. J Proteome Res. 10, 3060-3075.

Sours, K.M. and Ahn, N.G. (2010) Analysis of MAP kinases by hydrogen exchange mass spectrometry. In “MAP Kinase Signaling Protocols”, R. Seger, Ed., Methods in Molecular Biology, 661, 239-255.

Ring, A.Y., Sours, K.M., Lee, T., and Ahn, N.G. (2010) Distinct patterns of activation-dependent changes in conformational mobility between ERK1 and ERK2.  Intl. J. Mass Spectrometry, 302, 101-109.

Houel, S., Abernathy, R., Renganathan, K., Meyer-Arendt, K., Ahn, N.G. and Old, W.M. (2010) Quantifying the impact of chimera MS/MS spectra on peptide identification in large scale proteomics studies.  J. Proteome Res. 9, 4152-4160.

Oyeyemi, O., Sours, K.M., Lee, T., Resing, K.A., Ahn, N.G. and Klinman, J.P. (2010) Temperature dependence of protein motions in a thermophilic dihydrofolate reductase and its relationship to catalytic efficiency.  Proc. Natl. Acad. Sci., USA. 107:10074-10079.

Kabuyama, Y., Litman, E.S., Templeton, P., Metzner. S.I., Witze, E.S., Argast, G.M., Langer, S.J., Polvinen, K., Shellman, Y, Chan, D., Shabb, J.B., Fitzpatrick, J.E., Resing, K.A., Sousa, M.C., and Ahn, N.G. (2009)  A mediator of Rho-dependent signaling in melanoma moonlights as a methionine salvage enzyme.  Mol. Cell. Proteomics. 8(10):2308-2320.

Highlighted as an “Author’s Choice” article.

Argast, G.M., Croy, C.H., Couts, K.L., Zhang, Z., Litman, E.S., Chan, D.C. and Ahn, N.G. (2009) Cross-regulation of plexin B1 by B-Raf signaling in melanoma cells.  Oncogene 28(30):2697-2709.

Old, W.M., Shabb, J.S., Houel, S., Wang, H., Couts, K.H., Yen, C-Y., Litman, E.S., Croy, C.H, Meyer-Arendt, K., Miranda, J.G., Brown, R.A., Witze, E.S., Schweppe, R.E., Resing, K.A., and Ahn, N.G.  (2009) Functional proteomics identifies targets of phosphorylation by B-Raf signaling in melanoma. Molecular Cell, 34(1):115-131.

Yen, C.-Y., Meyer-Arendt, K., Eichelberger, B., Houel, S., Old, W.M., Knight, R.D., Ahn, N.G., Hunter, L.E., and Resing, K.A.  (2008) A theoretical MS/MS library for spectrum-to-spectrum searching in large-scale identification of proteins.  Mol. Cellular Proteomics, 8(4):857-869.

Gehrke, A.S., Sun, S., Kurgan, L., Ahn, N., Resing, K., Kafadar, K., and Cios, K. (2008) Improved Machine Learning Method for Analysis of Gas Phase Chemistry of Peptides.  BMC Bioinformatics, 9:515.

Levin-Salomon, V., Kogan, K., Ahn, N.G., Livnah, O., and Engelberg, D (2008). Isolation of intrinsically active (MEK- independent) variants of the ERK family of MAP kinases.  J. Biol. Chem. 283:34500-34510.

Sours, K.M., Kwok, S.C., Rachidi, T., Lee, T., Ring, A., Hoofnagle, A.N., Resing, K.A. and Ahn, N.G. (2008) Hydrogen exchange mass spectrometry reveals activation-induced changes in conformational mobility of p38a MAP kinase.  J. Mol. Biol., 379(5):1075-1093.

Witze, E.S., Litman, E.S., Argast, G.M., Moon, R.T., and Ahn, N.G. (2008) Wnt5A control of cell polarity and directional movement by polarized redistribution of adhesion receptors. Science, 320(5874):365-369.

Witze, E.S., Old, W.M., Resing, K.A. and Ahn, N.G. (2007) Mapping protein post-translational modifications with mass spectrometry.  Nat. Methods, 4, 798-806.

Ahn, N.G., Shabb J.S., Old, W.M., and Resing, K.A. (2007) Achieving in-depth proteomics profiling by mass spectrometry.  ACS Chemical Biology, 2:39-52.

Sun, S., Meyer-Arendt, K., Eichelberger, B., Brown, R., Yen, C.Y., Old, W.M., Pierce, K., Cios, K., Ahn, N.G., and Resing, K.A. (2007) Improved validation of peptide MS/MS assignments using spectral intensity prediction and full annotation of fragment ions.  Mol. Cell. Proteomics, 6,1-17.

Shi, Z., Resing, K.A. and Ahn, N.G. (2006) Networks for the allosteric control of protein kinases.  Curr. Op. Struct. Biol. 16, 686-692

Emrick, M.A., Lee, T., Starkey, P., Mumby, M.C., Resing, K.A., and Ahn, N.G. (2006) The gatekeeper residue in ERK2 controls autoactivation via a pathway of intramolecular connectivity. Proc. Natl. Acad. Sci. USA, 103, 18101-18106.

Schweppe, R.E., Cheung, T.H., and Ahn, N.G. (2006) Global gene expression analysis of ERK5 and ERK1/2 signaling reveals a role for HIF-1 in ERK5-mediated responses.  J. Biol. Chem., 281(30):20993-21003.

Roberts E.C., Hammond, K., Yin, H., Traish, A.M., Resing, K.A. and Ahn, N.G. (2006) Identification of G2/M targets for the MAP kinase pathway by functional proteomics.  Proteomics, 6(16):4541-53.

Ma, Z., Izumi, H., Kanai, M., Kabuyama, Y., Ahn, N.G., and Fukasawa, K. (2006) Mortalin controls centrosome duplication via modulating centrosomal localization of p53. Oncogene, 25(39):5377-90.

Kabuyama, Y., Langer, S.J., Polvinen, K., Homma, Y., Resing, K.A., and Ahn, N.G. (2006) Functional proteomics identifies protein tyrosine phosphatase 1B as a target of RhoA signaling.  Mol. Cell. Proteomics. 5(8):1359-67.

 

Lee, T., Croy, C.H., Resing, K.A. and Ahn, N.G. (2006) Hydrogen exchange measurements in proteins.  In "Handbook of Hydrogen Transfer" (Schowen, R.L., Klinman, J.P., eds), Wiley VHC, October 2006, Chapter 14, p 1361-1392..

Ruth, M.C., Old, W.M., Emrick, M.A., Meyer-Arendt, K., Aveline-Wolf, L.D., Pierce, K.G., Mendoza, A.M., Sevinsky, J.R., Hamady, M., Knight, R.D., Resing, K.A. and Ahn, N.G. (2006)  Analysis of membrane proteins from human chronic myelogenous leukemia cells: Comparison of extraction methods for multidimensional LC-MS/MS.  J. Proteome Res, 5(3):709-719.

Yen, C.Y., Russell, S., Mendoza, A.M., Meyer-Arendt, K., Sun, S.J., Cios, K.J., Ahn, N.G. and Resing, K.A.  (2006) Improving sensitivity in shotgun proteomics using a peptide-centric database with reduced complexity:  Protease cleavage and SCX elution rules from data mining of MS/MS spectra.  Anal. Chem., 78:1071-1084.

Lee, T., Hoofnagle, A.N., Resing, K.A., and Ahn, N.G. (2006)  Protein hydrogen exchange measured by electrospray ionization mass spectrometry.  in "Cell Biology: A Laboratory Handbook", Third Edition, J.E. Celis, Ed., Elsevier Science. v. 4: 443-449.

Lee, T., Hoofnagle, A.N, Resing, K.A., and Ahn, N.G. (2005)  Hydrogen exchange solvent protection by an ATP analogue reveals conformational changes in ERK2 upon activation.  J. Mol. Biol. 353:600-612.

Old, W.M., Meyer-Arendt, K., Aveline-Wolf, K., Pierce, K.G., Mendoza, A., Sevinsky, J.R., Resing, K.A., and Ahn, N.G. (2005) Comparison of label-free methods for quantifying human proteins by shotgun proteomics.  Mol. Cell. Proteomics, 4:1487-1502.

Kabuyama, Y., Resing, K.A., and Ahn, N.G. (2004)  Applying proteomics to signaling networks.  Current Opinions in Genetics and Development, 14(5):492-8.

Liang, Z.X., Tsigos, I., Lee,T., Bouriotis, V., Resing, K.A., Ahn, N.G., and Klinman J.P.(2004) Evidence for increased local flexibility in psychrophilic alcohol dehydrogenase relative to its thermophilic homologue.  Biochemistry 43(46):14676-83.

Resing, K.A., Meyer-Arendt, K., Mendoza, A.M., Aveline-Wolf, L.D., Jonscher, K.R., Pierce, K.G., Old, W.M., Cheung, H.T., Russell, S., Wattawa, J.L., Goehle, G.R., Knight, R.D., and Ahn, N.G. (2004) Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics.  Anal. Chem., 76:3556-68.

Liang, Z.-X., Lee, T., Resing, K.A., Ahn, N.G., and Klinman, J.P. (2004) Thermal-activated protein mobility and its correlation with catalysis in thermophilic alcohol dehydrogenase.  Proc. Natl. Acad. Sci. USA, 101:9556-61.

Kabuyama, Y., Polvinen, K., Resing, K.A. and Ahn, N.G. (2004) Two-dimensional electrophoresis for the identification of signaling targets.  in "Signal Transduction Protocols", R.C. Dickson, M. D. Mendenhall, Eds.  Methods in Mol. Biol. 284:37-49.

Lee, T., Hoofnagle A. N., Kabuyama, Y., Stroud, J., Min, X., Goldsmith, E.J., Chen, L., Resing, K.A., and Ahn, N.G. (2004) Docking site interactions in MAP kinases revealed by hydrogen exchange mass spectrometry.  Molecular Cell, 14:43-55

Sevinsky J.R., Whalen, A.M., and Ahn, N.G. (2004) ERK induces the megakaryocyte gene GPIIb/CD41 through MafB/Kreisler. Mol. Cell. Biol., 24(10):4534-45

Hoofnagle A. N., Resing, K. A., and Ahn, N.G. (2004)  Practical methods for deuterium exchange/mass spectrometry.  in "MAP kinase protocols", R. Seger, Ed., Meth. Mol. Biol. 250, 283-298.

Hoofnagle A. N., Stoner, J.W., Lee, T., Eaton, S.S. and Ahn, N.G. (2004)  Phosphorylation-dependent changes in structure and dynamics in ERK2 detected by site directed spin labelling and electron paramagnetic resonance.  Biophysical Journal, 86(1 Pt 1):395-403

Haydon, C.E., Eyers, P.A., Wolf, L.A., Resing, K.A., Maller, J.L., and Ahn, N.G. (2003)  Identification of novel phosphorylation sites on Xenopus laevis Aurora A and analysis of phosphopeptide enrichment by IMAC. Mol. Cell. Proteomics, 2(10):1055-1067.

Bernard, K., Litman, E., Fitzpatrick, J., Shellman,Y.,  Argast, G., Polvinen, K., Everett, A., Fukasawa, K., Norris, D., Ahn, N.G., and Resing, K.A. (2003)  Functional proteomic analysis of melanoma progression.  Cancer Res. 63:6716-6725.

 

Schweppe, R.E., Melton A.A., Brodsky, K.S., Aveline, L.D., Resing, K.A., Ahn, N.G. and Gutierrez-Hartmann, A. (2003) Purification and mass spectrometric identification of GABP as the functional pituitary Ets factor binding to the basal transcription element of the prolactin promoter. J. Biol. Chem, 278:16863-72.

Schweppe R.E., Resing, K. A., and Ahn, N.G. (2003)  The characterization of post-translational modifications by mass spectrometry. Accounts Chem. Res. 36, 453-61.

Hoofnagle A. N., Resing, K.A., and Ahn, N.G. (2003)  Protein analysis by hydrogen exchange mass spectrometry.  Ann. Rev. Biophys. Biomol. Struct. 32, 1-25.

 

Aurandt, J., Vikis, H.G., Gutkind, J.S., Ahn, N. and Guan, K.L. (2002)  The semaphorin receptor plexin B1 signals through a direct interaction with the Rho specific nucleotide exchanger, LARG.  Proc. Natl. Acad. Sci. USA 99, 12085-90.

Roberts, E.C., Shapiro, P.S., Nahreini, T.S., Pages, G., Pouyssegur, J. and Ahn, N.G. (2002)  Distinct cell cycle timing requirements for ERK and PI3K signaling pathways in somatic cell mitosis. Mol. Cell. Biol. 22, 7226-41.

Galasinski, S.C., Resing, K.A., Goodrich, J.A. and Ahn, N.G. (2002)  Phosphatase inhibition leads to histone deacetylase 1/2 phosphorylation and disruption of co-repressor interactions. J. Biol. Chem. 277, 19618-26.

Galasinski S., Louie D.F., Gloor, K.K., Resing, K.A., and Ahn, N.G. (2002) Global regulation of post-translational modifications on core histones.  J. Biol. Chem. 277, 2579-88

Emrick, M.A., Hoofnagle, A.N., Miller, A.S., Ten Eyck, L.F., and Ahn, N.G. (2001) Constitutive activation of extracellular signal-regulated kinase 2 by synergistic point mutations. J. Biol. Chem. 276, 46469-79.

Jesch S.A., Lewis, T.S., Ahn, N.G. and Linstedt, A.D. (2001) Mitotic phosphorylation of Golgi reassembly stacking protein 55 by mitogen activated protein kinase ERK2.  Mol. Biol. Cell 12, 1811-1817.

Hoofnagle A. N., Resing, K. A., Goldsmith,E.J., and Ahn, N.G. (2001)  Changes in protein conformational mobility upon activation of ERK2, as detected by hydrogen exchange.  Proc. Natl. Acad. Sci. USA 98, 956-961.

Lewis, T.S., Hunt, J., Aveline, L.D., Jonscher, K.R., Louie, D.F., Yeh, J., Nahreini T.S., Resing, K.A. and Ahn, N.G.  (2000) Identification of novel MAP kinase pathway signaling targets by functional proteomics and mass spectrometry.  Molecular Cell 6, 1343-1354.

Seiwert, S., Nahreini, T.S., Aigner, S., Ahn, N.G., and Uhlenbeck O.C. (2000)  RNA aptamers as pathway-specific MAP kinase inhibitors.  Chemistry and Biology 7, 833-843.

Prowse, C.N., Hagopian, J.C., Cobb, M.H., Ahn, N.G. and Lew J. (2000) Catalytic reaction pathway for the mitogen-activated protein kinase, ERK2.  Biochemistry, 39:6258-66

Rak, J., Mitsuhashi, Y., Sheehan, C., Tamir, A., Viloria-Petit, A., Filmus, J., Mansour, S.J., Ahn, N.G., Kerbel, R.S.  (2000)  Oncogenes and tumor angiogenesis: differential modes of vascular endothelial growth factor up-regulation in ras-transformed epithelial cells  and fibroblasts.  Cancer Res. 60, 490-498.

Louie, D.F., Gloor, K.K., Galasinski, S.C., Resing, K.A. and Ahn, N.G. (2000) Phosphorylation and subcellular redistribution of high mobility group proteins 14 and 17, analyzed by mass spectrometry.  Protein Sci. 9, 170-179.

 

Boeshans, K.M., Resing, K.A., Hunt, J.B., Ahn, N.G. and Shabb, J.B. (1999) Structural characterization of the membrane-associated regulatory subunit of type I cAMP dependent protein kinase by mass spectrometry:  Identification of Ser81 as the in vivo phosphorylation site of RIa.  Protein Sci. 8, 1515-1522.

Resing, K.A., Hoofnagle, A.N., and Ahn, N.G. (1999) Modeling deuterium exchange behavior of ERK2 using pepsin mapping to probe secondary structure.  J. Am. Soc. Mass Spec. 10, 685-702.

Shapiro, P.S., Whalen, A.M., Tolwinski, N.S., Froelich-Ammon, S.J., Garcia, M., Osheroff, N., and Ahn, N.G. (1999)  ERK activates topoisomerase IIa through a mechanism independent of phosphorylation.  Mol. Cell. Biol. 19, 3551-3560.

Tolwinski, N.S., Shapiro, P.S., Goueli, S., and Ahn, N.G.  (1999) Nuclear localization of MAP kinase kinase-1 is promoted by serum stimulation and G2/M progression. Requirement for phosphorylation at the activation lip and signaling downstream of MKK.  J. Biol. Chem. 274, 6168-6174.

Resing, K.A. and Ahn, N.G. (1999)  Applications of mass spectrometry to signal transduction.  Prog. Biophys. Mol. Biol. 71, 501-523.

Shapiro, P.S.,Vaisberg, E., Hunt, A.J., Tolwinski, N.S., Whalen, A.M., McIntosh, J.R. and Ahn, N.G. (1998) Activation of the MKK/ERK pathway during somatic cell mitosis.  Direct interactions of active ERK with kinetochores and regulation of the mitotic 3F3/2 phosphoantigen.  J. Cell Biol. 142, 1533-1545.

Duesbery, N.S., Webb, C., Leppla, S., Gordon, V.M., Klimpel, K.R., Copeland, T.D., Ahn, N.G., Oskarsson, M.K., Fukasawa, K., Paull, K.D., and Vande Woude, G.F. (1998) Proteolytic inactivation of MAPKK by anthrax lethal factor.  Science. 280, 734-737.

Lewis, T.S., Shapiro, P.S. and Ahn, N.G. (1998)  Signal transduction through MAP kinase cascades.  Adv. Cancer Res. 74, 49-139.

Shapiro, P.S. and Ahn, N.G. (1998) Feedback regulation of Raf-1 and mitogen activated protein kinase kinases 1 and 2 by MKP-1 phosphatase. J. Biol. Chem. 273, 1788-1793.

Resing, K.A. and Ahn, N.G. (1998)  Deuterium exchange mass spectrometry as a probe of protein kinase activation.  Analysis of wild type and constitutively active mutants of MAP kinase kinase 1.  Biochemistry 37, 463-475.

Resing, K.A. and Ahn, N.G. (1997) Protein phosphorylation analysis by electrospray ionization mass spectrometry.  Methods Enzymol. 283, 29-44.

Whalen, A.M., Galasinski, S.C., Shapiro, P.S., Nahreini, T.S. and Ahn, N.G. (1997)  Megakaryocytic differentiation induced by constitutive activation of MAP kinase kinase.  Mol. Cell. Biol. 17, 1947-1958.

Mansour, S.J., Candia, J.M., Matsuuda, J., Manning, M. and Ahn, N.G. (1996)  Interdependent domains controlling the enzymatic activity of MAP kinase kinase 1. Biochemistry 35, 15529-15536.

Louie, D.F., Resing, K.A., Lewis, T.S. and Ahn, N.G. (1996)  Mass spectrometric analysis of 40S ribosomal proteins from Rat-1 fibroblasts.  J. Biol. Chem. 271, 28189-28198.

Matten, W.T., Mansour, S.J., Copeland, T., Ahn, N.G., and Vande Woude, G.F. (1996) A positive feedback signal from MAPK to Mos during Xenopus oocyte maturation.  Dev. Biol. 179, 485-492.

 

Choi, T., Rulong, S., Resau, J., Fukasawa, K., Matten, W., Kuriyama, R., Mansour, S., Ahn, N., Vande Woude, G.F. (1996)  Mos/MAP kinase can induce early meiotic phenotypes in the absence of MPF:  A novel system for analyzing spindle formation during meiosis I, Proc. Natl. Acad. Sci. USA, 93, 4730-4735.

Mansour, S.J., Candia, J.M., Gloor, K. and Ahn, N.G. (1996)  Constitutively activated MAPKK1 and MAPKK2 mediate similar transcriptional and morphological responses.  Cell Growth Diff. 7, 243-250.

Resing, K.A., Mansour, S.J., Hermann, A.S., Johnson, R.S., Candia, J.M., Fukasawa, K., Vande Woude, G.F., and Ahn, N.G. (1995)  Determination of v-Mos catalyzed phosphorylation sites and autophosphorylation sites on MAP kinase kinase by ESI/MS.  Biochemistry 34, 2610-2620.

Mansour, S.J., Matten, W.T., Hermann, A.S., Candia, J.M., Rong, S., Fukasawa, K., Vande Woude, G.F., and Ahn, N.G. (1994)  Gain-of-function mutations in MAP kinase kinase promote mammalian cell transformation.  Science 265, 966-970.

Mansour, S.J., Resing, K.A., Candia, J.M., Hermann, A.S., Gloor, J.W., Herskind, K.R., Wartmann, M., Davis, R.J., and Ahn, N.G. (1994)  Mitogen-activated protein kinase phosphorylation of mitogen-activated protein kinase-kinase:  Analysis of in vitro phosphorylation sites.  J. Biochem. 116. 304-314.

Posada, J., Yew, N., Ahn, N.G., Vande Woude, G.F. and Cooper, J.A. (1993)  Mos stimulates MAP kinase in Xenopus oocytes and activates a MAP kinase kinase in vitro. Mol. Cell . Biol. 13, 2546-2553.

Ahn, N.G. (1993)  The MAP kinase cascade.  Discovery of a new signal transduction pathway.   Mol. Cell. Biochem. 127/128, 201-209.

Ahn, N.G., Campbell, J.S., Seger, R., Jensen, A.L., Graves, L.M. and Krebs, E.G. (1993) Metabolic labelling of mitogen-activated protein kinase kinase in A431 cells demonstrates phosphorylation on serine and threonine residues.  Proc. Natl. Acad. Sci. USA 90, 5143-5147.

Ahn, N.G., Seger, R. and Krebs, E.G. (1992) The mitogen-activated protein kinase activator. Curr. Op. Cell Biol. 4, 992-999.

Seger, R., Seger, D., Lozeman, F.J., Ahn, N.G., Graves, L.M., Campbell, J.S., Ericsson, L., Harrylock, M., Jensen, A.M. and Krebs, E.G. (1992)  Human T-cell mitogen-activated protein kinase kinases are related to yeast signal transduction kinases.  J. Biol. Chem. 267, 25628-25631.

Seger, R., Ahn, N.G., Posada, J., Munar, E.S., Jensen, A.J., Cooper, J.A., Cobb, M.H. and Krebs, E.G. (1992) Purification and characterization of mitogen-activated protein kinase activator(s) from epidermal growth factor-stimulated A431 cells. J. Biol Chem. 267, 14373-14381.

Ahn, N.G., Robbins, D.J., Haycock, J.W., Seger, R., Cobb, M.H. and Krebs, E.G. (1992) Identification of an activator of the MAP kinases ERK1 and ERK2 in PC12 cells stimulated with nerve growth factor or bradykinin.  J. Neurochem., 59, 147-156.

Haycock, J.W., Ahn, N.G., Cobb, M.H. and Krebs, E.G. (1992).  ERK1 and ERK2, two microtubule-associated protein 2 kinases, mediate the phosphorylation of tyrosine hydroxylase at serine 31 in situProc. Natl. Acad. Sci. USA, 89, 2365-2369.

Seger, R., Ahn, N.G., Boulton, T.G., Yancopoulos, G.D., Panayotatos, N., Radziejewska, E., Ericsson, L., Bratlien, R.L., Cobb, M.H., and Krebs, E.G. (1991).  Microtubule-associated protein 2 kinases, ERK1 and ERK2, undergo autophosphorylation on both tyrosine and threonine residues:  Implications for their mechanism of activation.  Proc. Natl. Acad. Sci. USA, 88, 6142-6146.

Ahn, N.G., Seger, R., Bratlien, R.L. and Krebs, E.G. (1991).  Growth factor stimulated phosphorylation cascades:  Activation of growth factor-stimulated MAP kinase. CIBA Foundation Symposia, 164, 113-131.

Ahn, N.G., Seger, R., Bratlien, R.L., Diltz, C.D., Tonks, N.K. and Krebs, E.G. (1991)  Multiple components in an epidermal growth factor-stimulated protein kinase cascade.  In vitro activation of a MBP/MAP2 kinase.  J. Biol. Chem. 256, 4220-4227.

Ahn, N.G. and Krebs, E.G. (1990)  Evidence for an epidermal growth factor-stimulated protein serine/threonine kinase cascade in Swiss 3T3 cells.  Activation of serine peptide kinase activity by myelin basic protein kinases in vitroJ. Biol. Chem. 265, 11495-11501.

Ahn, N.G., Weiel, J.E., Chan, C.P. and Krebs, E.G. (1990)  Identification of multiple epidermal growth factor-stimulated protein serine/threonine kinases from Swiss 3T3 cells.  J. Biol. Chem. 265, 11487-11494.

Ahn, N.G. and Klinman, J.P. (1989)  Nature of rate-limiting steps in a compartmentalized enzyme system.  Quantitation of dopamine transport and hydroxylation rates in resealed chromaffin granule ghosts.  J. Biol. Chem. 264, 12259-12265.

Ahn, N.G., Teller, D.C., Bienkowski, M.J., McMullen, B.A., Lipkin, E.W. and de Haën, C.  (1988)  Sedimentation equilibrium analysis of five lipocortin-related phospholipase A2 inhibitors from human placenta.  J. Biol. Chem. 263, 18657-18663.

Ahn, N. and Klinman, J.P. (1987)  Activation of dopamine b-monooxygenase by external and internal electron donors in resealed chromaffin granule ghosts.  J. Biol. Chem. 262, 1485-1492.

Ahn, N. and Klinman, J.P. (1983)  Mechanism of modulation of dopamine b-monooxygenase by pH and fumarate as deduced from initial rate and primary deuterium isotope effect studies.  Biochemistry 22, 3096-3106.