About

Professor Natalie Ahn completed her Ph.D. studies in mechanistic enzymology under Judith P. Klinman in the Department of Chemistry at the University of California, Berkeley. She pursued postdoctoral research at the University of Washington, Seattle, working first with Christoph de Haën in the Department of Medicine and then with Edwin G. Krebs in the Department of Pharmacology. During her time in the Krebs lab, she was among the first scientists to describe extracellular signal-activated protein kinases (ERKs) and MAP kinase kinases (MKKs, also known as MEKs). Professor Ahn began her academic career as an assistant professor at the University of Colorado Boulder in 1992, was promoted to full professor in 2003, and became a Distinguished Professor in 2018. She has held prestigious positions including investigator of the Howard Hughes Medical Institute, fellow of the American Academy of Arts and Sciences, and member of the U.S. National Academy of Sciences. Her leadership roles in the scientific community include serving as president of the American Society of Biochemistry and Molecular Biology and president of the U.S. Human Proteome Organization.

Research topics

• Mathematics
• Biochemistry
• Cell biology
• Biology
• Chemistry
• Computer Science
• Physics
• Organic chemistry
• Nuclear physics
• Pharmacology
• Cancer research
• Medicine
• Genetics
• Biophysics

Selected publications

• Variable thresholds for phosphorylation targets of the ERK signaling pathway

  Proceedings of the National Academy of Sciences · 2026-02-06 · 1 citations

  articleOpen accessSenior authorCorresponding

  Cell fates regulated by ERK respond to different thresholds of signaling strength. In mammalian cells, conditions that activate ERK to submaximal levels are sufficient to sustain proliferation, survival, and transformation, while stimuli that activate ERK to very high levels often lead to cell death or cell cycle arrest. But while this "Goldilocks effect" is well known, the mechanisms have never been fully explained. In particular, threshold responses have been shown at the level of transcription and cell state changes, but whether phosphorylation responses upstream of these events also respond to thresholds is unknown. Here, we used mass spectrometry-based phosphoproteomics to ask if molecular events in the ERK pathway respond to different thresholds of signaling strength, by quantifying changes in phosphorylation of pathway targets against the occupancy of the two activating phosphosites in ERK. The results show that most phosphorylation events track ERK activation faithfully, responding linearly with increasing 2P-ERK occupancy. But some sites respond nonlinearly, reaching maximal phosphorylation when 2P-ERK exceeds lower thresholds (10 to 40%), or increasing substantially after 2P-ERK exceeds higher thresholds (>60%). Low threshold sites are found on transcriptional repressors that facilitate proliferation when inactivated by ERK/ribosomal s6 kinase (RSK) phosphorylation. By contrast, high threshold sites are found on proteins that are recruited to double-stranded DNA breaks and mediate DNA repair. Measurement of phosphorylation occupancies also revealed unexpected differences between cell states not apparent from inhibitor fold-changes. Our findings demonstrate that signaling thresholds exist at the level of the phosphoproteome, providing potential mechanisms for regulating cellular responses to pathway strength.

  PublisherDOI

• Protocol for converting assigned nuclear Overhauser enhancement spectroscopy series peaks into exact distance restraints using MATLAB- or CYANA-eNORA

  STAR Protocols · 2025-02-28

  articleOpen access

  In the exact nuclear Overhauser enhancement (eNOE) method, tight upper and lower interatomic distance restraints for structure calculations and comparison are extracted from NMR nuclear Overhauser enhancement spectroscopy (NOESY) spectra of biomolecules recorded with different mixing times. Here, we present a protocol for exporting the resonance assignments of NOESY spectra from CCPNmr (v.2) into nmrDraw to obtain peak intensities. We then detail procedures for converting them into distances using either the CYANA- or MATLAB-based “exact NOE by relaxation matrix analysis” (eNORA) program. • Steps for peak picking in nmrDraw • Guidance on transferring resonance assignment from CCPNmr to nmrDraw peak list • Tutorial for fitting cross-peak buildups and diagonal decays in NOESY series • Instructions for extracting upper and lower distance limits using eNORA2 or CYANA Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. In the exact nuclear Overhauser enhancement (eNOE) method, tight upper and lower interatomic distance restraints for structure calculations and comparison are extracted from NMR nuclear Overhauser enhancement spectroscopy (NOESY) spectra of biomolecules recorded with different mixing times. Here, we present a protocol for exporting the resonance assignments of NOESY spectra from CCPNmr (v.2) into nmrDraw to obtain peak intensities. We then detail procedures for converting them into distances using either the CYANA- or MATLAB-based “exact NOE by relaxation matrix analysis” (eNORA) program.

  PublisherDOI

• Characterization of the Eya and PP2A-B55α interaction

  Structural Dynamics · 2025-03-01

  articleOpen access

  The Eyes Absent (Eya) proteins were first identified as co-activators of the Six homeobox family of transcription factors and are critical in embryonic development. These proteins are also re-expressed in cancers after development is complete, where they drive tumor progression. We have previously shown that the Eya3 N-terminal domain (NTD) contains Ser/Thr phosphatase activity through an interaction with the protein phosphatase 2A (PP2A)-B55α holoenzyme, and that this interaction increases the half-life of Myc through pT58 dephosphorylation. Here we showed that Eya3 directly interacted with the NTD of Myc, recruiting PP2A-B55α to Myc. We also showed that Eya3 increased the Ser/Thr phosphatase activity of PP2A-B55α but not PP2A-B56α. Furthermore, knockdown and phosphoproteomic analyses demonstrated that Eya3 and B55α affected highly similar phosphosite motifs with a preference for Ser/Thr followed by Pro, consistent with Eya3's apparent Ser/Thr phosphatase activity being mediated through its interaction with PP2A-B55α. Intriguingly, mutating this Pro to other amino acids in a Myc peptide dramatically increased dephosphorylation by PP2A. Not surprisingly, MycP59A, a naturally occurring mutation hotspot in several cancers, enhanced Eya3-PP2A-B55α mediated dephosphorylation of pT58 on Myc, leading to increased Myc stability and cell proliferation, underscoring the critical role of this phosphosite in regulating Myc stability. In addition, we demonstrated that the NTD (∼250 amino acids) of Eya3 was completely disordered, and it used a 38-residue segment to interact with B55α. We are in the process of determining the cryo-EM structure of the PP2A-B55α-Eya3 complex to illustrate the molecular details of the PP2A-B55α and Eya3 interaction. We are also designing a cell penetrating peptide fused Eya3 peptide to inhibit the PP2A-B55α and Eya3 interaction. This can be used as a research tool to study the function of Eya-PP2A-B55α interaction in Myc phosphorylation and stabilization in many cancers overexpressing Myc and as a potential therapy for these cancers.

  PublisherDOI

• Biochemical characterization of the Eya and PP2A-B55α interaction

  Journal of Biological Chemistry · 2024-05-23 · 7 citations

  articleOpen access

  The eyes absent (Eya) proteins were first identified as co-activators of the six homeobox family of transcription factors and are critical in embryonic development. These proteins are also re-expressed in cancers after development is complete, where they drive tumor progression. We have previously shown that the Eya3 N-terminal domain (NTD) contains Ser/Thr phosphatase activity through an interaction with the protein phosphatase 2A (PP2A)-B55α holoenzyme and that this interaction increases the half-life of Myc through pT58 dephosphorylation. Here, we showed that Eya3 directly interacted with the NTD of Myc, recruiting PP2A-B55α to Myc. We also showed that Eya3 increased the Ser/Thr phosphatase activity of PP2A-B55α but not PP2A-B56α. Furthermore, we demonstrated that the NTD (∼250 amino acids) of Eya3 was completely disordered, and it used a 38-residue segment to interact with B55α. In addition, knockdown and phosphoproteomic analyses demonstrated that Eya3 and B55α affected highly similar phosphosite motifs with a preference for Ser/Thr followed by Pro, consistent with Eya3's apparent Ser/Thr phosphatase activity being mediated through its interaction with PP2A-B55α. Intriguingly, mutating this Pro to other amino acids in a Myc peptide dramatically increased dephosphorylation by PP2A. Not surprisingly, Myc^P59A, a naturally occurring mutation hotspot in several cancers, enhanced Eya3-PP2A-B55α–mediated dephosphorylation of pT58 on Myc, leading to increased Myc stability and cell proliferation, underscoring the critical role of this phosphosite in regulating Myc stability.

  PublisherOA PDFDOI

• Conformation selection by ATP-competitive inhibitors and allosteric communication in ERK2

  eLife · 2024-03-27 · 16 citations

  articleOpen accessSenior author

  Activation of the extracellular signal-regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named ‘L’ and ‘R,’ where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here, we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P +1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.

  PublisherDOI

• Author Response: Conformation selection by ATP-competitive inhibitors and allosteric communication in ERK2

  2024-03-27

  peer-reviewOpen accessSenior author
  PublisherDOI

• Conformation Selection by ATP-competitive Inhibitors and Allosteric Communication in ERK2

  eLife · 2024-01-03

  preprintOpen accessSenior authorCorresponding

  Abstract Activation of the extracellular signal regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named “L” and “R”, where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.

  PublisherOA PDFDOI

• Latent allosteric control of protein interactions by ATP-competitive kinase inhibitors

  Current Opinion in Structural Biology · 2024-10-11 · 3 citations

  reviewOpen accessSenior authorCorresponding
  PublisherOA PDFDOI

• Author Response: Conformation Selection by ATP-competitive Inhibitors and Allosteric Communication in ERK2

  2024-01-03

  peer-reviewOpen accessSenior author

  Activation of the extracellular signal regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named “L” and “R”, where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.

  PublisherDOI

• Reviewer #2 (Public Review): Conformation Selection by ATP-competitive Inhibitors and Allosteric Communication in ERK2

  2023-09-28

  peer-reviewOpen accessSenior author

  Activation of the extracellular signal regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states, named “L” and “R”, where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.

  PublisherDOI

Recent grants

• Technologies to Define and Map Novel Interorganelle Macromolecular Interactions

  NIH · $1.6M · 2013–2018

• NIH Grant R01CA118972

  NIH · $1.3M · 2013

• NIH Grant R01GM048521

  NIH · $2.5M · 2006

• Molecular and Cellular Dynamics in Mammalian Signal Transduction

  NIH · $4.2M · 2020–2030

• Linking Dynamics to Catalysis and Inhibition in ERK2

  NIH · $1.3M · 2015–2020

Frequent coauthors

• Katheryn A. Resing

  Howard Hughes Medical Institute

  144 shared

• William M. Old

  University of Colorado Boulder

  57 shared

• George F. Vande Woude

  46 shared

• Thomas Lee

  University of Colorado Boulder

  46 shared

• Laurel M. Pegram

  43 shared

• Stéphane Houel

  Thermo Fisher Scientific (United States)

  43 shared

• Kenji Fukasawa

  NTT (Japan)

  41 shared

• John G. Moffat

  37 shared

Labs

• Ahn LabPI

  Mechanistic enzymology, extracellular signal-activated protein kinases (ERKs), MAP kinase kinases (MKKs, aka MEKs), and cell signaling mechanisms

Education

• Ph.D.

  University of California, Berkeley

  1985

• Other

  University of Washington, Seattle

Awards & honors

• Searle Scholar (1993-1996)
• Merck Fellow (1988-1991)
• American Academy of Arts and Sciences Member
• Howard Hughes Medical Institute Investigator
• National Academy of Sciences Member