Natalie Ahn

Summary

Affiliation: University of Colorado
Country: USA

Publications

  1. ncbi request reprint Hydrogen exchange solvent protection by an ATP analogue reveals conformational changes in ERK2 upon activation
    Thomas Lee
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    J Mol Biol 353:600-12. 2005
  2. pmc A mediator of Rho-dependent invasion moonlights as a methionine salvage enzyme
    Yukihito Kabuyama
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309 0215, USA
    Mol Cell Proteomics 8:2308-20. 2009
  3. pmc Plexin B1 is repressed by oncogenic B-Raf signaling and functions as a tumor suppressor in melanoma cells
    G M Argast
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309 0215, USA
    Oncogene 28:2697-709. 2009
  4. pmc Oncogenic B-Raf signaling in melanoma cells controls a network of microRNAs with combinatorial functions
    K L Couts
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309 0215, USA
    Oncogene 32:1959-70. 2013
  5. pmc IsoformResolver: A peptide-centric algorithm for protein inference
    Karen Meyer-Arendt
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309 0215, USA
    J Proteome Res 10:3060-75. 2011
  6. pmc Improved machine learning method for analysis of gas phase chemistry of peptides
    Allison Gehrke
    Department of Computer Science and Engineering, University of Colorado at Denver, USA
    BMC Bioinformatics 9:515. 2008
  7. ncbi request reprint Achieving in-depth proteomics profiling by mass spectrometry
    Natalie G Ahn
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
    ACS Chem Biol 2:39-52. 2007
  8. ncbi request reprint Cell biology. Lessons in rational drug design for protein kinases
    Natalie G Ahn
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Science 308:1266-7. 2005
  9. ncbi request reprint Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics
    Katheryn A Resing
    Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309 0215, USA
    Anal Chem 76:3556-68. 2004
  10. pmc Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies
    Stephane Houel
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
    J Proteome Res 9:4152-60. 2010

Research Grants

  1. Biochemical Analysis of MKK/ERK Pathway
    Natalie Ahn; Fiscal Year: 2005
  2. AB-4000 QTRAP MASS SPECTROMETER
    Natalie Ahn; Fiscal Year: 2005
  3. Regulation of Map Kinase by Protein Motions
    Natalie G Ahn; Fiscal Year: 2010
  4. Protein Phosphorylation and Cellular Regulation
    Natalie Ahn; Fiscal Year: 2002

Detail Information

Publications42

  1. ncbi request reprint Hydrogen exchange solvent protection by an ATP analogue reveals conformational changes in ERK2 upon activation
    Thomas Lee
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    J Mol Biol 353:600-12. 2005
    ..The finding provides novel evidence that phosphorylation of ERK2 facilitates interdomain closure, allowing proper orientation between ATP and substrate to facilitate phosphoryl transfer...
  2. pmc A mediator of Rho-dependent invasion moonlights as a methionine salvage enzyme
    Yukihito Kabuyama
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309 0215, USA
    Mol Cell Proteomics 8:2308-20. 2009
    ..Thus, mechanisms used by signal transduction pathways to control cell movement have evolved from proteins with ancient function in amino acid metabolism...
  3. pmc Plexin B1 is repressed by oncogenic B-Raf signaling and functions as a tumor suppressor in melanoma cells
    G M Argast
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309 0215, USA
    Oncogene 28:2697-709. 2009
    ..Our findings suggest that B-Raf/MKK/ERK provides a permissive environment for melanoma genesis by modulating plexin B1...
  4. pmc Oncogenic B-Raf signaling in melanoma cells controls a network of microRNAs with combinatorial functions
    K L Couts
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309 0215, USA
    Oncogene 32:1959-70. 2013
    ..The findings highlight the potential for complex interactions between coordinately regulated miRNAs within a network...
  5. pmc IsoformResolver: A peptide-centric algorithm for protein inference
    Karen Meyer-Arendt
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309 0215, USA
    J Proteome Res 10:3060-75. 2011
    ..Finally, we examine the relatedness of proteins within IsoformResolver groups and compare its performance to other protein inference software...
  6. pmc Improved machine learning method for analysis of gas phase chemistry of peptides
    Allison Gehrke
    Department of Computer Science and Engineering, University of Colorado at Denver, USA
    BMC Bioinformatics 9:515. 2008
    ..Improved discrimination is achieved with theoretical spectra that are based on simulating gas phase chemistry of the peptides, but the limited understanding of those processes affects the accuracy of predictions from theoretical spectra...
  7. ncbi request reprint Achieving in-depth proteomics profiling by mass spectrometry
    Natalie G Ahn
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
    ACS Chem Biol 2:39-52. 2007
    ..We review recent progress in approaching these problems and present examples of successful applications and the outlook for the future...
  8. ncbi request reprint Cell biology. Lessons in rational drug design for protein kinases
    Natalie G Ahn
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Science 308:1266-7. 2005
  9. ncbi request reprint Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics
    Katheryn A Resing
    Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309 0215, USA
    Anal Chem 76:3556-68. 2004
    ..Analysis of soluble proteins from a human K562 cells identified 5130 unique proteins, with approximately 100 false positive protein assignments...
  10. pmc Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies
    Stephane Houel
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
    J Proteome Res 9:4152-60. 2010
    ..The results provide a framework for identifying chimeras and characterizing their contribution to the poorly understood false negative class of MS/MS...
  11. ncbi request reprint Comparison of label-free methods for quantifying human proteins by shotgun proteomics
    William M Old
    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder 80309 0215, USA
    Mol Cell Proteomics 4:1487-502. 2005
    ..Protein changes identified with p<0.1 showed good correlations with parallel measurements of changes in mRNA expression...
  12. ncbi request reprint Proteomics strategies for protein identification
    Katheryn A Resing
    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309 0215, USA
    FEBS Lett 579:885-9. 2005
    ..Here, we discuss strategies to improve accuracy and sensitivity of peptide identification, distinguish represented protein isoforms, and quantify relative changes in protein abundance...
  13. ncbi request reprint Methods in functional proteomics: two-dimensional polyacrylamide gel electrophoresis with immobilized pH gradients, in-gel digestion and identification of proteins by mass spectrometry
    Karine R Bernard
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA
    Methods Mol Biol 250:263-82. 2004
  14. pmc A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins
    Chia Yu Yen
    Department of Chemistry and Biochemistry and paragraph signHoward Hughes Medical Institute, University of Colorado, Boulder, Colorado 80309, USA
    Mol Cell Proteomics 8:857-69. 2009
    ....
  15. ncbi request reprint Phosphatase inhibition leads to histone deacetylases 1 and 2 phosphorylation and disruption of corepressor interactions
    Scott C Galasinski
    Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado 80309, USA
    J Biol Chem 277:19618-26. 2002
    ....
  16. ncbi request reprint Global regulation of post-translational modifications on core histones
    Scott C Galasinski
    Howard Hughes Medical Institute, The Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
    J Biol Chem 277:2579-88. 2002
    ..These results provide novel evidence that global covalent modifications of chromatin-bound histones are regulated through phosphorylation-dependent mechanisms...
  17. ncbi request reprint Functional proteomics identifies protein-tyrosine phosphatase 1B as a target of RhoA signaling
    Yukihito Kabuyama
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309 0215, USA
    Mol Cell Proteomics 5:1359-67. 2006
    ..Thus, protein profiling reveals a novel role for PTP1B as a mediator of RhoA-dependent phosphorylation of p130Cas...
  18. pmc Functional proteomics identifies targets of phosphorylation by B-Raf signaling in melanoma
    William M Old
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309 0215, USA
    Mol Cell 34:115-31. 2009
    ....
  19. ncbi request reprint Applying proteomics to signaling networks
    Yukihito Kabuyama
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
    Curr Opin Genet Dev 14:492-8. 2004
    ..Improved technologies that have emerged for comprehensive and high-throughput protein analysis yield novel insights into cell regulation...
  20. ncbi request reprint Two-dimensional gel electrophoresis for the identification of signaling targets
    Yukihito Kabuyama
    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado at Boulder, USA
    Methods Mol Biol 284:37-49. 2004
    ..In this chapter, optimized protocols for 2-DE using extracts from tissue culture are provided. Protocols for in-gel digestion of gel-resolved proteins, which allow protein identification by mass spectrometry are also discussed...
  21. ncbi request reprint Functional proteomic analysis of melanoma progression
    Karine Bernard
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
    Cancer Res 63:6716-25. 2003
    ..Thus, expression of this antigen likely reports a reduced dependence of protein expression on epidermal interactions...
  22. ncbi request reprint Practical methods for deuterium exchange/mass spectrometry
    Andrew N Hoofnagle
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA
    Methods Mol Biol 250:283-98. 2004
  23. ncbi request reprint Docking motif interactions in MAP kinases revealed by hydrogen exchange mass spectrometry
    Thomas Lee
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
    Mol Cell 14:43-55. 2004
    ..In vitro assays confirm the dependence of Elk1 and nucleoporin binding on ERK2 phosphorylation, and provide a structural basis for preferential involvement of active ERK in substrate binding and nuclear pore protein interactions...
  24. ncbi request reprint Identification of novel phosphorylation sites on Xenopus laevis Aurora A and analysis of phosphopeptide enrichment by immobilized metal-affinity chromatography
    Claire E Haydon
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
    Mol Cell Proteomics 2:1055-67. 2003
    ..Moreover, we demonstrate a significant difference in enrichment of phosphopeptides when different resins are used for Fe3+-IMAC and characterize the strengths and limitations of this methodology for the study of phosphoproteomics...
  25. pmc Wnt5a control of cell polarity and directional movement by polarized redistribution of adhesion receptors
    Eric S Witze
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO80309, USA
    Science 320:365-9. 2008
    ..Thus, cell-autonomous mechanisms allow Wnt5a to control cell orientation, polarity, and directional movement in response to positional cues from chemokine gradients...
  26. ncbi request reprint Identification of G2/M targets for the MAP kinase pathway by functional proteomics
    Elisabeth C Roberts
    Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder 80309 0215, USA
    Proteomics 6:4541-53. 2006
    ....
  27. ncbi request reprint Protein analysis by hydrogen exchange mass spectrometry
    Andrew N Hoofnagle
    Department of Chemistry and Biochemistry University of Colorado, Boulder, Colorado 80309, USA
    Annu Rev Biophys Biomol Struct 32:1-25. 2003
    ..In addition, recent studies illustrate the utility of hydrogen exchange mass spectrometry toward detecting protein motions relevant to allostery, covalent modifications, and enzyme function...
  28. ncbi request reprint Monitoring post-translational modification of proteins with allosteric ribozymes
    Narendra K Vaish
    Ribozyme Pharmaceuticals, Inc, 2950 Wilderness Place, Boulder, CO 80301, USA
    Nat Biotechnol 20:810-5. 2002
    ..This approach is generally applicable to the development of ribozymes capable of monitoring post-translational modification of specific proteins...
  29. ncbi request reprint Mapping protein post-translational modifications with mass spectrometry
    Eric S Witze
    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, Colorado 80309 0215, USA
    Nat Methods 4:798-806. 2007
    ..The aim of this review is introduce biologists to current strategies in mass spectrometry-based proteomics that are used to characterize protein post-translational modifications, noting strengths and shortcomings of various approaches...
  30. ncbi request reprint The characterization of protein post-translational modifications by mass spectrometry
    Rebecca E Schweppe
    Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado 80309, USA
    Acc Chem Res 36:453-61. 2003
    ..Here, we discuss current mass spectrometric and proteomic approaches for the identification of proteins and their covalent modifications, and we highlight high-throughput strategies for comprehensive analysis of cell proteomes...
  31. pmc The gatekeeper residue controls autoactivation of ERK2 via a pathway of intramolecular connectivity
    Michelle A Emrick
    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 103:18101-6. 2006
    ..Thus, an N-terminal hydrophobic cluster that includes the gatekeeper forms a novel structural unit, which functions to maintain the "off" state of ERK2 before cell signal activation...
  32. pmc Extracellular signal-regulated kinase induces the megakaryocyte GPIIb/CD41 gene through MafB/Kreisler
    Joel R Sevinsky
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
    Mol Cell Biol 24:4534-45. 2004
    ..Thus, ERK promotes megakaryocyte differentiation by coordinate regulation of nuclear factors that synergize in GPIIb promoter regulation. These results establish a novel role for MafB as a regulator of ERK-induced gene expression...
  33. ncbi request reprint Improved validation of peptide MS/MS assignments using spectral intensity prediction
    Shaojun Sun
    Department of Computer Science and Engineering, University of Colorado at Denver and Health Sciences Center, Denver, Colorado 80217 3364, USA
    Mol Cell Proteomics 6:1-17. 2007
    ....
  34. pmc Thermal-activated protein mobility and its correlation with catalysis in thermophilic alcohol dehydrogenase
    Zhao Xun Liang
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 101:9556-61. 2004
    ..The data provide support for the hypothesis that protein dynamics play a key role in controlling hydrogen tunneling at enzyme active sites...
  35. ncbi request reprint Purification and mass spectrometric identification of GA-binding protein (GABP) as the functional pituitary Ets factor binding to the basal transcription element of the prolactin promoter
    Rebecca E Schweppe
    Department of Medicine, Program in Molecular Biology, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
    J Biol Chem 278:16863-72. 2003
    ..Thus, we have identified GABPalpha/GABPbeta1 as a critical and functionally relevant Ets factor that regulates rPRL promoter activity via the BTE site...
  36. ncbi request reprint RhoC promotes human melanoma invasion in a PI3K/Akt-dependent pathway
    Mariah C Ruth
    Department of Dermatology, University of Colorado Health Science Center at Fitzsimons, Aurora, Colorado 80045, USA
    J Invest Dermatol 126:862-8. 2006
    ..We propose that RhoC promotes melanoma progression via separate mechanisms that regulate the PI3K/Akt pathway and the ROCK signaling pathway...
  37. ncbi request reprint 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
    Chia Yu Yen
    Department of Computer Science and Engineering, University of Colorado at Denver and Health Sciences Center, Denver, CO 80217 3364, USA
    Anal Chem 78:1071-84. 2006
    ....
  38. ncbi request reprint Analysis of membrane proteins from human chronic myelogenous leukemia cells: comparison of extraction methods for multidimensional LC-MS/MS
    Mariah C Ruth
    Yale University School of Medicine, New Haven, Connecticut 06510, USA
    J Proteome Res 5:709-19. 2006
    ..Proteins most highly abundant in the membrane samples showed enrichment of integral membrane protein identifications, consistent with their isolation by differential centrifugation...
  39. ncbi request reprint Incorporating expression data in metabolic modeling: a case study of lactate dehydrogenase
    Joshua Downer
    Department of Applied Mathematics, University of Colorado at Boulder, 526 UCB, CO 80309 0526, USA
    J Theor Biol 240:464-74. 2006
    ..Changes in the isoform ratio are not the primary determinant of the production of lactate. Rather, the total concentration of LDH controls the lactate concentration...
  40. pmc Proteomics and genomics: perspectives on drug and target discovery
    Natalie G Ahn
    Curr Opin Chem Biol 12:1-3. 2008
  41. pmc Phosphorylation-dependent changes in structure and dynamics in ERK2 detected by SDSL and EPR
    Andrew N Hoofnagle
    School of Medicine, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
    Biophys J 86:395-403. 2004
    ..Thus, electron paramagnetic resonance indicates reproducible changes in nanosecond side-chain mobilities at specific residues within the interdomain region, far from the site of phosphorylation and conformational change...
  42. doi request reprint Human Proteinpedia enables sharing of human protein data
    Suresh Mathivanan
    Nat Biotechnol 26:164-7. 2008

Research Grants5

  1. Biochemical Analysis of MKK/ERK Pathway
    Natalie Ahn; Fiscal Year: 2005
    ....
  2. AB-4000 QTRAP MASS SPECTROMETER
    Natalie Ahn; Fiscal Year: 2005
    ..An internal advisory committee consisting of faculty users and non-users will ensure equitable distribution of instrument time and fairness in fee schedules for use of the instrument. ..
  3. Regulation of Map Kinase by Protein Motions
    Natalie G Ahn; Fiscal Year: 2010
    ..abstract_text> ..
  4. Protein Phosphorylation and Cellular Regulation
    Natalie Ahn; Fiscal Year: 2002
    ..Our goal is to provide participants with a venue to learn perspectives and the forefront of each discipline, as well as opportunities to crossfertilize and establish new contacts and collaborations. ..