Adrian Hegeman

Summary

Affiliation: University of Minnesota–Twin Cities
Location: Saint Paul, United States
URL: http://www.horticulture.umn.edu/Who_sWho/Faculty/AdrianHegeman/

Publications

  1. ncbi request reprint Sequence of the cDNA for the heart/muscle isoform of mouse cytochrome c oxidase subunit VIII
    A D Hegeman
    Department of Anatomy and Cell Biology, University of Michigan, Ann Arbor 48109 0616, USA
    Biochim Biophys Acta 1261:311-4. 1995
  2. ncbi request reprint Comparison of full versus partial metabolic labeling for quantitative proteomics analysis in Arabidopsis thaliana
    Edward L Huttlin
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    Mol Cell Proteomics 6:860-81. 2007
  3. ncbi request reprint Implications of 15N-metabolic labeling for automated peptide identification in Arabidopsis thaliana
    Clark J Nelson
    Department of Comparative Biosciences, University of Wisconsin, Madison, WI, USA
    Proteomics 7:1279-92. 2007
  4. ncbi request reprint Stable isotope assisted assignment of elemental compositions for metabolomics
    Adrian D Hegeman
    Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    Anal Chem 79:6912-21. 2007
  5. ncbi request reprint New bioinformatics resources for metabolomics
    John L Markley
    Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    Pac Symp Biocomput . 2007
  6. doi request reprint Metabolite identification via the Madison Metabolomics Consortium Database
    Qiu Cui
    Nat Biotechnol 26:162-4. 2008
  7. ncbi request reprint The Radical SAM Superfamily
    Perry A Frey
    Department of Biochemistry, University of Madison, Wisconin Madison, Wisconsin 53726, USA
    Crit Rev Biochem Mol Biol 43:63-88. 2008
  8. pmc Cyanogenesis of wild lima bean (Phaseolus lunatus L.) is an efficient direct defence in nature
    Daniel J Ballhorn
    Department of General Botany Plant Ecology, Universitat Duisburg Essen, Essen, Germany
    PLoS ONE 4:e5450. 2009
  9. pmc Discovery and validation of colonic tumor-associated proteins via metabolic labeling and stable isotopic dilution
    Edward L Huttlin
    Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 106:17235-40. 2009
  10. pmc Analyzing plant defenses in nature
    Daniel J Ballhorn
    Department of General Botany Plant Ecology, , FB BioGeo, Essen, Germany
    Plant Signal Behav 4:743-5. 2009

Collaborators

Detail Information

Publications34

  1. ncbi request reprint Sequence of the cDNA for the heart/muscle isoform of mouse cytochrome c oxidase subunit VIII
    A D Hegeman
    Department of Anatomy and Cell Biology, University of Michigan, Ann Arbor 48109 0616, USA
    Biochim Biophys Acta 1261:311-4. 1995
    ..The deduced protein sequence enables us to compare the heart/muscle COX VIII isoforms from several species and to determine that the most highly conserved region of this subunit is the C-terminal domain...
  2. ncbi request reprint Comparison of full versus partial metabolic labeling for quantitative proteomics analysis in Arabidopsis thaliana
    Edward L Huttlin
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    Mol Cell Proteomics 6:860-81. 2007
    ..This difference is especially pronounced at extreme ratios. Ultimately both full metabolic labeling and partial metabolic labeling prove to be well suited for quantitative proteomics characterization...
  3. ncbi request reprint Implications of 15N-metabolic labeling for automated peptide identification in Arabidopsis thaliana
    Clark J Nelson
    Department of Comparative Biosciences, University of Wisconsin, Madison, WI, USA
    Proteomics 7:1279-92. 2007
    ..However, by determining the nitrogen count from each pair of labeled and unlabeled peptides we may improve our confidence in both heavy and light identifications...
  4. ncbi request reprint Stable isotope assisted assignment of elemental compositions for metabolomics
    Adrian D Hegeman
    Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    Anal Chem 79:6912-21. 2007
    ..These results demonstrate that metabolic labeling can be used to provide additional constraints for higher confidence formula assignments over an extended mass range...
  5. ncbi request reprint New bioinformatics resources for metabolomics
    John L Markley
    Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    Pac Symp Biocomput . 2007
    ..Sesame was designed to help coordinate research efforts in laboratories with high sample throughput and multiple investigators and to track all of the actions that have taken place in a particular study...
  6. doi request reprint Metabolite identification via the Madison Metabolomics Consortium Database
    Qiu Cui
    Nat Biotechnol 26:162-4. 2008
  7. ncbi request reprint The Radical SAM Superfamily
    Perry A Frey
    Department of Biochemistry, University of Madison, Wisconin Madison, Wisconsin 53726, USA
    Crit Rev Biochem Mol Biol 43:63-88. 2008
    ....
  8. pmc Cyanogenesis of wild lima bean (Phaseolus lunatus L.) is an efficient direct defence in nature
    Daniel J Ballhorn
    Department of General Botany Plant Ecology, Universitat Duisburg Essen, Essen, Germany
    PLoS ONE 4:e5450. 2009
    ..Our results indicate the general importance of analysing 'multiple defence syndromes' rather than single defence mechanisms in future functional analyses of plant defences...
  9. pmc Discovery and validation of colonic tumor-associated proteins via metabolic labeling and stable isotopic dilution
    Edward L Huttlin
    Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 106:17235-40. 2009
    ..Our work demonstrates the power of metabolic labeling combined with stable isotopic dilution as an integrated strategy for the identification and validation of differentially expressed proteins using rodent models of human disease...
  10. pmc Analyzing plant defenses in nature
    Daniel J Ballhorn
    Department of General Botany Plant Ecology, , FB BioGeo, Essen, Germany
    Plant Signal Behav 4:743-5. 2009
    ....
  11. doi request reprint Plant metabolomics--meeting the analytical challenges of comprehensive metabolite analysis
    Adrian D Hegeman
    Department of Horticultural Science, Microbial and Plant Genomics Institute, University of Minnesota, USA
    Brief Funct Genomics 9:139-48. 2010
    ..New strategies to address spatial distribution of metabolites via mass spectrometry-based imaging are also reviewed...
  12. doi request reprint Measuring the turnover rates of Arabidopsis proteins using deuterium oxide: an auxin signaling case study
    Xiao Yuan Yang
    Department of Plant Biology, University of Minnesota, St Paul, MN 55108, USA
    Plant J 63:680-95. 2010
    ..These considerations suggest a prescription for specific experimental designs that minimize interference resulting from the induction of treatment-specific gene expression in the results obtained...
  13. doi request reprint Microscale analysis of amino acids using gas chromatography-mass spectrometry after methyl chloroformate derivatization
    Wen Ping Chen
    Department of Horticultural Science, University of Minnesota, Saint Paul, MN 55108, United States
    J Chromatogr B Analyt Technol Biomed Life Sci 878:2199-208. 2010
    ..Sample preparation was facile, rapid, economical, and the method is easily modified for integration into robotic systems for analysis with large numbers of samples...
  14. pmc An automated growth enclosure for metabolic labeling of Arabidopsis thaliana with 13C-carbon dioxide - an in vivo labeling system for proteomics and metabolomics research
    Wen Ping Chen
    Department of Horticultural Science, University of Minnesota, Saint Paul, USA
    Proteome Sci 9:9. 2011
    ..abstract:..
  15. doi request reprint Easy and accurate high-performance liquid chromatography retention prediction with different gradients, flow rates, and instruments by back-calculation of gradient and flow rate profiles
    Paul G Boswell
    Department of Horticultural Science and the Microbial and Plant Genomics Institute, University of Minnesota, 1970 Folwell Avenue, St Paul, MN 55108, USA
    J Chromatogr A 1218:6742-9. 2011
    ..This approach provides a simple way to correct for all instrument-related factors affecting retention, allowing dramatically streamlined and improved retention projection across gradients, flow rates, and HPLC instruments...
  16. doi request reprint A study on retention "projection" as a supplementary means for compound identification by liquid chromatography-mass spectrometry capable of predicting retention with different gradients, flow rates, and instruments
    Paul G Boswell
    Department of Horticultural Science and the Microbial and Plant Genomics Institute, University of Minnesota, 1970 Folwell Avenue, St Paul, MN 55108, USA
    J Chromatogr A 1218:6732-41. 2011
    ..Thus, these two factors must be taken into account to accurately project retention on diverse instrumentation...
  17. pmc Prediction of error associated with false-positive rate determination for peptide identification in large-scale proteomics experiments using a combined reverse and forward peptide sequence database strategy
    Edward L Huttlin
    Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    J Proteome Res 6:392-8. 2007
    ..Finally, we consider how these approaches may be applied to more complicated data sets, as when peptides are separated by charge state prior to false-positive determination...
  18. ncbi request reprint Free radical mechanisms in enzymology
    Perry A Frey
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
    Chem Rev 106:3302-16. 2006
  19. ncbi request reprint Identification of genes expressed after noise exposure in the chick basilar papilla
    T W Gong
    Kresge Hearing Research Institute, Department of Otolaryngology Head Neck Surgery, University of Michigan Medical School, Ann Arbor 48109 0648, USA
    Hear Res 96:20-32. 1996
    ..These results indicate the potential involvement of both Ca2+/calmodulin-mediated signaling and GTPase cascades in the response to noise damage and during hair cell regeneration in the chick basilar papilla...
  20. ncbi request reprint Structural analysis of UDP-sugar binding to UDP-galactose 4-epimerase from Escherichia coli
    J B Thoden
    Institute for Enzyme Research, College of Agricultural and Life Sciences, University of Wisconsin Madison 53705, USA
    Biochemistry 36:6294-304. 1997
    ..24 A. The only significant differences between the various enzyme/UDP-sugar models occur in two of the dihedral angles defining the conformation of the UDP-sugar ligands...
  21. ncbi request reprint Novel genes expressed in the chick otocyst during development: identification using differential display of RNA
    T W Gong
    Kresge Hearing Research Institute, Department of Otolaryngology Head Neck Surgery, University of Michigan Medical School, Ann Arbor 48109 0648, USA
    Int J Dev Neurosci 15:585-94. 1997
    ..These results identified both the avian and human homologues of an evolutionarily conserved gene encoding a small acidic protein of unknown function; however, expression of this gene was not restricted to otocysts...
  22. ncbi request reprint Characterization of enzymatic processes by rapid mix-quench mass spectrometry: the case of dTDP-glucose 4,6-dehydratase
    J W Gross
    Department of Biochemistry, College of Agricultural Life Sciences, University of Wisconsin Madison, Madison, Wisconsin 53705, USA
    Biochemistry 39:13633-40. 2000
    ..The transient formation and reaction of dTDP-4-ketoglucose could not be observed, because this intermediate did not accumulate to detectable concentrations...
  23. ncbi request reprint Probing catalysis by Escherichia coli dTDP-glucose-4,6-dehydratase: identification and preliminary characterization of functional amino acid residues at the active site
    A D Hegeman
    Department of Biochemistry, University of Wisconsin Madison, 53705, USA
    Biochemistry 40:6598-610. 2001
    ..Additional steady-state techniques were employed in an attempt to further limit the assignment of rate limitation. The results are discussed within the context of the 4,6-dehydratase active site model and chemical mechanism...
  24. ncbi request reprint Dehydration is catalyzed by glutamate-136 and aspartic acid-135 active site residues in Escherichia coli dTDP-glucose 4,6-dehydratase
    J W Gross
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53705, USA
    Biochemistry 40:12497-504. 2001
    ..Thus, the decrease in the rate of catalysis ( approximately 2 orders of magnitude) of the exchange reaction observed with Glu136 variants demonstrates this residue's importance in base catalysis of dehydration...
  25. ncbi request reprint Toward a structural understanding of the dehydratase mechanism
    Simon T M Allard
    Centre for Biomolecular Sciences, North Haugh, The University, St Andrews, Fife KY16 9ST, Scotland, United Kingdom
    Structure 10:81-92. 2002
    ..We conclude that the substrate is required to move within the active site to complete the catalytic cycle and that this movement is driven by the elimination of water. The results provide insight into members of the SDR superfamily...
  26. ncbi request reprint Concerted and stepwise dehydration mechanisms observed in wild-type and mutated Escherichia coli dTDP-glucose 4,6-dehydratase
    Adrian D Hegeman
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53705, USA
    Biochemistry 41:2797-804. 2002
    ..We postulate that the switch from a concerted to stepwise dehydration mechanism observed in the aspartic acid variants is due to the loss of control over the glucosyl C5-C6 bond rotation in the active site...
  27. ncbi request reprint The structure of NADH in the enzyme dTDP-d-glucose dehydratase (RmlB)
    Konstantinos Beis
    Centre for Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
    J Am Chem Soc 125:11872-8. 2003
    ..These results demonstrate the ability of dehydratase enzymes to fine-tune the redox potential of NADH through conformational changes in the nicotinamide ring...
  28. ncbi request reprint An isotope labeling strategy for quantifying the degree of phosphorylation at multiple sites in proteins
    Adrian D Hegeman
    Biotechnology Center, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    J Am Soc Mass Spectrom 15:647-53. 2004
    ....
  29. pmc Autophosphorylation and subcellular localization dynamics of a salt- and water deficit-induced calcium-dependent protein kinase from ice plant
    E Wassim Chehab
    Department of Biochemistry MS200, University of Nevada, Reno, Nevada 89557 0014, USA
    Plant Physiol 135:1430-46. 2004
    ....
  30. ncbi request reprint Crystal structure of At2g03760, a putative steroid sulfotransferase from Arabidopsis thaliana
    David W Smith
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Proteins 57:854-7. 2004
  31. pmc A transcriptome-based characterization of habituation in plant tissue culture
    Melissa S Pischke
    University of Wisconsin Biotechnology Center and Department of Biochemistry, Madison, Wisconsin 53706, USA
    Plant Physiol 140:1255-78. 2006
    ....
  32. ncbi request reprint A quantitative analysis of Arabidopsis plasma membrane using trypsin-catalyzed (18)O labeling
    Clark J Nelson
    Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USA
    Mol Cell Proteomics 5:1382-95. 2006
    ....
  33. ncbi request reprint A phyloproteomic characterization of in vitro autophosphorylation in calcium-dependent protein kinases
    Adrian D Hegeman
    University of Wisconsin Biotechnology Center, Madison, 53706, USA
    Proteomics 6:3649-64. 2006
    ..Homology models were generated for the protein kinase and calmodulin-like domains, each containing two of the five conserved sites, to allow intelligent speculation regarding subsequent lines of investigation...
  34. pmc Protocol: High-throughput and quantitative assays of auxin and auxin precursors from minute tissue samples
    Xing Liu
    Plant Biological Sciences Graduate Program, Department of Horticultural Science, and Microbial and Plant Genomics Institute, University of Minnesota, 1970 Folwell Avenue, Saint Paul, MN, 55108, USA
    Plant Methods 8:31. 2012
    ..abstract:..