Research Topics
Genomes and Genes | Adrian HegemanSummaryAffiliation: University of Minnesota–Twin Cities Location: Saint Paul, United States URL: http://www.horticulture.umn.edu/Who_sWho/Faculty/AdrianHegeman/ Publications
| Collaborators
|
Detail Information
Publications
Sequence of the cDNA for the heart/muscle isoform of mouse cytochrome c oxidase subunit VIIIA 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...- Comparison of full versus partial metabolic labeling for quantitative proteomics analysis in Arabidopsis thalianaEdward 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... - Implications of 15N-metabolic labeling for automated peptide identification in Arabidopsis thalianaClark 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... - Stable isotope assisted assignment of elemental compositions for metabolomicsAdrian 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... - New bioinformatics resources for metabolomicsJohn 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... - Metabolite identification via the Madison Metabolomics Consortium DatabaseQiu Cui
Nat Biotechnol 26:162-4. 2008 - The Radical SAM SuperfamilyPerry A Frey
Department of Biochemistry, University of Madison, Wisconin Madison, Wisconsin 53726, USA
Crit Rev Biochem Mol Biol 43:63-88. 2008.... 
Cyanogenesis of wild lima bean (Phaseolus lunatus L.) is an efficient direct defence in natureDaniel 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...- Discovery and validation of colonic tumor-associated proteins via metabolic labeling and stable isotopic dilutionEdward 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... - Analyzing plant defenses in natureDaniel J Ballhorn
Department of General Botany Plant Ecology, , FB BioGeo, Essen, Germany
Plant Signal Behav 4:743-5. 2009.... 
Plant metabolomics--meeting the analytical challenges of comprehensive metabolite analysisAdrian 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...- Measuring the turnover rates of Arabidopsis proteins using deuterium oxide: an auxin signaling case studyXiao 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... - Microscale analysis of amino acids using gas chromatography-mass spectrometry after methyl chloroformate derivatizationWen 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... - An automated growth enclosure for metabolic labeling of Arabidopsis thaliana with 13C-carbon dioxide - an in vivo labeling system for proteomics and metabolomics researchWen Ping Chen
Department of Horticultural Science, University of Minnesota, Saint Paul, USA
Proteome Sci 9:9. 2011..abstract:.. - Easy and accurate high-performance liquid chromatography retention prediction with different gradients, flow rates, and instruments by back-calculation of gradient and flow rate profilesPaul 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... - 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 strategyEdward 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... - Free radical mechanisms in enzymologyPerry A Frey
Department of Biochemistry, University of Wisconsin-Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
Chem Rev 106:3302-16. 2006 - A phyloproteomic characterization of in vitro autophosphorylation in calcium-dependent protein kinasesAdrian 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... - Identification of genes expressed after noise exposure in the chick basilar papillaT 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... - Structural analysis of UDP-sugar binding to UDP-galactose 4-epimerase from Escherichia coliJ 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... - Novel genes expressed in the chick otocyst during development: identification using differential display of RNAT 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... - Characterization of enzymatic processes by rapid mix-quench mass spectrometry: the case of dTDP-glucose 4,6-dehydrataseJ 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... - Probing catalysis by Escherichia coli dTDP-glucose-4,6-dehydratase: identification and preliminary characterization of functional amino acid residues at the active siteA 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... - Dehydration is catalyzed by glutamate-136 and aspartic acid-135 active site residues in Escherichia coli dTDP-glucose 4,6-dehydrataseJ 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... - Toward a structural understanding of the dehydratase mechanismSimon 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... - Concerted and stepwise dehydration mechanisms observed in wild-type and mutated Escherichia coli dTDP-glucose 4,6-dehydrataseAdrian 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... - 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... - An isotope labeling strategy for quantifying the degree of phosphorylation at multiple sites in proteinsAdrian D Hegeman
Biotechnology Center, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
J Am Soc Mass Spectrom 15:647-53. 2004.... - Autophosphorylation and subcellular localization dynamics of a salt- and water deficit-induced calcium-dependent protein kinase from ice plantE Wassim Chehab
Department of Biochemistry/MS200, University of Nevada, Reno, Nevada 89557-0014, USA
Plant Physiol 135:1430-46. 2004.... - Crystal structure of At2g03760, a putative steroid sulfotransferase from Arabidopsis thalianaDavid W Smith
Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
Proteins 57:854-7. 2004 - A transcriptome-based characterization of habituation in plant tissue cultureMelissa S Pischke
University of Wisconsin Biotechnology Center and Department of Biochemistry, Madison, Wisconsin 53706, USA
Plant Physiol 140:1255-78. 2006.... - A quantitative analysis of Arabidopsis plasma membrane using trypsin-catalyzed (18)O labelingClark J Nelson
Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USA
Mol Cell Proteomics 5:1382-95. 2006.... - 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 instrumentsPaul 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...