Vanderbilt-Ingram Cancer Center

The VICC.ORG Investigator Directory

Amy-Joan Lorna Ham, Ph.D.

Research Associate Professor of Biochemistry
VICC Member
Researcher

Contact Information:

Vanderbilt University Medical Center
465 21st Avenue South
U1213 MRB III
Nashville, TN 37232-6350
615-322-2948

Publications:

• Tomasiak, TM, Archuleta, TL, Andréll, J, Luna-Chávez, C, Davis, TA, Sarwar, M, Ham, AJ, McDonald, WH, Yankovskaya, V, Stern, HA, Johnston, JN, Maklashina, E, Cecchini, G, Iverson, TM Geometric restraint drives on- and off-pathway catalysis by the Escherichia coli menaquinol:fumarate reductase. J Biol Chem, 286(4), 3047-56, 2011.
• Zhang, H, Liu, Q, Zimmerman, LJ, Ham, AJ, Slebos, RJ, Rahman, J, Kikuchi, T, Massion, PP, Carbone, DP, Billheimer, D, Liebler, DC Methods for Peptide and protein quantitation by liquid chromatography-multiple reaction monitoring mass spectrometry. Mol Cell Proteomics, 10(6), M110.006593, 2011.
• Rexer, BN, Ham, AJ, Rinehart, C, Hill, S, de Matos Granja-Ingram, N, González-Angulo, AM, Mills, GB, Dave, B, Chang, JC, Liebler, DC, Arteaga, CL Phosphoproteomic mass spectrometry profiling links Src family kinases to escape from HER2 tyrosine kinase inhibition. Oncogene, 2011.
• Ma, ZQ, Chambers, MC, Ham, AJ, Cheek, KL, Whitwell, CW, Aerni, HR, Schilling, B, Miller, AW, Caprioli, RM, Tabb, DL ScanRanker: Quality Assessment of Tandem Mass Spectra via Sequence Tagging. J Proteome Res, 2011.
• Baucum, AJ, Jalan-Sakrikar, N, Jiao, Y, Gustin, RM, Carmody, LC, Tabb, DL, Ham, AJ, Colbran, RJ Identification and validation of novel spinophilin-associated proteins in rodent striatum using an enhanced ex vivo shotgun proteomics approach. Mol Cell Proteomics, 9(6), 1243-59, 2010.
• Tabb, DL, Vega-Montoto, L, Rudnick, PA, Variyath, AM, Ham, AJ, Bunk, DM, Kilpatrick, LE, Billheimer, DD, Blackman, RK, Cardasis, HL, Carr, SA, Clauser, KR, Jaffe, JD, Kowalski, KA, Neubert, TA, Regnier, FE, Schilling, B, Tegeler, TJ, Wang, M, Wang, P, Whiteaker, JR, Zimmerman, LJ, Fisher, SJ, Gibson, BW, Kinsinger, CR, Mesri, M, Rodriguez, H, Stein, SE, Tempst, P, Paulovich, AG, Liebler, DC, Spiegelman, C Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J Proteome Res, 9(2), 761-76, 2010.
• Dasari, S, Chambers, MC, Slebos, RJ, Zimmerman, LJ, Ham, AJ, Tabb, DL TagRecon: high-throughput mutation identification through sequence tagging. J Proteome Res, 9(4), 1716-26, 2010.
• Vanacore, R, Ham, AJ, Voehler, M, Sanders, CR, Conrads, TP, Veenstra, TD, Sharpless, KB, Dawson, PE, Hudson, BG A sulfilimine bond identified in collagen IV. Science, 325(5945), 1230-4, 2009.
• Raman, D, Neel, NF, Sai, J, Mernaugh, RL, Ham, AJ, Richmond, AJ Characterization of chemokine receptor CXCR2 interacting proteins using a proteomics approach to define the CXCR2 "chemosynapse". Methods Enzymol, 460315-30, 2009.
• Cai, Y, Xu, Z, Xie, J, Ham, AJ, Koury, MJ, Hiebert, SW, Brandt, SJ Eto2/MTG16 and MTGR1 are heteromeric corepressors of the TAL1/SCL transcription factor in murine erythroid progenitors. Biochem Biophys Res Commun, 390(2), 295-301, 2009.
• Falin, RA, Morrison, R, Ham, AJ, Strange, K Identification of regulatory phosphorylation sites in a cell volume- and Ste20 kinase-dependent ClC anion channel. J Gen Physiol, 133(1), 29-42, 2009.
• Kolobova, E, Efimov, A, Kaverina, I, Rishi, AK, Schrader, JW, Ham, AJ, Larocca, MC, Goldenring, JR Microtubule-dependent association of AKAP350A and CCAR1 with RNA stress granules. Exp Cell Res, 315(3), 542-55, 2009.
• Erickson, JR, Joiner, ML, Guan, X, Kutschke, W, Yang, J, Oddis, CV, Bartlett, RK, Lowe, JS, O''Donnell, SE, Aykin-Burns, N, Zimmerman, MC, Zimmerman, K, Ham, AJ, Weiss, RM, Spitz, DR, Shea, MA, Colbran, RJ, Mohler, PJ, Anderson, ME A dynamic pathway for calcium-independent activation of CaMKII by methionine oxidation. Cell, 133(3), 462-74, 2008.
• Vanacore, RM, Ham, AJ, Cartailler, JP, Sundaramoorthy, M, Todd, P, Pedchenko, V, Sado, Y, Borza, DB, Hudson, BG A role for collagen IV cross-links in conferring immune privilege to the Goodpasture autoantigen: structural basis for the crypticity of B cell epitopes. J Biol Chem, 283(33), 22737-48, 2008.
• Tabb, DL, Ma, ZQ, Martin, DB, Ham, AJ, Chambers, MC DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring. J Proteome Res, 7(9), 3838-46, 2008.
• Slebos, RJ, Brock, JW, Winters, NF, Stuart, SR, Martinez, MA, Li, M, Chambers, MC, Zimmerman, LJ, Ham, AJ, Tabb, DL, Liebler, DC Evaluation of Strong Cation Exchange versus Isoelectric Focusing of Peptides for Multidimensional Liquid Chromatography-Tandem Mass Spectrometry. J Proteome Res, 2008.
• Yang, Z, Browning, CF, Hallaq, H, Yermalitskaya, L, Esker, J, Hall, MR, Link, AJ, Ham, AJ, McGrath, MJ, Mitchell, CA, Murray, KT Four and a half LIM protein 1: a partner for KCNA5 in human atrium. Cardiovasc Res, 78(3), 449-57, 2008.
• Luo, W, Slebos, RJ, Hill, S, Li, M, Brábek, J, Amanchy, R, Chaerkady, R, Pandey, A, Ham, AJ, Hanks, SK Global impact of oncogenic Src on a phosphotyrosine proteome. J Proteome Res, 7(8), 3447-60, 2008.
• Fang, WB, Brantley-Sieders, DM, Hwang, Y, Ham, AJ, Chen, J Identification and functional analysis of phosphorylated tyrosine residues within EphA2 receptor tyrosine kinase. J Biol Chem, 283(23), 16017-26, 2008.
• Brown, KA, Ham, AJ, Clark, CN, Meller, N, Law, BK, Chytil, A, Cheng, N, Pietenpol, JA, Moses, HL Identification of novel Smad2 and Smad3 associated proteins in response to TGF-beta1. J Cell Biochem, 105(2), 596-611, 2008.
• Chetyrkin, SV, Mathis, ME, Ham, AJ, Hachey, DL, Hudson, BG, Voziyan, PA Propagation of protein glycation damage involves modification of tryptophan residues via reactive oxygen species: inhibition by pyridoxamine. Free Radic Biol Med, 44(7), 1276-85, 2008.
• Burgess, EF, Ham, AJ, Tabb, DL, Billheimer, D, Roth, BJ, Chang, SS, Cookson, MS, Hinton, TJ, Cheek, KL, Hill, S, Pietenpol, JA Prostate cancer serum biomarker discovery through proteomic analysis of alpha-2 macroglobulin protein complexes. Proteomics Clin Appl, 2(9), 1223, 2008.
• Cao, Z, Li, C, Higginbotham, JN, Franklin, JL, Tabb, DL, Graves-Deal, R, Hill, S, Cheek, K, Jerome, WG, Lapierre, LA, Goldenring, JR, Ham, AJ, Coffey, RJ Use of fluorescence-activated vesicle sorting for isolation of Naked2-associated, basolaterally targeted exocytic vesicles for proteomics analysis. Mol Cell Proteomics, 7(9), 1651-67, 2008.
• Lapierre, LA, Avant, KM, Caldwell, CM, Ham, AJ, Hill, S, Williams, JA, Smolka, AJ, Goldenring, JR Characterization of immunoisolated human gastric parietal cells tubulovesicles: identification of regulators of apical recycling. Am J Physiol Gastrointest Liver Physiol, 292(5), G1249-62, 2007.
• Myers, JS, Zhao, R, Xu, X, Ham, AJ, Cortez, D Cyclin-dependent kinase 2 dependent phosphorylation of ATRIP regulates the G2-M checkpoint response to DNA damage. Cancer Res, 67(14), 6685-90, 2007.
• Mohler, PJ, Zhu, MY, Blade, AM, Ham, AJ, Shelness, GS, Swift, LL Identification of a novel isoform of microsomal triglyceride transfer protein. J Biol Chem, 282(37), 26981-8, 2007.
• Druckova, A, Mernaugh, RL, Ham, AJ, Marnett, LJ Identification of the protein targets of the reactive metabolite of teucrin A in vivo in the rat. Chem Res Toxicol, 20(10), 1393-408, 2007.
• Donowitz, M, Singh, S, Salahuddin, FF, Hogema, BM, Chen, Y, Gucek, M, Cole, RN, Ham, A, Zachos, NC, Kovbasnjuk, O, Lapierre, LA, Broere, N, Goldenring, J, deJonge, H, Li, X Proteome of murine jejunal brush border membrane vesicles. J Proteome Res, 6(10), 4068-79, 2007.
• Bender, RP, Ham, AJ, Osheroff, N Quinone-induced enhancement of DNA cleavage by human topoisomerase IIalpha: adduction of cysteine residues 392 and 405. Biochemistry, 46(10), 2856-64, 2007.
• Hill, KE, Zhou, J, Austin, LM, Motley, AK, Ham, AJ, Olson, GE, Atkins, JF, Gesteland, RF, Burk, RF The selenium-rich C-terminal domain of mouse selenoprotein P is necessary for the supply of selenium to brain and testis but not for the maintenance of whole body selenium. J Biol Chem, 282(15), 10972-80, 2007.
• Wu, ZL, Bartleson, CJ, Ham, AJ, Guengerich, FP Heterologous expression, purification, and properties of human cytochrome P450 27C1. Arch Biochem Biophys, 445(1), 138-46, 2006.
• Luka, Z, Ham, AJ, Norris, JL, Yeo, EJ, Yermalitsky, V, Glenn, B, Caprioli, RM, Liebler, DC, Wagner, C Identification of phosphorylation sites in glycine N-methyltransferase from rat liver. Protein Sci, 15(4), 785-94, 2006.
• Grueter, CE, Abiria, SA, Dzhura, I, Wu, Y, Ham, AJ, Mohler, PJ, Anderson, ME, Colbran, RJ L-type Ca2+ channel facilitation mediated by phosphorylation of the beta subunit by CaMKII. Mol Cell, 23(5), 641-50, 2006.
• Ducharme, NA, Hales, CM, Lapierre, LA, Ham, AJ, Oztan, A, Apodaca, G, Goldenring, JR MARK2/EMK1/Par-1Balpha phosphorylation of Rab11-family interacting protein 2 is necessary for the timely establishment of polarity in Madin-Darby canine kidney cells. Mol Biol Cell, 17(8), 3625-37, 2006.
• Popescu, DC, Ham, AJ, Shieh, BH Scaffolding protein INAD regulates deactivation of vision by promoting phosphorylation of transient receptor potential by eye protein kinase C in Drosophila. J Neurosci, 26(33), 8570-7, 2006.
• Tabb, DL, Friedman, DB, Ham, AJ Verification of automated peptide identifications from proteomic tandem mass spectra. Nat Protoc, 1(5), 2213-22, 2006.
• Vanacore, RM, Friedman, DB, Ham, AJ, Sundaramoorthy, M, Hudson, BG Identification of S-hydroxylysyl-methionine as the covalent cross-link of the noncollagenous (NC1) hexamer of the alpha1alpha1alpha2 collagen IV network: a role for the post-translational modification of lysine 211 to hydroxylysine 211 in hexamer assembly. J Biol Chem, 280(32), 29300-10, 2005.
• Pedchenko, VK, Chetyrkin, SV, Chuang, P, Ham, AJ, Saleem, MA, Mathieson, PW, Hudson, BG, Voziyan, PA Mechanism of perturbation of integrin-mediated cell-matrix interactions by reactive carbonyl compounds and its implication for pathogenesis of diabetic nephropathy. Diabetes, 54(10), 2952-60, 2005.
• Hansen, BT, Davey, SW, Ham, AJ, Liebler, DC P-Mod: an algorithm and software to map modifications to peptide sequences using tandem MS data. J Proteome Res, 4(2), 358-68, 2005.
• Manza, LL, Stamer, SL, Ham, AJ, Codreanu, SG, Liebler, DC Sample preparation and digestion for proteomic analyses using spin filters. Proteomics, 5(7), 1742-5, 2005.
• Ham, AJ, Engelward, BP, Koc, H, Sangaiah, R, Meira, LB, Samson, LD, Swenberg, JA New immunoaffinity-LC-MS/MS methodology reveals that Aag null mice are deficient in their ability to clear 1,N6-etheno-deoxyadenosine DNA lesions from lung and liver in vivo. DNA Repair (Amst), 3(3), 257-65, 2004.
• Morinello, EJ, Ham, AJ, Ranasinghe, A, Nakamura, J, Upton, PB, Swenberg, JA Molecular dosimetry and repair of N(2),3-ethenoguanine in rats exposed to vinyl chloride. Cancer Res, 62(18), 5189-95, 2002.
• Morinello, EJ, Ham, AJ, Ranasinghe, A, Sangaiah, R, Swenberg, JA Simultaneous quantitation of N(2),3-ethenoguanine and 1,N(2)-ethenoguanine with an immunoaffinity/gas chromatography/high-resolution mass spectrometry assay. Chem Res Toxicol, 14(3), 327-34, 2001.
• Ham, AJ, Ranasinghe, A, Koc, H, Swenberg, JA 4-Hydroxy-2-nonenal and ethyl linoleate form N(2),3-ethenoguanine under peroxidizing conditions. Chem Res Toxicol, 13(12), 1243-50, 2000.
• Swenberg, JA, Ham, A, Koc, H, Morinello, E, Ranasinghe, A, Tretyakova, N, Upton, PB, Wu, K DNA adducts: effects of low exposure to ethylene oxide, vinyl chloride and butadiene. Mutat Res, 464(1), 77-86, 2000.
• Hussain, SP, Amstad, P, Raja, K, Ambs, S, Nagashima, M, Bennett, WP, Shields, PG, Ham, AJ, Swenberg, JA, Marrogi, AJ, Harris, CC Increased p53 mutation load in noncancerous colon tissue from ulcerative colitis: a cancer-prone chronic inflammatory disease. Cancer Res, 60(13), 3333-7, 2000.
• Swenberg, JA, Bogdanffy, MS, Ham, A, Holt, S, Kim, A, Morinello, EJ, Ranasinghe, A, Scheller, N, Upton, PB Formation and repair of DNA adducts in vinyl chloride- and vinyl fluoride-induced carcinogenesis. IARC Sci Publ, (150), 29-43, 1999.
• Liebler, DC, Burr, JA, Ham, AJ Gas chromatography-mass spectrometry analysis of vitamin E and its oxidation products. Methods Enzymol, 299309-18, 1999.
• Ham, AJ, Ranasinghe, A, Morinello, EJ, Nakamura, J, Upton, PB, Johnson, F, Swenberg, JA Immunoaffinity/gas chromatography/high-resolution mass spectrometry method for the detection of N(2),3-ethenoguanine. Chem Res Toxicol, 12(12), 1240-6, 1999.
• Ham, AJ, Liebler, DC Antioxidant reactions of vitamin E in the perfused rat liver: product distribution and effect of dietary vitamin E supplementation. Arch Biochem Biophys, 339(1), 157-64, 1997.
• Liebler, DC, Burr, JA, Philips, L, Ham, AJ Gas chromatography-mass spectrometry analysis of vitamin E and its oxidation products. Anal Biochem, 236(1), 27-34, 1996.
• Ham, AJ, Liebler, DC Vitamin E oxidation in rat liver mitochondria. Biochemistry, 34(17), 5754-61, 1995.
• Sharpe, AL, Carter, DE Substrate specificity of rat liver aldehyde dehydrogenase with chloroacetaldehydes. J Biochem Toxicol, 8(3), 155-60, 1993.