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MSRC Proteomics Lab

MSRC Proteomics Laboratory Publications

2009

Franco AT, Friedman DB, Nagy TA, Romero-Gallo J, Krishna U, Kendall A, Israel DA, Tegtmeyer N, Washington MK, Peek RM Jr. Delineation of a carcinogenic Helicobacter pylori proteome. Mol Cell Proteomics. 2009 Aug;8(8):1947-58. Epub 2009 May 25. PubMed PMID: 19470446; PubMed Central PMCID: PMC2722763. 

Voehler MW, Eoff RL, McDonald WH, Guengerich FP, Stone MP. Modulation of the structure, catalytic activity, and fidelity of african Swine Fever virus DNA polymerase x by a reversible disulfide switch. J Biol Chem. 2009 Jul 3;284(27):18434-44. Epub 2009 May 5. PubMed PMID: 19419958; PubMed Central PMCID: PMC2709365.

Friedman, D. B., and Lilley, K. S. (2009). Difference gel electrophoresis (DIGE). In ‘‘The Protein Protocols Handbook’’ (Walker John, ed.), 3rd edn. pp. 379–408,.Humana Press, Totowa, NJ.

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.  2009 Sep 4;325(5945):1230-4. PubMed PMID: 19729652. 

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. 2009;460:315-30. PubMed PMID: 19446732. 

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. 2009 Jan;133(1):29-42. Epub 2008 Dec 15. PubMed PMID: 19088383; PubMed Central PMCID: PMC2606941. 

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. 2009 Feb 1;315(3):542-55. Epub 2008 Dec 3. PubMed  PMID: 19073175. 

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. 2008 Aug;7(8):3447-60. Epub 2008 Jun 19. PubMed PMID: 18563927; PubMed Central PMCID: PMC2579752. 

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. 2008 Sep;7(9):1651-67. Epub 2008 May 25. PubMed PMID: 18504258; PubMed Central PMCID: PMC2528074. 

Friedman DB, Lilley KS. Optimizing the difference gel electrophoresis (DIGE) technology. Methods Mol Biol. 2008;428:93-124. PubMed PMID: 18287770. 

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. 2008 Aug 15;283(33):22737-48. Epub 2008 May 22. PubMed PMID: 18499662; PubMed Central PMCID: PMC2504875. 

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. 2008 Jun 6;283(23):16017-26. Epub 2008 Apr 3. PubMed PMID: 18387945; PubMed Central PMCID: PMC2414276. 

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. 2008 Jun 1;78(3):449-57. Epub  2008 Feb 15. PubMed PMID: 18281375. 

Robertson PD, Warren EM, Zhang H, Friedman DB, Lary JW, Cole JL, Tutter AV, Walter JC, Fanning E, Eichman BF. Domain architecture and biochemical characterization of vertebrate Mcm10. J Biol Chem. 2008 Feb 8;283(6):3338-48. Epub 2007 Dec 6. PubMed PMID: 18065420.

Meyrick BO, Friedman DB, Billheimer DD, Cogan JD, Prince MA, Phillips JA 3rd,  Loyd JE. Proteomics of transformed lymphocytes from a family with familial pulmonary arterial hypertension. Am J Respir Crit Care Med. 2008 Jan 1;177(1):99-107. Epub 2007 Oct 11. PubMed PMID: 17932379; PubMed Central PMCID: PMC2176118. 

2007

Friedman DB, Wang SE, Whitwell CW, Caprioli RM, Arteaga CL. Multivariable difference gel electrophoresis and mass spectrometry: a case study on transforming growth factor-beta and ERBB2 signaling. Mol Cell Proteomics. 2007 Jan;6(1):150-69. Epub 2006 Oct 5. PubMed PMID: 17028091. 

Viquez OM, Valentine HL, Friedman DB, Olson SJ, Valentine WM. Peripheral nerve protein expression and carbonyl content in N,N-diethlydithiocarbamate myelinopathy. Chem Res Toxicol. 2007 Mar;20(3):370-9. Epub 2007 Feb 27. PubMed PMID: 17323979; PubMed Central PMCID: PMC2525616. 

Khoshnoodi J, Hill S, Tryggvason K, Hudson B, Friedman DB. Identification of  N-linked glycosylation sites in human nephrin using mass spectrometry. J Mass Spectrom. 2007 Mar;42(3):370-9. PubMed PMID: 17212372. 

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. 2008 Apr 1;44(7):1276-85. Epub 2007 Oct 4. PubMed PMID: 18374270. 

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. 2007 Oct;20(10):1393-408. Epub 2007 Sep 25. PubMed PMID: 17892266. 

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. 2007 Jul 15;67(14):6685-90. PubMed PMID: 17638878; PubMed Central PMCID: PMC2728292. 

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. 2007 Apr 13;282(15):10972-80. Epub 2007 Feb 20. PubMed PMID: 17311913. 

Bender RP, Ham AJ, Osheroff N. Quinone-induced enhancement of DNA cleavage by human topoisomerase IIalpha: adduction of cysteine residues 392 and 405. Biochemistry. 2007 Mar 13;46(10):2856-64. Epub 2007 Feb 14. PubMed PMID: 17298034. 

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. 2007 May;292(5):G1249-62. Epub 2007 Jan 25. PubMed PMID: 17255364. 

Pollins AC, Friedman DB, Nanney LB. Proteomic investigation of human burn wounds by 2D-difference gel electrophoresis and mass spectrometry. J Surg Res. 2007 Sep;142(1):143-52. Epub 2007 Jun 29. PubMed PMID: 17604053; PubMed Central PMCID: PMC2696121.  <

Haas KF, Miller SL, Friedman DB, Broadie K. The ubiquitin-proteasome system postsynaptically regulates glutamatergic synaptic function. Mol Cell Neurosci. 2007 May;35(1):64-75. Epub 2007 Feb 8. PubMed PMID: 17363264; PubMed Central PMCID: PMC1936977. 

Wang SE, Narasanna A, Whitell CW, Wu FY, Friedman DB, Arteaga CL. Convergence of p53 and transforming growth factor beta (TGFbeta) signaling on activating expression of the tumor suppressor gene maspin in mammary epithelial cells. J Biol Chem. 2007 Feb 23;282(8):5661-9. Epub 2007 Jan 4. PubMed PMID: 17204482. 

Keller JW, Franklin JL, Graves-Deal R, Friedman DB, Whitwell CW, Coffey RJ. Oncogenic KRAS provides a uniquely powerful and variable oncogenic contribution among RAS family members in the colonic epithelium. J Cell Physiol. 2007 Mar;210(3):740-9. PubMed PMID: 17133351. 

2006

Friedman DB, Stauff DL, Pishchany G, Whitwell CW, Torres VJ, Skaar EP. Staphylococcus aureus redirects central metabolism to increase iron availability. PLoS Pathog. 2006 Aug;2(8):e87. PubMed PMID: 16933993; PubMed Central PMCID: PMC1557832. 

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. 2006 Sep 1;23(5):641-50. PubMed PMID: 16949361. 

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. 2006 Aug 16;26(33):8570-7. PubMed PMID: 16914683; PubMed Central PMCID: PMC1577681. 

Tabb DL, Friedman DB, Ham AJ. Verification of automated peptide identifications from proteomic tandem mass spectra. Nat Protoc. 2006;1(5):2213-22. PubMed PMID: 17406459. 

Anumanthan G, Halder SK, Friedman DB, Datta PK. Oncogenic serine-threonine kinase receptor-associated protein modulates the function of Ewing sarcoma protein through a novel mechanism. Cancer Res. 2006 Nov 15;66(22):10824-32. PubMed PMID: 17108118. 

Wang SE, Shin I, Wu FY, Friedman DB, Arteaga CL. HER2/Neu (ErbB2) signaling to Rac1-Pak1 is temporally and spatially modulated by transforming growth factor  beta. Cancer Res. 2006 Oct 1;66(19):9591-600. PubMed PMID: 17018616. 

Busler VJ, Torres VJ, McClain MS, Tirado O, Friedman DB, Cover TL. Protein-protein interactions among Helicobacter pylori cag proteins. J Bacteriol. 2006 Jul;188(13):4787-800. PubMed PMID: 16788188; PubMed Central PMCID: PMC1482994. 

Tian C, Breyer RM, Kim HJ, Karra MD, Friedman DB, Karpay A, Sanders CR. Solution NMR spectroscopy of the human vasopressin V2 receptor, a G protein-coupled receptor. J Am Chem Soc. 2005 Jun 8;127(22):8010-1. Erratum in: J Am Chem Soc. 2006 Apr 19;128(15):5300. PubMed PMID: 15926814.

Selected papers pre-2006

Lilley KS, Friedman DB. All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev Proteomics. 2004 Dec;1(4):401-9. PubMed PMID: 15966837.

Friedman DB, Hill S, Keller JW, Merchant NB, Levy SE, Coffey RJ, Caprioli RM.  Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics. 2004 Mar;4(3):793-811. PubMed  PMID: 14997500. 

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. 2005 Aug 12;280(32):29300-10. Epub 2005 Jun 10. PubMed PMID: 15951440.

Gerbasi VR, Weaver CM, Hill S, Friedman DB, Link AJ. Yeast Asc1p and mammalian RACK1 are functionally orthologous core 40S ribosomal proteins that repress gene  expression. Mol Cell Biol. 2004 Sep;24(18):8276-87. PubMed PMID: 15340087; PubMed Central PMCID: PMC515043. 

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