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July 2015
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Pharmacology and Molecular Sciences Archives

1. Cox PM and Bumpus NN. Structure-activity studies reveal the oxazinone ring is a determinant of cytochrome P450 2B6 activity toward efavirenz. ACS Med Chem Lett. 2014 Sep 4;5(10):1156-1161.
Key words: cytochromes P450; drug metabolism; mass spectrometry; efavirenz; structure-activity
http://www.ncbi.nlm.nih.gov/pubmed/25309681

2. Lu Y, Fuchs EJ, Hendrix CW, Bumpus NN. CYP3A5 Genotype Impacts Maraviroc Concentrations in Healthy Volunteers. Drug Metab Dispos. 2014 Nov;42(11):1796-802.
Key words: Pharmacogenetics, maraviroc, HIV, drug metabolism and pharmacokinetics
http://www.ncbi.nlm.nih.gov/pubmed/25117426

3. Prendergast J, Umanah GK, Yoo SW, Lagerlöf O, Motari MG, Cole RN, Huganir RL, Dawson TM, Dawson VL, Schnaar RL. Ganglioside regulation of AMPA receptor trafficking. J Neurosci. 2014 Sep 24;34(39):13246-58.
Key words: AMPA receptor, ganglioside, GluR2, N-ethylmaleimide-sensitive factor, Nicalin; Thorase
http://www.ncbi.nlm.nih.gov/pubmed/25253868

1. Cieniewicz AM, Moreland L, Ringel AE, Mackintosh SG, Raman A, Gilbert TM, Wolberger C, Tackett AJ, Taverna SD. The bromodomain of Gcn5 regulates site-specificity of lysine acetylation on histone H3. Molecular and Cellular Proteomics. 2014 Aug 8. pii: mcp.M114.038174. [Epub ahead of print]
Key words: Gcn5, histone, acetylation, bromodomain, chromatin

http://www.ncbi.nlm.nih.gov/pubmed/25106422

2. Gilbert TM, McDaniel SL, Byrum SD, Cades JA, Dancy BCR, Wade H, Tackett AJ, Strahl BD, Taverna SD. An H3K36me3 binding PWWP protein targets the NuA3 acetyltransferase complex to coordinate transcriptional elongation at coding regions. Molecular and Cellular Proteomics. 2014 Aug 6. pii: mcp.M114.038224. [Epub ahead of print]
Key words: Histone, transcription, acetylation, methylation, chromatin
http://www.ncbi.nlm.nih.gov/pubmed/25104842

3. Papazyan R, Voronina E, Chapman JR, Luperchio TR, Gilbert TM, Meier E, Mackintosh SG, Shabanowitz J, Tackett AJ, Reddy KL, Coyne RS, Hunt DF, Liu Y, Taverna SD. Methylation of histone H3K23 blocks DNA damage in pericentric heterochromatin during meiosis.
eLife. 2014 Aug 26;3:e02996. doi: 10.7554/eLife.02996
Key words: Histone, DNA damage, methylation, meiosis, genome integrity
http://www.ncbi.nlm.nih.gov/pubmed/25161194

4. Waldrip ZJ, Byrum SD, Storey A, Gao J, Byrd AK, Mackintosh SG, Wahls WP, Taverna SD, Raney KD, Tackett AJ. A CRISPR-based approach for proteomic analysis of a single genomic locus. Epigenetics. 2014; 9(9). [Epub ahead of print]
Key words: Transcription, histone post-translational modifications, epigenetics, CRISPR, mass spectrometry
http://www.ncbi.nlm.nih.gov/pubmed/25147920

1. Mehta S, Aye-Han NN, Ganesan A, Oldach L, Gorshkov K, Zhang J. Calmodulin-controlled spatial decoding of oscillatory Ca2+ signals by calcineurin. Elife. 2014 Jul 23:e03765. doi: 10.7554/eLife.03765. [Epub ahead of print]
Key words: calcium; oscillation; FRET; biosensor; live-cell imaging
http://www.ncbi.nlm.nih.gov/pubmed/25056880

1. Brammer Basta LA, Patel H, Kakalis L, Jordan F, Freel Meyers CL. Defining critical residues for substrate binding to 1-deoxy-d-xylulose 5-phosphate synthase - active site substitutions stabilize the predecarboxylation intermediate C2?-lactylthiamin diphosphate. FEBS J. 2014 June;281(12):2820-37.
Key words: CD; DXP synthase; enzymology; protein fluorescence; thiamin

http://www.ncbi.nlm.nih.gov/pubmed/24767541

1. Tullman JA, Harmon M-E, Delannoy M, Gibson W. Recovery of an HMWP/hmwBP (pUL48/pUL47) complex from virions of human cytomegalovirus: subunit interactions, oligomers composition, deubiquitylase activity. J Virology. 2014 May 14. pii: JVI.00971-14. [Epub ahead of print.]
Key words: Cytomegalovirus, herpesvirus, protein-protein interactions, ubiquitin, deubiquitylase, virus structure
http://www.ncbi.nlm.nih.gov/pubmed/24829352

1. Calcaterra NE, Barrow JC. Classics in Chemical Neuroscience: Diazepam (Valium). ACS Chem. Neurosci. 2014 Apr 16;5(4):253-60.
Key words: Diazepam, Valium, benzodiazepine, GABA, anxiety, hypnotic, sedative
http://www.ncbi.nlm.nih.gov/pubmed/24552479

1. Hersman EM, Bumpus NN. A targeted proteomics approach for profiling murine cytochrome P450 expression. J Pharmacol Exp Ther. 2014 May;349(2):221-8.
Key words: cytochrome P450; mass spectrometry; drug metabolism
http://www.ncbi.nlm.nih.gov/pubmed/24594750

1. Webster MR, Kamat C, Connis N, Zhao M, Weeraratna AT, Rudek MA, Hann CL, Freel Meyers CL. Bisphosphonamidate clodronate prodrug exhibits selective cytototxic activity against melanoma cell lines. Mol Cancer Ther. 2014 Feb;13(2):297-306.
Key words: prodrug, bisphosphonate, melanoma, clodronate
http://www.ncbi.nlm.nih.gov/pubmed/24310621

1. Kiwamoto T, Brummet ME, Wu F, Motari MG, Smith DF, Schnaar RL, Zhu Z, Bochner BS. Mice deficient in the St3gal3 gene product ?2,3 sialyltransferase (ST3Gal-III) exhibit enhanced allergic eosinophilic airway inflammation. J Allergy Clin Immunol. 2014 Jan;133(1):240-247.
Key words: asthma, airway, inflammation, eosinophil, lung
http://www.ncbi.nlm.nih.gov/pubmed/23830412

1. Avery LB and Bumpus NN. Valproic acid is a novel activator of AMP-activated protein kinase and decreases liver mass, hepatic fat accumulation, and serum glucose in obese mice. Molecular Pharmacology. 2014 Jan;85(1):1-10.
Key words: Valproic Acid; AMP-activated Protein Kinase; Metabolomics; Mass Spectrometry; Cytochrome P450
http://www.ncbi.nlm.nih.gov/pubmed/24105977

2. Teng X, Dayhoff-Brannigan M, Cheng WC, Gilbert CE, Sing CN, Diny NL, Wheelan SJ, Dunham MJ, Boeke JD, Pineda FJ, Hardwick JM. Genome-wide consequences of deleting any single gene. Mol Cell. 2013 Nov 21;52(4):485-94.
Key words: genome evolution, yeast, cancer, amino acid-sensing, cell death
http://www.ncbi.nlm.nih.gov/pubmed/24211263

1. Byrum SD, Taverna SD, and Tackett AJ. (2013) Purification of a specific native genomic locus for proteomic analysis. Nucleic Acids Res. 2013 Nov 1;41(20), e195, doi:10.1093/nar/gkt822
Key words: Epigenetics, Transcription, Histone post-translational modifications, Acetylation, Mass spectromery
http://www.ncbi.nlm.nih.gov/pubmed/24030711

2. Hu S, Wan J, Su Y, Song Q, Zeng Y, Nguyen HN, Shin J, Cox E, Rho H-S, Woodard C, Xia S, Liu S, Lu H, Ming G, Wade H, Song H, Qian J, Zhu H. DNA methylation presents distinct binding sites for human transcription factors. eLife. 2013; 2:e00726.
Key words: DNA methylation, transcription, protein microarrays, KLF4, CpG
http://www.ncbi.nlm.nih.gov/pubmed/24015356

3. Lade JM, Avery LB, Bumpus NN. 2013. Human biotransformation of the non-nucleoside reverse transcriptase inhibitor rilpivirine and a cross species metabolism comparison. Antimicrobial Agents and Chemotherapy. 2013 Oct; 57(10):5067-5079.
Key words: cytochrome P450; HIV; antiretroviral; mass spectrometry; drug metabolism
http://www.ncbi.nlm.nih.gov/pubmed/23917319

4. To EE, Hendrix CW, Bumpus NN. 2013. Dissimilarities in the metabolism of antiretroviral drugs used in HIV pre-exposure prophylaxis in colon and vagina tissues. Biochemical Pharmacology. 2013 Oct 1; 86(7):979-990.
Key words: cytochrome P450; HIV; antiretroviral; mass spectrometry; drug metabolism
http://www.ncbi.nlm.nih.gov/pubmed/23965226

1. Hu S, Feng Y, Henson B, Wang B, Huang X, Li M, Desai P, Zhu H. VirD - A virion display array for profiling functional membrane proteins. Anal Chem. 2013 Sep 3;85(17):8046?8054.
Key words: VirD; multi-pass membrane proteins, virions, protein microarrays, GPCR
http://www.ncbi.nlm.nih.gov/pubmed/23941274

2. Woodard CL, Goodwin CR, Wan J, Xia S, Hu J, Newman RH, Zhang J, Hayward SD, Qian J, Laterra J, Zhu H. Profiling the dynamics of a human phosphorylome reveals new components in HGF/c-Met signaling. PLoS One 2013 Sept 2; 8(9):e72671.
Key words: Phosphorylation, lysate, protein microarrays, c-Met, signal transduction
http://www.ncbi.nlm.nih.gov/pubmed/24023761

1. Morris F, Vierling R, Boucher L, Bosch J, Freel Meyers C.L. DXP synthase-catalyzed C-N bond formation: nitroso substrate specificity studies guide selective inhibitor design. ChemBioChem. 2013 Jul 22;14(11):1309-1315.
Key words: isoprenoid biosynthesis, selective enzyme inhibitors, thiamin diphosphate

http://www.ncbi.nlm.nih.gov/pubmed/23824585

1. Smith J, Vierling RJ, Freel Meyers CL. Selective inhibition of E. coli 1-deoxy-D-xylulose-5-phosphate synthase by acetylphosphonates. MedChemComm. 2012; 3(1): 65-67.
Key words: isoprenoid biosynthesis, DXP synthase, anti-infectives, acetylphosphonate
http://www.ncbi.nlm.nih.gov/pubmed/23326631

1. Patel H, Nemeria N, Brammer L, Freel Meyers C, Jordan F. Observation of thiamin-bound intermediates and microscopic rate constants for their interconversion on 1-deoxy-D-xylulose 5-phosphate synthase: 600-fold rate acceleration of pyruvate decarboxylation by D-glyceraldehyde-3-phosphate. J Am Chem Soc 2012;134:18374-79.
Key words: thiamin diphosphate, isoprenoid biosynthesis, anti-infectives
http://www.ncbi.nlm.nih.gov/pubmed/23072514

1. Mountney A, Zahner MR, Sturgill ER, Riley CJ, Aston JW, Oudega M, Schramm LP, Hurtado A, Schnaar RL. Sialidase, chondroitinase ABC and combination therapy after spinal cord contusion injury. J Neurotrauma. 2012 Aug 31. [Epub ahead of print]
Key words: Spinal cord injury; axon regeneration; ganglioside; motor behavior; serotonergic axons
http://www.ncbi.nlm.nih.gov/pubmed/22934782

2. Shim JS, Rao R, Beebe K, Neckers L, Han I, Nahta R, Liu JO. Selective inhibition of HER2-positive breast cancer cells by the HIV protease inhibitor nelfinavir. J Natl Cancer Inst. 2012 Oct 5. [Epub ahead of print]
Key words include: Nelfinavir, Johns Hopkins Drug Library, Her2, breast cancer, and drug resistance
http://www.ncbi.nlm.nih.gov/pubmed/23042933

3. Sturgill ER, Aoki K, Lopez PH, Colacurcio D, Vajn K, Lorenzini I, Majic S, Yang WH, Heffer M, Tiemeyer M, Marth JD, Schnaar RL. Biosynthesis of the major brain gangliosides GD1a and GT1b. Glycobiology. 2012 Oct;22(10):1289-301. Epub 2012 Jun 26.
Key words: Brain, ganglioside, myelin, sialic acid, sialyltransferase
http://www.ncbi.nlm.nih.gov/pubmed/22735313

1. Byrum SD, Raman A, Taverna SD, Tackett AJ. ChAP-MS: A method for identification of proteins and histone posttranslational modifications at a single genomic locus. Cell Reports. 2012 July 26;2(1):198-205.
Key words: Histone, chromatin, affinity purification, transcription, mass spectrometry
http://www.ncbi.nlm.nih.gov/pubmed/22840409

2. Jung KO, Khan AM, Tan BY, Hu Y, Simon GG, Nascimento EJ, Lemonnier F, Brusic V, Miotto O, Tan TW, Marques ET, Dhalia R, Salmon J, August JT. West nile virus T-cell ligand sequences shared with other flaviviruses: a multitude of variant sequences as potential altered Peptide ligands. J Virol. 2012 July; 86(14):7616-7624.
Key words: West Nile virus, T-cell ligand, flaviviruses, altered peptide ligands, immune cross-reactivity
http://www.ncbi.nlm.nih.gov/pubmed/22573867

1. Barrow, JC. Inhibitors of catechol-o-methyltransferase. CNS Neurol Disord Drug Targets, 2012 May;11(3):324-332.
Key words: Catechol-O-methyltransferase; COMT; dopamine; L-DOPA; Parkinson's disease
http://www.ncbi.nlm.nih.gov/pubmed/22483290

2. Calabrese V, Cornelius C, Dinkova-Kostova AT, Iavicoli I, Di Paola R, Koverech A, Cuzzocrea S, Rizzarelli E, Calabrese EJ. Cellular stress responses, hormetic phytochemicals and vitagenes in aging and longevity. Biochim Biophys Acta. 2012 May;1822(5):753-83.
Key words: Nrf2, Keap1, stress, sulforaphane, hormesis
http://www.ncbi.nlm.nih.gov/pubmed/22108204

3. Dedecker P, Mo GCH, Dertinger T, Zhang J. A widely accessible method for superresolution fluorescence imaging of living systems. Proc. Natl. Acad. Sci. USA. 2012 Jul 3;109(27):10909-10914. [Epub ahead of print]
Key words: subdiffraction-limit, two-color imaging, membrane rafts
http://www.ncbi.nlm.nih.gov/pubmed/22711840

4. Dinkova-Kostova AT, Kostov R. Glucosinolates and isothiocyanates in health and disease. Trends Mol Med. 2012 Jun;18(6):337-47.
Key words: NQO1, sulforaphane, phenethylisothiocyanate, cancer, neurodegenerative disease
http://www.ncbi.nlm.nih.gov/pubmed/22578879

5. Ibbotson SH, Dawe RS, Dinkova-Kostova AT, Weidlich S, Farr PM, Ferguson J, Wolf CR, Smith G. Glutathione S-transferase genotype is associated with sensitivity to psoralen-UVA (PUVA) photochemotherapy. Br J Dermatol. 2012; 166: 380-388.
Key words: GST, psoralen, UVA, 8-MOP, photochemotherapy
http://www.ncbi.nlm.nih.gov/pubmed/21967523

6. Kalra S, Knatko EV, Zhang Y, Honda T, Yamamoto M, Dinkova-Kostova AT. Highly potent activation of Nrf2 by topical tricyclic bis(cyano enone): Implications for protection against UV radiation during thiopurine therapy. Cancer Prev Res (Phila). 2012 Jul;5(7):973-81.
Key words: cyanoenone, Nrf2, NQO1, skin cancer, ultraviolet radiation
http://www.ncbi.nlm.nih.gov/pubmed/22659146

7. Zheng S, Laxmi Y R S, David E, Dinkova-Kostova AT, Shiavoni KH, Ren Y, Zheng Y, Trevino I, Bumeister R, Ojima I, Wigley WC, Bliska J, Mierke DF, Honda T. Synthesis, chemical reactivity as Michael acceptors, and biological potency of monocyclic cyanoenones, novel and highly potent anti-inflammatory and cytoprotective agents. J Med Chem. 2012 May 24; 55(10): 4837-4846.
Key words: Keap1, Michael acceptor, NQO1, iNOS, cyanoenone
http://www.ncbi.nlm.nih.gov/pubmed/22533790

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