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So many roads traveled: A career in science and administration.

Halpert JR.

J Biol Chem. 2020 Jan 17;295(3):822-832. doi: 10.1074/jbc.X119.012206.


Crystal Structure of CYP2B6 in Complex with an Efavirenz Analog.

Shah MB, Zhang Q, Halpert JR.

Int J Mol Sci. 2018 Mar 29;19(4). pii: E1025. doi: 10.3390/ijms19041025.


Role of cytochrome P450 2B sequence variation and gene copy number in facilitating dietary specialization in mammalian herbivores.

Kitanovic S, Orr TJ, Spalink D, Cocke GB, Schramm K, Wilderman PR, Halpert JR, Dearing MD.

Mol Ecol. 2018 Feb;27(3):723-736. doi: 10.1111/mec.14480. Epub 2018 Jan 29.


Use of Phenoxyaniline Analogues To Generate Biochemical Insights into the Interactio n of Polybrominated Diphenyl Ether with CYP2B Enzymes.

Chen C, Liu J, Halpert JR, Wilderman PR.

Biochemistry. 2018 Feb 6;57(5):817-826. doi: 10.1021/acs.biochem.7b01024. Epub 2017 Dec 19.


Rational Re-Engineering of the O-Dealkylation of 7-Alkoxycoumarin Derivatives by Cytochromes P450 2B from the Desert Woodrat Neotoma lepida.

Huo L, Liu J, Dearing MD, Szklarz GD, Halpert JR, Wilderman PR.

Biochemistry. 2017 Apr 25;56(16):2238-2246. doi: 10.1021/acs.biochem.7b00097. Epub 2017 Apr 12.


Halogen-π Interactions in the Cytochrome P450 Active Site: Structural Insights into Human CYP2B6 Substrate Selectivity.

Shah MB, Liu J, Zhang Q, Stout CD, Halpert JR.

ACS Chem Biol. 2017 May 19;12(5):1204-1210. doi: 10.1021/acschembio.7b00056. Epub 2017 Apr 6.


Correction to Concurrent Cooperativity and Substrate Inhibition in the Epoxidation of Carbamazepine by Cytochrome P450 3A4 Active Site Mutants Inspired by Molecular Dynamics Simulations.

Müller CS, Knehans T, Davydov DR, Bounds PL, von Mandach U, Halpert JR, Caflisch A, Koppenol WH.

Biochemistry. 2016 Oct 4;55(39):5647. Epub 2016 Sep 21. No abstract available.


The draft genome sequence and annotation of the desert woodrat Neotoma lepida.

Campbell M, Oakeson KF, Yandell M, Halpert JR, Dearing D.

Genom Data. 2016 Jun 23;9:58-9. doi: 10.1016/j.gdata.2016.06.008. eCollection 2016 Sep.


Effect of detergent binding on cytochrome P450 2B4 structure as analyzed by X-ray crystallography and deuterium-exchange mass spectrometry.

Shah MB, Jang HH, Wilderman PR, Lee D, Li S, Zhang Q, Stout CD, Halpert JR.

Biophys Chem. 2016 Sep;216:1-8. doi: 10.1016/j.bpc.2016.05.007. Epub 2016 Jun 1.


Conformational Mobility in Cytochrome P450 3A4 Explored by Pressure-Perturbation EPR Spectroscopy.

Davydov DR, Yang Z, Davydova N, Halpert JR, Hubbell WL.

Biophys J. 2016 Apr 12;110(7):1485-1498. doi: 10.1016/j.bpj.2016.02.026.


Coumarin Derivatives as Substrate Probes of Mammalian Cytochromes P450 2B4 and 2B6: Assessing the Importance of 7-Alkoxy Chain Length, Halogen Substitution, and Non-Active Site Mutations.

Liu J, Shah MB, Zhang Q, Stout CD, Halpert JR, Wilderman PR.

Biochemistry. 2016 Apr 5;55(13):1997-2007. doi: 10.1021/acs.biochem.5b01330. Epub 2016 Mar 24.


Structure-Function Analysis of Mammalian CYP2B Enzymes Using 7-Substituted Coumarin Derivatives as Probes: Utility of Crystal Structures and Molecular Modeling in Understanding Xenobiotic Metabolism.

Shah MB, Liu J, Huo L, Zhang Q, Dearing MD, Wilderman PR, Szklarz GD, Stout CD, Halpert JR.

Mol Pharmacol. 2016 Apr;89(4):435-45. doi: 10.1124/mol.115.102111. Epub 2016 Jan 29.


Using the Specialization Framework to Determine Degree of Dietary Specialization in a Herbivorous Woodrat.

Skopec MM, Kohl KD, Schramm K, Halpert JR, Dearing MD.

J Chem Ecol. 2015 Dec;41(12):1059-68. doi: 10.1007/s10886-015-0654-y. Epub 2015 Dec 2.


Functional importance of a peripheral pocket in mammalian cytochrome P450 2B enzymes.

Jang HH, Liu J, Lee GY, Halpert JR, Wilderman PR.

Arch Biochem Biophys. 2015 Oct 15;584:61-9. doi: 10.1016/ Epub 2015 Aug 28.


Structural and biophysical characterization of human cytochromes P450 2B6 and 2A6 bound to volatile hydrocarbons: analysis and comparison.

Shah MB, Wilderman PR, Liu J, Jang HH, Zhang Q, Stout CD, Halpert JR.

Mol Pharmacol. 2015 Apr;87(4):649-59. doi: 10.1124/mol.114.097014. Epub 2015 Jan 13.


Concurrent cooperativity and substrate inhibition in the epoxidation of carbamazepine by cytochrome P450 3A4 active site mutants inspired by molecular dynamics simulations.

Müller CS, Knehans T, Davydov DR, Bounds PL, von Mandach U, Halpert JR, Caflisch A, Koppenol WH.

Biochemistry. 2015 Jan 27;54(3):711-21. doi: 10.1021/bi5011656. Epub 2015 Jan 15. Erratum in: Biochemistry. 2016 Oct 4;55(39):5647.


Interactions among cytochromes P450 in microsomal membranes: oligomerization of cytochromes P450 3A4, 3A5, and 2E1 and its functional consequences.

Davydov DR, Davydova NY, Sineva EV, Halpert JR.

J Biol Chem. 2015 Feb 6;290(6):3850-64. doi: 10.1074/jbc.M114.615443. Epub 2014 Dec 22.


The role of cytochrome P450 2B6 and 2B4 substrate access channel residues predicted based on crystal structures of the amlodipine complexes.

Jang HH, Davydov DR, Lee GY, Yun CH, Halpert JR.

Arch Biochem Biophys. 2014 Mar 1;545:100-7. doi: 10.1016/ Epub 2014 Jan 18.


A large-scale allosteric transition in cytochrome P450 3A4 revealed by luminescence resonance energy transfer (LRET).

Sineva EV, Rumfeldt JA, Halpert JR, Davydov DR.

PLoS One. 2013 Dec 23;8(12):e83898. doi: 10.1371/journal.pone.0083898. eCollection 2013.


Functional characterization of cytochromes P450 2B from the desert woodrat Neotoma lepida.

Wilderman PR, Jang HH, Malenke JR, Salib M, Angermeier E, Lamime S, Dearing MD, Halpert JR.

Toxicol Appl Pharmacol. 2014 Feb 1;274(3):393-401. doi: 10.1016/j.taap.2013.12.005. Epub 2013 Dec 19.


An in vivo assay for elucidating the importance of cytochromes P450 for the ability of a wild mammalian herbivore (Neotoma lepida) to consume toxic plants.

Skopec MM, Malenke JR, Halpert JR, Denise Dearing M.

Physiol Biochem Zool. 2013 Sep-Oct;86(5):593-601. doi: 10.1086/672212. Epub 2013 Aug 14.


Structural and thermodynamic basis of (+)-α-pinene binding to human cytochrome P450 2B6.

Wilderman PR, Shah MB, Jang HH, Stout CD, Halpert JR.

J Am Chem Soc. 2013 Jul 17;135(28):10433-40. doi: 10.1021/ja403042k. Epub 2013 Jul 3.


Pivotal role of P450-P450 interactions in CYP3A4 allostery: the case of α-naphthoflavone.

Davydov DR, Davydova NY, Sineva EV, Kufareva I, Halpert JR.

Biochem J. 2013 Jul 15;453(2):219-30. doi: 10.1042/BJ20130398.


A structural snapshot of CYP2B4 in complex with paroxetine provides insights into ligand binding and clusters of conformational states.

Shah MB, Kufareva I, Pascual J, Zhang Q, Stout CD, Halpert JR.

J Pharmacol Exp Ther. 2013 Jul;346(1):113-20. doi: 10.1124/jpet.113.204776. Epub 2013 Apr 30.


CYP261 enzymes from deep sea bacteria: a clue to conformational heterogeneity in cytochromes P450.

Davydov DR, Sineva EV, Davydova NY, Bartlett DH, Halpert JR.

Biotechnol Appl Biochem. 2013 Jan-Feb;60(1):30-40. doi: 10.1002/bab.1083. Epub 2013 Jan 25.


Steroid-based facial amphiphiles for stabilization and crystallization of membrane proteins.

Lee SC, Bennett BC, Hong WX, Fu Y, Baker KA, Marcoux J, Robinson CV, Ward AB, Halpert JR, Stevens RC, Stout CD, Yeager MJ, Zhang Q.

Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):E1203-11. doi: 10.1073/pnas.1221442110. Epub 2013 Mar 11.


X-ray crystal structure of the cytochrome P450 2B4 active site mutant F297A in complex with clopidogrel: insights into compensatory rearrangements of the binding pocket.

Shah MB, Jang HH, Zhang Q, David Stout C, Halpert JR.

Arch Biochem Biophys. 2013 Feb 15;530(2):64-72. doi: 10.1016/ Epub 2013 Jan 4.


Potent mechanism-based inactivation of cytochrome P450 2B4 by 9-ethynylphenanthrene: implications for allosteric modulation of cytochrome P450 catalysis.

Zhang H, Gay SC, Shah M, Foroozesh M, Liu J, Osawa Y, Zhang Q, Stout CD, Halpert JR, Hollenberg PF.

Biochemistry. 2013 Jan 15;52(2):355-64. doi: 10.1021/bi301567z. Epub 2013 Jan 4.


Stereoselective formation and metabolism of 4-hydroxy-retinoic Acid enantiomers by cytochrome p450 enzymes.

Shimshoni JA, Roberts AG, Scian M, Topletz AR, Blankert SA, Halpert JR, Nelson WL, Isoherranen N.

J Biol Chem. 2012 Dec 7;287(50):42223-32. doi: 10.1074/jbc.M112.404475. Epub 2012 Oct 15.


Conformational adaptation of human cytochrome P450 2B6 and rabbit cytochrome P450 2B4 revealed upon binding multiple amlodipine molecules.

Shah MB, Wilderman PR, Pascual J, Zhang Q, Stout CD, Halpert JR.

Biochemistry. 2012 Sep 18;51(37):7225-38. doi: 10.1021/bi300894z. Epub 2012 Sep 4.


Plasticity of CYP2B enzymes: structural and solution biophysical methods.

Wilderman PR, Halpert JR.

Curr Drug Metab. 2012 Feb;13(2):167-76. Review.


Peripheral ligand-binding site in cytochrome P450 3A4 located with fluorescence resonance energy transfer (FRET).

Davydov DR, Rumfeldt JA, Sineva EV, Fernando H, Davydova NY, Halpert JR.

J Biol Chem. 2012 Feb 24;287(9):6797-809. doi: 10.1074/jbc.M111.325654. Epub 2011 Dec 22.


Investigation by site-directed mutagenesis of the role of cytochrome P450 2B4 non-active-site residues in protein-ligand interactions based on crystal structures of the ligand-bound enzyme.

Wilderman PR, Gay SC, Jang HH, Zhang Q, Stout CD, Halpert JR.

FEBS J. 2012 May;279(9):1607-20. doi: 10.1111/j.1742-4658.2011.08411.x. Epub 2011 Nov 25.


The structural basis for homotropic and heterotropic cooperativity of midazolam metabolism by human cytochrome P450 3A4.

Roberts AG, Yang J, Halpert JR, Nelson SD, Thummel KT, Atkins WM.

Biochemistry. 2011 Dec 20;50(50):10804-18. doi: 10.1021/bi200924t. Epub 2011 Nov 22. Erratum in: Biochemistry. 2012 Feb 14;51(6):1332.


Structures of cytochrome P450 2B6 bound to 4-benzylpyridine and 4-(4-nitrobenzyl)pyridine: insight into inhibitor binding and rearrangement of active site side chains.

Shah MB, Pascual J, Zhang Q, Stout CD, Halpert JR.

Mol Pharmacol. 2011 Dec;80(6):1047-55. doi: 10.1124/mol.111.074427. Epub 2011 Aug 29.


Structural analysis of mammalian cytochrome P450 2B4 covalently bound to the mechanism-based inactivator tert-butylphenylacetylene: insight into partial enzymatic activity.

Gay SC, Zhang H, Wilderman PR, Roberts AG, Liu T, Li S, Lin HL, Zhang Q, Woods VL Jr, Stout CD, Hollenberg PF, Halpert JR.

Biochemistry. 2011 Jun 7;50(22):4903-11. doi: 10.1021/bi200482g. Epub 2011 May 13.


Structure and function of cytochromes P450 2B: from mechanism-based inactivators to X-ray crystal structures and back.

Halpert JR.

Drug Metab Dispos. 2011 Jul;39(7):1113-21. doi: 10.1124/dmd.111.039719. Epub 2011 Apr 18.


NMR-derived models of amidopyrine and its metabolites in complexes with rabbit cytochrome P450 2B4 reveal a structural mechanism of sequential N-dealkylation.

Roberts AG, Sjögren SE, Fomina N, Vu KT, Almutairi A, Halpert JR.

Biochemistry. 2011 Mar 29;50(12):2123-34. doi: 10.1021/bi101797v. Epub 2011 Mar 4.


Institutional Profile: University of California San Diego Pharmacogenomics Education Program (PharmGenEd™): bridging the gap between science and practice.

Kuo GM, Ma JD, Lee KC, Halpert JR, Bourne PE, Ganiats TG, Taylor P.

Pharmacogenomics. 2011 Feb;12(2):149-53. doi: 10.2217/pgs.10.213.


Comparison of in vitro metabolism of ticlopidine by human cytochrome P450 2B6 and rabbit cytochrome P450 2B4.

Talakad JC, Shah MB, Walker GS, Xiang C, Halpert JR, Dalvie D.

Drug Metab Dispos. 2011 Mar;39(3):539-50. doi: 10.1124/dmd.110.037101. Epub 2010 Dec 14.


Multiple substrate-binding sites are retained in cytochrome P450 3A4 mutants with decreased cooperativity.

Fernando H, Rumfeldt JA, Davydova NY, Halpert JR, Davydov DR.

Xenobiotica. 2011 Apr;41(4):281-9. doi: 10.3109/00498254.2010.538748. Epub 2010 Dec 14.


Structural features of cytochromes P450 and ligands that affect drug metabolism as revealed by X-ray crystallography and NMR.

Gay SC, Roberts AG, Halpert JR.

Future Med Chem. 2010 Sep;2(9):1451-68. Review. Erratum in: Future Med Chem. 2010 Oct;2(10):1612.


Plasticity of cytochrome P450 2B4 as investigated by hydrogen-deuterium exchange mass spectrometry and X-ray crystallography.

Wilderman PR, Shah MB, Liu T, Li S, Hsu S, Roberts AG, Goodlett DR, Zhang Q, Woods VL Jr, Stout CD, Halpert JR.

J Biol Chem. 2010 Dec 3;285(49):38602-11. doi: 10.1074/jbc.M110.180646. Epub 2010 Sep 28.


Structures of cytochrome P450 2B4 complexed with the antiplatelet drugs ticlopidine and clopidogrel .

Gay SC, Roberts AG, Maekawa K, Talakad JC, Hong WX, Zhang Q, Stout CD, Halpert JR.

Biochemistry. 2010 Oct 12;49(40):8709-20. doi: 10.1021/bi100914z. Epub 2010 Sep 15.


Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole at 2.0-A resolution.

Gay SC, Shah MB, Talakad JC, Maekawa K, Roberts AG, Wilderman PR, Sun L, Yang JY, Huelga SC, Hong WX, Zhang Q, Stout CD, Halpert JR.

Mol Pharmacol. 2010 Apr;77(4):529-38. doi: 10.1124/mol.109.062570. Epub 2010 Jan 8.


Electron transfer in the complex of membrane-bound human cytochrome P450 3A4 with the flavin domain of P450BM-3: the effect of oligomerization of the heme protein and intermittent modulation of the spin equilibrium.

Davydov DR, Sineva EV, Sistla S, Davydova NY, Frank DJ, Sligar SG, Halpert JR.

Biochim Biophys Acta. 2010 Mar;1797(3):378-90. doi: 10.1016/j.bbabio.2009.12.008. Epub 2009 Dec 21.


Rational engineering of cytochromes P450 2B6 and 2B11 for enhanced stability: Insights into structural importance of residue 334.

Talakad JC, Wilderman PR, Davydov DR, Kumar S, Halpert JR.

Arch Biochem Biophys. 2010 Feb 15;494(2):151-8. doi: 10.1016/ Epub 2009 Nov 26.


Ligand diversity of human and chimpanzee CYP3A4: activation of human CYP3A4 by lithocholic acid results from positive selection.

Kumar S, Qiu H, Oezguen N, Herlyn H, Halpert JR, Wojnowski L.

Drug Metab Dispos. 2009 Jun;37(6):1328-33. doi: 10.1124/dmd.108.024372. Epub 2009 Mar 19.


Dehydrogenation of the indoline-containing drug 4-chloro-N-(2-methyl-1-indolinyl)-3-sulfamoylbenzamide (indapamide) by CYP3A4: correlation with in silico predictions.

Sun H, Moore C, Dansette PM, Kumar S, Halpert JR, Yost GS.

Drug Metab Dispos. 2009 Mar;37(3):672-84. doi: 10.1124/dmd.108.022707. Epub 2008 Dec 12.

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