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Critical Role of Water Molecules in Proton Translocation by the Membrane-Bound Transhydrogenase.

Padayatti PS, Leung JH, Mahinthichaichan P, Tajkhorshid E, Ishchenko A, Cherezov V, Soltis SM, Jackson JB, Stout CD, Gennis RB, Zhang Q.

Structure. 2017 Jul 5;25(7):1111-1119.e3. doi: 10.1016/j.str.2017.05.022. Epub 2017 Jun 22.


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.


Role of the Conserved Valine 236 in Access of Ligands to the Active Site of Thermus thermophilus ba3 Cytochrome Oxidase.

Funatogawa C, Li Y, Chen Y, McDonald W, Szundi I, Fee JA, Stout CD, Einarsdóttir Ó.

Biochemistry. 2017 Jan 10;56(1):107-119. doi: 10.1021/acs.biochem.6b00590. Epub 2016 Dec 27.


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.


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.


Review and Hypothesis. New insights into the reaction mechanism of transhydrogenase: Swivelling the dIII component may gate the proton channel.

Jackson JB, Leung JH, Stout CD, Schurig-Briccio LA, Gennis RB.

FEBS Lett. 2015 Jul 22;589(16):2027-33. doi: 10.1016/j.febslet.2015.06.027. Epub 2015 Jul 2. Review.


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.


Structural biology. Division of labor in transhydrogenase by alternating proton translocation and hydride transfer.

Leung JH, Schurig-Briccio LA, Yamaguchi M, Moeller A, Speir JA, Gennis RB, Stout CD.

Science. 2015 Jan 9;347(6218):178-81. doi: 10.1126/science.1260451.


Contributions of ionic interactions and protein dynamics to cytochrome P450 2D6 (CYP2D6) substrate and inhibitor binding.

Wang A, Stout CD, Zhang Q, Johnson EF.

J Biol Chem. 2015 Feb 20;290(8):5092-104. doi: 10.1074/jbc.M114.627661. Epub 2015 Jan 1.


Towards novel therapeutics for HIV through fragment-based screening and drug design.

Tiefendbrunn T, Stout CD.

Prog Biophys Mol Biol. 2014 Nov-Dec;116(2-3):124-40. Review.


Conserved glycine 232 in the ligand channel of ba3 cytochrome oxidase from Thermus thermophilus.

McDonald W, Funatogawa C, Li Y, Chen Y, Szundi I, Fee JA, Stout CD, Einarsdóttir O.

Biochemistry. 2014 Jul 15;53(27):4467-75. doi: 10.1021/bi500289h. Epub 2014 Jul 7.


Crystallographic fragment-based drug discovery: use of a brominated fragment library targeting HIV protease.

Tiefenbrunn T, Forli S, Happer M, Gonzalez A, Tsai Y, Soltis M, Elder JH, Olson AJ, Stout CD.

Chem Biol Drug Des. 2014 Feb;83(2):141-8. doi: 10.1111/cbdd.12227. Epub 2013 Oct 30.


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.


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.


AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery.

Tsai Y, McPhillips SE, González A, McPhillips TM, Zinn D, Cohen AE, Feese MD, Bushnell D, Tiefenbrunn T, Stout CD, Ludaescher B, Hedman B, Hodgson KO, Soltis SM.

Acta Crystallogr D Biol Crystallogr. 2013 May;69(Pt 5):796-803. doi: 10.1107/S0907444913001984. Epub 2013 Apr 11.


Structural diversity of eukaryotic membrane cytochrome p450s.

Johnson EF, Stout CD.

J Biol Chem. 2013 Jun 14;288(24):17082-90. doi: 10.1074/jbc.R113.452805. Epub 2013 Apr 30. Review.


Antifungal Azoles: Structural Insights into Undesired Tight Binding to Cholesterol-Metabolizing CYP46A1.

Mast N, Zheng W, Stout CD, Pikuleva IA.

Mol Pharmacol. 2013 Jul;84(1):86-94. doi: 10.1124/mol.113.085902. Epub 2013 Apr 19.


Small molecule regulation of protein conformation by binding in the Flap of HIV protease.

Tiefenbrunn T, Forli S, Baksh MM, Chang MW, Happer M, Lin YC, Perryman AL, Rhee JK, Torbett BE, Olson AJ, Elder JH, Finn MG, Stout CD.

ACS Chem Biol. 2013;8(6):1223-31. doi: 10.1021/cb300611p. Epub 2013 Mar 29.


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.


Binding of a cyano- and fluoro-containing drug bicalutamide to cytochrome P450 46A1: unusual features and spectral response.

Mast N, Zheng W, Stout CD, Pikuleva IA.

J Biol Chem. 2013 Feb 15;288(7):4613-24. doi: 10.1074/jbc.M112.438754. Epub 2013 Jan 3.


Ligand access to the active site in Thermus thermophilus ba(3) and bovine heart aa(3) cytochrome oxidases.

McDonald W, Funatogawa C, Li Y, Szundi I, Chen Y, Fee JA, Stout CD, Einarsdóttir Ó.

Biochemistry. 2013 Jan 29;52(4):640-52. doi: 10.1021/bi301358a. Epub 2013 Jan 18.


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.


The novel purification and biochemical characterization of a reversible CYP24A1:adrenodoxin complex.

Hartfield KA, Stout CD, Annalora AJ.

J Steroid Biochem Mol Biol. 2013 Jul;136:47-53. doi: 10.1016/j.jsbmb.2012.11.001. Epub 2012 Nov 16. Review.


Structural characterization of human cytochrome P450 2C19: active site differences between P450s 2C8, 2C9, and 2C19.

Reynald RL, Sansen S, Stout CD, Johnson EF.

J Biol Chem. 2012 Dec 28;287(53):44581-91. doi: 10.1074/jbc.M112.424895. Epub 2012 Nov 1.


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.


In silico and intuitive predictions of CYP46A1 inhibition by marketed drugs with subsequent enzyme crystallization in complex with fluvoxamine.

Mast N, Linger M, Clark M, Wiseman J, Stout CD, Pikuleva IA.

Mol Pharmacol. 2012 Nov;82(5):824-34. doi: 10.1124/mol.112.080424. Epub 2012 Aug 2.


Mobility of Xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase.

Luna VM, Fee JA, Deniz AA, Stout CD.

Biochemistry. 2012 Jun 12;51(23):4669-76. doi: 10.1021/bi3003988. Epub 2012 May 29.


Crystal structure of human cytochrome P450 2D6 with prinomastat bound.

Wang A, Savas U, Hsu MH, Stout CD, Johnson EF.

J Biol Chem. 2012 Mar 30;287(14):10834-43. doi: 10.1074/jbc.M111.307918. Epub 2012 Feb 3.


Structural changes that occur upon photolysis of the Fe(II)(a3)-CO complex in the cytochrome ba(3)-oxidase of Thermus thermophilus: a combined X-ray crystallographic and infrared spectral study demonstrates CO binding to Cu(B).

Liu B, Zhang Y, Sage JT, Soltis SM, Doukov T, Chen Y, Stout CD, Fee JA.

Biochim Biophys Acta. 2012 Apr;1817(4):658-65. doi: 10.1016/j.bbabio.2011.12.010. Epub 2011 Dec 27.


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.


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.


High resolution structure of the ba3 cytochrome c oxidase from Thermus thermophilus in a lipidic environment.

Tiefenbrunn T, Liu W, Chen Y, Katritch V, Stout CD, Fee JA, Cherezov V.

PLoS One. 2011;6(7):e22348. doi: 10.1371/journal.pone.0022348. Epub 2011 Jul 21.


Structural basis for drug and substrate specificity exhibited by FIV encoding a chimeric FIV/HIV protease.

Lin YC, Perryman AL, Olson AJ, Torbett BE, Elder JH, Stout CD.

Acta Crystallogr D Biol Crystallogr. 2011 Jun;67(Pt 6):540-8. doi: 10.1107/S0907444911011681. Epub 2011 May 12.


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.


Three clusters of conformational states in p450cam reveal a multistep pathway for closing of the substrate access channel.

Lee YT, Glazer EC, Wilson RF, Stout CD, Goodin DB.

Biochemistry. 2011 Feb 8;50(5):693-703. doi: 10.1021/bi101726d. Epub 2011 Jan 11.


Structural basis for three-step sequential catalysis by the cholesterol side chain cleavage enzyme CYP11A1.

Mast N, Annalora AJ, Lodowski DT, Palczewski K, Stout CD, Pikuleva IA.

J Biol Chem. 2011 Feb 18;286(7):5607-13. doi: 10.1074/jbc.M110.188433. Epub 2010 Dec 15.


Structural characterization of the complex between alpha-naphthoflavone and human cytochrome P450 1B1.

Wang A, Savas U, Stout CD, Johnson EF.

J Biol Chem. 2011 Feb 18;286(7):5736-43. doi: 10.1074/jbc.M110.204420. Epub 2010 Dec 8.


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.


Structural basis of drug binding to CYP46A1, an enzyme that controls cholesterol turnover in the brain.

Mast N, Charvet C, Pikuleva IA, Stout CD.

J Biol Chem. 2010 Oct 8;285(41):31783-95. doi: 10.1074/jbc.M110.143313. Epub 2010 Jul 28.


Fragment-based screen against HIV protease.

Perryman AL, Zhang Q, Soutter HH, Rosenfeld R, McRee DE, Olson AJ, Elder JE, Stout CD.

Chem Biol Drug Des. 2010 Mar;75(3):257-68. doi: 10.1111/j.1747-0285.2009.00943.x. Epub 2010 Jan 19.


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.


Crystal structure of CYP24A1, a mitochondrial cytochrome P450 involved in vitamin D metabolism.

Annalora AJ, Goodin DB, Hong WX, Zhang Q, Johnson EF, Stout CD.

J Mol Biol. 2010 Feb 19;396(2):441-51. doi: 10.1016/j.jmb.2009.11.057. Epub 2009 Dec 1.


X-ray structures of the hexameric building block of the HIV capsid.

Pornillos O, Ganser-Pornillos BK, Kelly BN, Hua Y, Whitby FG, Stout CD, Sundquist WI, Hill CP, Yeager M.

Cell. 2009 Jun 26;137(7):1282-92. doi: 10.1016/j.cell.2009.04.063. Epub 2009 Jun 11.


A copper(I)-catalyzed 1,2,3-triazole azide-alkyne click compound is a potent inhibitor of a multidrug-resistant HIV-1 protease variant.

Giffin MJ, Heaslet H, Brik A, Lin YC, Cauvi G, Wong CH, McRee DE, Elder JH, Stout CD, Torbett BE.

J Med Chem. 2008 Oct 23;51(20):6263-70. doi: 10.1021/jm800149m. Epub 2008 Sep 30.


Crystal structures of substrate-bound and substrate-free cytochrome P450 46A1, the principal cholesterol hydroxylase in the brain.

Mast N, White MA, Bjorkhem I, Johnson EF, Stout CD, Pikuleva IA.

Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9546-51. doi: 10.1073/pnas.0803717105. Epub 2008 Jul 9.


Use of complementary cation and anion heavy-atom salt derivatives to solve the structure of cytochrome P450 46A1.

White MA, Mast N, Bjorkhem I, Johnson EF, Stout CD, Pikuleva IA.

Acta Crystallogr D Biol Crystallogr. 2008 May;64(Pt 5):487-95. doi: 10.1107/S0907444908004046. Epub 2008 Apr 19.

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