Stout Lab Publications

Publications

Click the PubMed button for abstracts by C.D. Stout, Ph.D on NCBI PubMed.

For Quick Search:

Copy the PMID or PMCID number from the listings below
Click on PubMed button
Paste the ID number in the search box

Transhydrogenase

Sundaresan, V., Chartron, J., Yamaguchi, M. and Stout, C.D. (2005) Conformational Diversity in
NAD(H) and Interacting Transhydrogenase Nicotinamide Nucleotide Binding Domains. J. Mol. Biol.
346; 617-629. PMID: 15670609

Sundaresan, V., Yamaguchi, M., Chartron, J. and Stout, C.D. (2003) Conformational change in the
NADP(H) binding domain of transhydrogenase defines four states. Biochem. 42; 12143-12153. PMID: 14567675

Yamaguchi, M. and Stout, C.D. (2003) Essential Glycine in the Proton Channel of Escherichia coli
Transhydrogenase. J. Biol. Chem. 278; 45333-45339. PMID: 12952962

CYP24A1

Mast, N., Zheng, W., Stout, C.D., Pikuleva, I.A. (2013) Antifungal Azoles: Structural Insights into Undesired Tight Binding to Cholesterol-Metabolizing CYP46A1. Mol Pharmacol 84(1); 86-94. PMCID: PMC3684827

Hartfield, K.A., Stout, C.D., Annalora, A.J. (2012) The novel purification and biochemical characterization of a reversible CYP24A1: adrenodoxin complex. J Steroid Biochem Mol Biol, S0960-0760, 00234-00238. PMID: 23165146. "Not NIH Funded"

Mast, N., Linger, M., Clark, M., Wiseman, J., Stout, C.D., Pikuleva, I.A. (2012) In silico and intuitive predictions of CYP46A1 inhibition by marketed drugs with subsequent enzyme crystallization in complex with fluvoxamine. Mol Pharmacol. 82; 824-834, PMCID: PMC3477228

Annalora, A., Goodin, D.B., Hong, W.-X., Zhang, Q., Johnson, E.F. and Stout, C.D. (2009) The crystal structure of CYP24A1, a mitochondrial cytochrome P450 involved in vitamin D metabolism. J. Mol. Biol. 19, 396(2); 441-451. PMCID: PMC2830900

HIV Protease

Tsai, Y., McPhillips, S.E., Gonzalez, A., McPhillips, T.M., Zinn, D., Cohen, A.E., Feese, M.D., Bushnell, D., Tiefenbrunn, T., Stout, C.D., Ludaescher, B., Hedman, B., Hodgson, K.O., Soltis, S.M. (2013) AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery. Acta Crystallogr D Biol Crystallogr, 69; 796-803. PMCID: PMC3640469

Tiefenbrunn, T., Forli, S., Baksh, M.M., Chang, M.W., Happer, M., Lin, Y.C., Perryman, AlL., Rhee, J.K., Torbett, B.E., Olson, A.J., Elder, J.H., Finn, M.G., Stout, C.D. (2013) Small Molecule Regulation of Protein Conformation by Binding in the Flap of HIV Protease. ACS Chem Biol PMID: 23540839 "PMC Journal In-Process"

Lin, Y-C., Perryman, A.L., Olson, A.J., Torbett, B.E., Elder, J.H. and Stout, C.D. (2011) Structural basis for drug and substrate specificity exhibited by FIV encoding a chimeric FIV/HIV protease. Acta Cryst D. 67(pt.6); 540-548. PMCID: PMC3107052

Perryman, A.L., Zhang, Q., Soutter, H.H., Rosenfeld, R., McRee, D.E., Olson, A.J., Elder, J.E. and
Stout, C.D. (2010) Fragment-Based Screen against HIV Protease. Chem. Biol. & Drug Design, 75;
275-268. PMCID: PMC2911974

Pornillos, O., Ganser-Pornillos, B.K. Kelly, B.N., Hua, Y., Whitby, F.G., Stout, C.D., Sundquist, W.I.,
Hill, C.P. and Yeager, M. (2009) X-ray structures of the hexameric building block of the HIV capsid, Cell 137; 1282-1292. PMCID: PMC2840706

Giffin, M.J., Heaslet, H.A., Brik, A., Lin, Y.-C., Cauvi, G., Wong, C.-H., McRee, D.E., Elder, J.H., Stout, C.D. and Torbett, B.E. (2008) AB2, an azide-alkyne click compound, is a potent protease inhibitor of multidrug-resistant HIV-1. J. Med. Chem. 51; 6263-6270, PMCID: PMC2744648.

Heaslet, H., Lin, Y-C., Tam, K., Torbett, B.E., Elder, J.E. and Stout, C.D. (2007) Crystal Structure of an FIV/HIV Chimeric Protease Complexed with the Broad-based Inhibitor, TL-3. Retrovirology 4:1. PMID: 17212810

Heaslet, H., Rosenfeld, R., Giffin, M., Lin, Y.-C., Tam, K., Torbett, B.E., Elder, J.H., McRee, D.E. and Stout, C.D. (2007) Conformational flexibility in the flap domains of ligand free HIV protease. Acta Cryst. D63; 866-875. PMID: 17642513

Heaslet, H., Kutilek, V., Morris, G.M., Lin, Y-C., Elder, J.H., Torbett, B.E. and Stout C.D. (2006)
Structural Insights into the Mechanisms of Drug Resistance in HIV-1 Protease NL4-3. J. Mol. Biol. 356; 967-981. PMID: 16403521

Cytochrome ba3 oxidase

Lee, S.C., Bennett, B.C., Hong, W.X., Fu, Y., Baker, K.A., Maracoux, J., Robinson, C.V., Ward, A.B., Halpert, J.R., Stevens, R.C., Stout, C.D., Yeager, M.J., Zhange, Q. (2013) Steroid-based facial amphiphiles for stabilization and crystallization of membrane proteins. Proc Natl Acad Sci., 110 E1203-E1211. PMCID: PMC3612649

McDonald W., Funatogawa, C., Li, Y., Szundi, I., Chen, Y., Fee, J.A., Stout, C.D., Einarsdottir, O. (2013) Ligand Access to the Active Site in Thermus thermophilusba(3) and Bovine Heart aa(3) Cytochrome Oxidases. Biochemistry, 52; 640-652. PMCID: PMC3569493

Luna, V.M., Fee, J.A., Deniz, A.A., Stout, C.D. (2012) Mobility of Xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase. Biochemistry 51; 4669-4676. PMCID: PMC3431459

Liu, B., Zhang, Y., Sage, J.T., Soltis, S.M., Doukov, T., Chen, Y., Stout, C.D. and Fee, J.A. (2011) Structural changes that occur upon photolysis of the Fe(II)a3 - CO complex in the cytochrome ba3-oxidase of Thermus thermophilus: A combined X-ray crystallographic and infrared spectral study demonstrates CO binding to CuB. Biochem. Biophys. Acta, 1817; 658-665. PMCID: PMC3294259

Tiefenbrunn, T., Liu, W., Chen, Y., Katritch, V., Stout, C.D., Fee, J.A. and Cherezov, V. (2011) High Resolution Structure of the ba3 Cytochrome c Oxidase from Thermus thermophilus in a Lipidic Environment, PLoS One 6(7): e22348. doi:10.1371/journal.pone.0022348. PMCID: PMC3141039

Liu, B., Chen, Y., Doukov, T., Soltis, S.M., Stout C.D., Fee, J.A. (2009) Combined
microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme. Biochemistry 48; 820-826. PMCID: PMC2638058

Luna, V.M., Chen, Y., Fee, J.A. and Stout, C.D. (2008) Crystallographic studies of Xe and Kr binding within the large internal cavity of cytochrome ba3 from Thermus thermophilus: Structural analysis and role of oxygen transport channels in the heme-Cu oxidases. Biochemistry 47; 4657-4665. PMID: 18376849.

Liu, B., Luna, V.M., Chen, Y., Stout, C.D. and Fee, J.A. (2007) An unexpected outcome of surface-
engineering an integral membrane protein: Improved crystallization of cytochrome ba3 from Thermus thermophilus. Acta Cryst. F63; 1029-1034. PMCID: PMC2344090

Hunsicker-Wang, L.M., Pacoma, R.L., Chen, Y., Fee, J.A. and Stout, C.D. (2005) A Novel
Cryoprotection Scheme for Enhancing Diffraction of Crystals from Recombinant Cytochrome ba3
Oxidase from Thermus thermophilus. Acta Cryst. D61; 340-343. PMID: 15735345

Cytochrome P450s

Wilderman, P.R., Shah, M.B., Jang, H.H., Stout, C.D., Halpert, J.R. (2013) Structural and Thermodynamic Basis of (+)-a-Pinene Binding to Human Cytochrome P450 2B6. J Am Chem Soc, 135; 10433-10440. PMID: 23786449 "PMC Journal In-Process"

Shah, M.B., Kufareva, I., Pascual, J., Zhang, Q., Stout, C.D., Halpert, J.R. (2013) A Structural Snapshot of Cytochrome P4502B4 in Complex with Paroxetine Provides insights into Ligand Binding and Clusters of Conformational States. J Pharmacol Exp Ther 346(1); 113-120. PMCID: PMC3684837

Johnson, E.F., Stout, C.D. (2013) Structural Diversity of Eukaryotic Membrane Cytochromes P450. J Biol Chem. 288; 17082-17090. PMCID: PMC3682514

Mast, N., Zheng, W., Stout, C.D., Pikuleva, I.A. (2013) Binding of a Cyano- and Fluoro-Containing Drug Bicalutamide to Cytochrome P450 46A1: Unusual Features and Spectral Response. J Biol Chem, 288; 4613-4624. PMCID: PMC3576067

Zhang, H., Gay, S.C., Shah, M., Foroozesh, M., Liu, J., Osawa, Y., Zhang, Q., Stout, C.D., Halpert, J.R., Hollenberg, P.F. (2013) Potent Mechanism-Based Inactivation of Cytochrome P450 2B4 by 9-Ethynylphenanthrene: Implications for Allosteric Modulation of Cytochrome P450 Catalysis. Biochemistry 52; 355-364. PMCID: PMC3612649

Reynald R.L., Sansen, S., Stout, C.D., Johnson, E.F. (2012) Structural Characterization of Human Cytochrome P450 2C19: ACTIVE SITE DIFFERENCES BETWEEN P450s 2C8, 2C9, AND 2C19. J Biol Chem, 287; 44581-44591. PMCID: PMC3531772

Shah, M.B., Wilderman, P.R., Pascual, J., Zhang, Q., Stout, C.D., Halpert, J.R. ((2012) Conformational adaptation of human cytochrome P450 2B6 and rabbit cytochrome P450 2B4 revealed upon binding multiple amlodipine molecules.Biochemistry, 51; 7225-7238. PMCID: PMC3485383

Lee, Y.T., Glazer, E.C., Wilson, R.F., Stout, C.D., Goodin, D.B. (2011) Three clusters of conformational States in P450cam reveal a multistep pathway for closing of the substrate access channel. Biochemistry 5; 693-703. PMCID: PMC3032038

Wilderman, P.R., Gay, S., Jang, H.-H., Qinghai, Z., Stout, C.D. and Halpert, J. (2011) 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. FEBS J., 279; 1607-1620. PMID: 22051155

Wang, A., Savas, U., Stout, C.D. and Johnson, E.F. (2011) Crystal Structure of Human Cytochrome P450 2D6 with prinomastat (AG3320) Bound. J. Biol. Chem., 287; 10834-10843. PMCID: PMC3322812

Shah, M.B., Pascual, J., Zhang, Q., Stout, C.D. and Halpert, J.R. (2011) Structures of Cytochrome P450 2B6 Bound to Inhibitors 4-Benzylpyridine and 4-(4-Nitrobenzyl)pyridine: Insight into Inhibitor Binding and Rearrangement of Active Site Side Chains. Mol. Pharmacol. 80; 1047-1055, PMCID: PMC3228530

Gay, S.C., Zhang, H., Wilderman, P.R., Roberts, A.G., Liu, T., Li, S., Lin, H.-I., Zhang, Q., Woods, V.L., Stout, C.D., Hollenberg, P.F. and Halpert, J.R. (2011) Structural Analysis of Mammalian Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator tert-Butylphenylacetylene: Insight into Partial Enzymatic Activity, Biochemistry 50; 4903-4911. PMCID: PMC3105221

Mast, N., Annalora, A.J., Lodowski, D.T., Palczewski, K., Stout, C.D., Pikuleva, I.A. (2011) Structural basis for three-step sequential catalysis by the cholesterol side chain cleavage enzyme CYP11A1.J. Biol. Chem. 286; 5607-5613. PMCID: PMC3037674

Wang, A., Savas, U., Stout, C.D., and Johnson, E.F. (2011) Structural characterization of the complex between α-naphthoflavone and human cytochrome P450 1B1. J. Biol. Chem. 286; 5736-5743. PMCID: PMC3037686

Gay, S.C., Roberts, A., Maekawa, K., Talakad, J., Hong, W.-X., Zhang, Q., Stout, C.D. and Halpert, J.R. (2010) Structures of Cytochrome P450 2B4 Complexed with the Antiplatelet Drugs Ticlopidine and Clopidogrel. Biochemistry 40; 8709-8720. PMCID: PMC3005796

Wilderman, P.R., Shah, M.B., Liu, T., Li, S., Hsu, S., Roberts, A.G., Goodlett, D.R., Woods, V.L., Stout, C.D. and Halpert, J.R. (2010) Plasticity of Cytochrome P450 2B4 as Investigated by Hydrogen-Deuterium Exchange Mass Spectrometry and X-Ray Crystallograpy. J. Biol Chem. 49; 38602-38611. PMCID: PMC2992292

Mast, N., Charvet, C., Pikuleva, I. and Stout, C.D. (2010) Structural basis of drug binding to CYP46A1, an enzyme that controls cholesterol turnover in the brain. J. Biol. Chem. 41; 31783-31795. PMCID: PMC2951250

Gay, S.C., Shah, M.B., Talakad, J.C., Maekawa, K., Roberts, A.G., Wilderman, P.R., Sun, L., Yang,
J.Y., Huelga, S.C., Zhang, Q., Stout, C.D. and Halpert, J.R. (2010) Crystal Structure of a Cytochrome P450 2B6 Genetic Variant in Complex with the Inhibitor 4-(4-Chlorophenyl)imidazole at 2.0 Å Resolution. Mol. Pharmacol. 77; 529-538. PMCID: PMC2845937

Gay, S.C., Sun, L., Maekawa, K., Halpert, J.R. and Stout, C.D. (2009) Crystal structures of cytochrome P450 2B4 in complex with the inhibitor 1-biphenyl-4-methyl-1H-imidazole: ligand induced structural response through a-helical repositioning. Biochemistry 48; 4762-4771 PMCID: 2764533

Mast, N., White, M.A., Bjorkhem, I., Johnson, E.F., Stout, C.D. and Pikuleva, I.A. (2008) Crystal
structures of substrate bound and substrate-free cytochrome P450 46A1, the principal cholesterol
hydroxylase in the brain. Proc. Natl. Acad. Sci. USA, 105; 9546-9551. PMCID: PMC2474539

White, M.A., Mast, N., Bjorkhem, I., Johnson, E.F., Stout, C.D. and Pikuleva, I.A. (2008) Use of
complementary cation and anion heavy-atom salt derivatives to solve the structure of cytochrome P450 46A1. Acta Cryst. D64; 487-495. PMCID: PMC2467524

Schoch, G.A., Yano, J.K., Sansen, S., Dansette, P.M, Stout, C.D. and Johnson, E.F. (2008)
Determinants of Cytochrome P450 2C8 Substrate Binding: Structures of Complexes with Montelukast, Troglitazone, Felodipine, and 9-cis-Retinoic Acid. J. Biol. Chem. 283; 17227-17237. PMCID: PMC2427337

Sansen, S., Yano, J.K., Reynald, R.L., Schoch, G.A., Griffin, K.J., Stout, C.D. and Johnson, E.F. (2007) Adaptations for the Oxidation of Polycyclic Aromatic Hydrocarbons Exhibited by the Structure of Human P450 1A2. J. Biol. Chem. 282; 14348-14355. PMID: 17311915

Sansen, S., Hsu, M.-H., Stout, C.D. and Johnson, E.F. (2007) Structural Insight into the Altered
Substrate Specificity of Human Cytochrome P450 2A6 Mutants. Arch. Biochem. Biophys. 464; 197-
206. PMID: 17540336

Smith, B.D., Sanders, J.L., Porubsky, P.R., Lushington, G.H., Stout, C.D. and Scott, E.E. (2007)
Structure of the Human Lung Cytochrome P450 2A13. J. Biol. Chem. 282; 17306-17313. PMID:
17428784

Zhao, Y., Sun, L., Muralidhara, B.K., Kumar, S., White, M.A., Stout, C.D. and Halpert, J.R. (2007)
Structural and Thermodynamic Consequences of 1-(4-Chlorophenyl)imidazole Binding to Cytochrome P450 2B4. Biochemistry 46; 11559-11567. PMCID: PMC2566820

Zhao, Y., White, M.A., Muralidhara, B.K., Sun, L., Halpert, J.R. and Stout, C.D. (2006) Structure of
Microsomal Cytochrome P450 2B4 Complexed with the Antifungal Drug Bifonazole: Insight into P450 Conformational Plasticity and Membrane Interaction. J. Biol. Chem. 281; 5973-5981. PMID: 16373351

Johnson, E.F. and Stout, C.D. (2005) Structural Diversity of Human Xenobiotic-Metabolizing
Cytochrome P450 Monooxygenases. Biochem. Biophys. Res. Comm. 338; 331-336. PMID: 16157296

Yano, J.K., Hsu, M.-H., Griffin, K.J., Stout, C.D. and Johnson, E.F. (2005) The structure of human
microsomal cytochrome P450 2A6 complexed with coumarin and methoxsalen. Nature Struct. Mol.
Biol. 12; 822-823. PMID: 16086027

Yano, J.K., Wester, M.R., Schoch, G.A., Griffin, K.J., Stout, C.D. and Johnson, E.F. (2004) The
structure of human microsomal cytochrome P450 3A4 determined by X-ray crystallography to 2.05 Å resolution. J. Biol. Chem. 279; 38091-38094. PMID: 15258162

Wester, M.R., Yano, J.K, Schoch, G.A., Yang, C., Griffin, K.J., Stout, C.D. and Johnson, E.F. (2004) The Structure of Human Cytochrome P450 2C9 Complexed with Flurbiprofen at 2.0 Å Resolution. J.
Biol. Chem. 279; 35630-35637. PMID: 15181000

Scott, E.E., White, M.A., He, Y.A., Johnson, E.F., Stout, C.D. and Halpert, J.R. (2004) Structure of
Mammalian Cytochrome P450 2B4 Complexed with 4-(4-chlorophenyl)imidazole at 1.9 Å Resolution: Insight into the Range of P450 Conformations and Coordination of Redox Partner Binding. J. Biol. Chem. 279; 27294-27301. PMID: 15100217

Schoch, G.A., Yano, J.K., Wester, M.R., Griffin, K.J., Stout, C.D. and Johnson, E.F. (2004) Structure of human microsomal cytochrome P450 2C8: Evidence for a peripheral fatty acid binding site. J. Biol. Chem. 279; 9497-9503. PMID: 14676196

Scott, E.E., He, Y.A., Wester, M.R., White, M.A., Chin, C.C., Halpert, J.R., Johnson, E.F. and Stout,
C.D. (2003) An Open Conformation of Mammalian Cytochrome P450 2B4 at 1.6 Å Resolution. Proc. Natl. Acad. Sci. USA. 100; 13196-13201. PMID: 14563924

Wester, M.R., Johnson, E.F., Marques-Soares, C., Dijols, S., Dansette, P., Mansuy, D. and Stout, C.D. (2003) The Structure of Mammalian Cytochrome P450 2C5 Complexed with Diclofenac at 2.1 Å Resolution: Evidence for an Induced Fit Model of Substrate Binding. Biochem. 42; 9335-9345. PMID: 12899620