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    Goodin Lab Publications

 
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2013

Myers, W.K., Lee, Y.-T., Britt, R. D. and Goodin, D.B. (2013) "The Conformation of P450cam in Complex with Putidaredoxin Is Dependent on Oxidation State", J. Am. Chem. Soc 135, 11732.
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2013

Barelier, S., Boyce, S.E., Fish, I., Fischer, M., Goodin, D.B., and Shoichet, B.K. (2013) "Roles for Ordered and Bulk Solvent in Ligand Recognition and Docking in Two Related Cavities", PLoS ONE 8, 69153.
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2012

Stoll, S., Lee, Y.-T., Zhang, M., Wilson, R.F., Britt, R.D. and Goodin, D.B. (2012) "Double electron-electron resonance shows cytochrome P450cam undergoes a conformational change in solution upon binding substrate", Proc. Natl. Acad. Sci. USA, 109, 12888-12893.
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2011

Markwick, Phineus R.L., Pierce, Levi C.T., Goodin, David B. and McCammon, J. Andrew (2011) "Adaptive accelerated molecular dynamics reveals the molecular plasticity of P450cam", J. Phys. Chem. Lett., 2, 158-164.
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2011

Lee, Y.-T., Glazer, E.C., Wilson, R.F., Stout, C.D. and Goodin, D.B. (2011) "Three clusters of conformational states in P450cam reveal a multi-step pathway for closing of the substrate access channel", Biochemistry, 50, 693-703.
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2011

Jensen, G.M. and Goodin, D.B. (2011) "Impact of proximal and distal pocket site-directed mutations on the ferric/ferrous heme redox potential of yeast cytochrome c peroxidase", Theor. Chem. Acc., 130, 1185-1196.
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2010

Nigro, A.P., and Goodin, D.B. (2010) “Reaction of N-hydroxyguanidine with the ferrous-oxy state of a heme peroxidase cavity mutant: A model for the reactions of nitric oxide synthase”, Arch. Biochem. Biophys., 500, 66-73.
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2010

Lee, Y.-T., Wilson, R.F., Rupniewski, I. and Goodin, D.B. (2010) “P450cam visits an open conformation in the absence of substrate”, Biochemistry 49, 3412-3419.
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2010

Annalora, A. J., Goodin, D.B., Hong, W.-X., Zang, Q., Johnson, E.F., Stout, C.D. (2010) “Crystal Structure of CYP24A1, a Mitochondrial Cytochrome P450 Involved in Vitamin D Metabolism”, J. Mol. Biol. 396, 441-451.
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2009

Putnam, A.-M. A. H., Lee, Y.-T. and Goodin D.B. (2009) “Replacement of an Electron Transfer Pathway in Cytochrome c Peroxidase with a Surrogate Peptide”, Biochemistry, 48, 1.
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2009
Vetter, Stefan W., Terentis, A.C., Osborne, R., Dawson, J.H. and Goodin, D.B. (2009) “Replacement of the Axial Histidine Heme Ligand with Cysteine in Nitrophorin I: Spectroscopic and Crystallographic Characterization”, J. Biol. Inorg. Chem, 14, 179.
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2008

Glazer, E.C., Le Nguyen, Y.H., Gray, H.B., and Goodin, D.B. (2008) “Probing Inducible Nitric Oxide Synthase with a Pterin-Ru(II) Sensitizer Wire”, Angew. Chemie, 47, 898.
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2007

Contakes, S.M., Nguyen, Y.H.L., Gray, H.B., Glazer, E.C., Hays, A.-M.A., and Goodin,
D.B. (2006) “Conjugates of Heme-Thiolate Enzymes with Photoactive Metal-Diimine
Wires”, in Structure & Bonding, Springer-Verlag, Berlin/Heidelberg, 123,177.
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2006

Brenk, R., Vetter, S., Boyce, S.E., Goodin, D.B., and Shoichet, B. (2006) “Probing
Molecular Docking in a Charged Model Binding Site,” J. Mol. Biol, 357, 1449.
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2005

Udit, A.K., Belliston-Bittner, W., Glazer, E.C., Nguyen, Y.H.L., Gillan, J.M., Hill, M.G.,
Marletta, M.A., Goodin, D.B., Gray, H.B. (2005) “Redox Couples of Inducible Nitric
Oxide Synthase,” J. Am. Chem. Soc 127, 11212.
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2004

Hays, A.-M.A., Dunn, A.R., Chiu, R., Gray, H.B., Stout, C.D., and Goodin, D.B. (2004)
“Conformational States of Cytochrome P450cam Revealed by Trapping of Synthetic
Molecular Wires,” J. Mol. Biol 344, 455.
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2004

Kroeck, L., Shivanyuk, A., Goodin, D.B., and Rebek, J., Jr. (2004) "Spin Labeling
Monitors Weak Host-Guest Interactions,” Chemical Communications 3, 272.
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2003

Rosenfeld, R.J., Goodsell, D.S., Musah, R.A., Morris, G.M., Goodin, D.B., and Olson,
A.J. (2003) "Automated Docking of Ligands to an Artificial Active Site: Augmenting
Crystallographic Analysis with Computer Modeling,” Journal of Computer-Aided
Molecular Design 17, 525.
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2003

Voegtle, H.L., Sono, M., Adak, S., Pond, A.E., Tomita, T., Perera, R., Goodin, D.B.,
Ikeda-Saito, M., Stuehr, D.J., and Dawson, J.H. (2003) "Spectroscopic Characterization
of Five- and Six-Coordinate Ferrous-NO Heme Complexes. Evidence for Heme Fe-
Proximal Cys Bond Cleavage in the Ferrous-NO Adducts of the Trp-409Tyr/Phe
Proximal Environment Mutants of Neuronal NOS,” Biochemistry 42, 2475.
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2003

Hays, A.-M.A., Gray, H.B., and Goodin, D.B. (2003) "Trapping of Peptide-Based
Surrogates in an Artificially Created Channel of Cytochrome c Peroxidase,” Protein
Science 12, 278.
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2003

Bonagura, C.A., Bhaskar, B., Shimizu, H., Li, H., Sundaramoorthy, M., McRee, D.E.,
Goodin, D.B., and Poulos, T.L. (2003) "High-Resolution Crystal Structures and
Spectroscopy of Native and Compound I Cytochrome c Peroxidase,” Biochemistry 42,
5600.
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2002

Rosenfeld, R.J., Hays, A.-M.A., Musah, R.A., and Goodin, D.B. (2002) "Excision of a
Proposed Electron Transfer Pathway in CCP and its Replacement by a Ligand-Binding
Channel,” Protein Sci 11, 1251.
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2002

Pond, A.E., Hirst, J., Goodin, D.B., and Dawson, J.H. (2002) in Oxygen and Life -
Oxygenases, Oxidases and Lipid Mediators (Ishimura, Y. Ed) pp 25-35, Elsevier,
Amsterdam.
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2002

Musah, R.A., Jensen, G.M., Bunte, S.W., Rosenfeld, R.J., and Goodin, D.B. (2002)
"Artificial Protein Cavities as Specific Ligand-Binding Templates: Characterization of an
Engineered Heterocyclic Cation Binding Site that Preserves the Evolved Specificity of
the Parent Protein,” J. Mol. Biol 315, 845.
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2002

Dunn, A.R., Hays, A.-M.A., Goodin, D.B., Stout, C.D., Chiu, R., Winkler, J.R., and
Gray, H.B. (2002) "Fluorescent Probes for Cytochrome P450 Structural Characterization
and Inhibitor Screening,” J. Am. Chem. Soc 124, 10254.
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2001

Pond, A.E., Ledbetter, A.P., Sono, M., Goodin, D.B., and Dawson, J.H. (2001) “Redox
Enzymes: Correlation of Three-Dimensional Structure and Mechanism for Heme-
Containing Oxygenases and Peroxidases,” in Electron Transfer in Chemistry (Balzani,
V., Ed.) pp 56-104, Wiley-VCH, Weinheim.
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2001

Ivancich, A., Dorlet, P., Goodin, D.B., and Un, S. (2001) "Multifrequency High-field
EPR Study of the Trp and Tyr Radical Intermediates in WT and the W191G Mutant of
CCP,” J. Am. Chem. Soc 123, 5050.
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2001

Hirst, J., Wilcox, S.K., Ai, J., Moënne-Loccoz, P., Loehr, T.M., and Goodin, D.B. (2001)
"Replacement of the Axial Histidine Ligand with Imidazole in Cytochrome c
Peroxidase.2. Effects on Heme Coordination and Function,” Biochemistry 40, 1274.
Link to PDF
 
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2001

Hirst, J., Wilcox, S.K., Williams, P.A., Blankenship, J., McRee, D.E., and Goodin, D.B.
(2001) "Replacement of the Axial Histidine Ligand with Imidazole in Cytochrome c
Peroxidase. 1. Effects on Structure,” Biochemistry 40, 1265.
Link to PDF
 
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2001

Bunte, S.W., Jensen, G.M., McNesby, K.L., Goodin, D.B., Chabalowski, C.F., Neiminen,
R.M., Suhai, S., and Jalkanen, K.J. (2001) "Theoretical Determination of the Vibrational
Absorption and Raman Spectra of 3-methylindole and 3-methylindole Radicals,”
Chemical Physics 265, 13.
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2001

Bateman, L., Léger, C., Goodin, D.B., and Armstrong, F.A. (2001) "A Distal Histidine
Mutant (H52Q) of Yeast CcP Catalyzes the Oxidation of H2O2 instead of its Reduction,”
J. Am. Chem. Soc 123, 9260.
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2000

Vaino, A.R., Goodin, D.B., and Janda, K.D. (2000) "Investigating Resins for Solid Phase
Organic Synthesis: The Relationship Between Swelling and Microenvironment As
Probed By EPR and Fluorescence,” J. Comb. Chem 2, 330.
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1999

Hirst, J., and Goodin, D.B. (2000) "Unusual oxidative chemistry of Nω-hydroxyarginine
and N-hydroxyguanidine catalyzed at an engineered cavity in a heme peroxidase,” J.
Biol. Chem 275, 8582.
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1999

Viles, J.H., Cohen, F.E., Prusiner, S.B., Goodin, D.B., Wright, P.E., and Dyson, H.J.
(1999) "Copper binding to prion protein: Structural implications of four identical
cooperative binding sites,” Proc. Natl. Acad. Sci. USA 96, 2042.
Link to PDF
 
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1999

Schipke, C.G., Goodin, D.B., McRee, D.E., and Stout, C.D. (1999) "Oxidized and
Reduced Azotobacter vinelandii Ferredoxin I at 1.4 Å Resolution: Conformational
Change of Surface Residues without Significant Change in the [3Fe-4S]+/0 Cluster,”
Biochemistry 38, 8228.
Link to PDF
 
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1999

Pond, A.E., Sono, M., Elenkova, E.A., Goodin, D.B., English, A.M., and Dawson, J.H.
(1999) "Influence of Protein Environment on Magnetic Circular Dichroism Spectral
Properties of Ferric and Ferrous Ligand Complexes of Yeast Cytochrome c Peroxidase,”
Biospectroscopy 5, 42.
Link to PDF
 
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1999

Pond, A.E., Sono, M., Elenkova, E.A., McRee, D.E., Goodin, D.B., English, A.M., and
Dawson, J.H. (1999) "MCD Studies of Cytochrome c Peroxidase From Yeast:
Investigation of the Effects of Aging and pH on the Active Site Heme Coordination
Sphere of the Ligand-Free Ferric State,” J. Inorg. Biochem 76, 165.
Link to PDF
 
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1998

Wilcox, S.K., Putnam, C.D., Sastry, M., Blankenship, J., Chazin, W.J., McRee, D.E., and
Goodin, D.B. (1998) "Rational Design of a Functional Metalloenzyme: Introduction of a
Site for Manganese Binding and Oxidation into a Heme Peroxidase,” Biochemistry 37,
16853.
Link to PDF
 
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1998

Wilcox, S.K., Putnam, C.D., Sastry, M., Blankenship, J., Chazin, W.J., McRee, D.E., and
Goodin, D.B. (1998) "Rational Design of a Functional Metalloenzyme: Introduction of a
Site for Manganese Binding and Oxidation into a Heme Peroxidase,” Biochemistry 37,
16853.
Link to PDF
 
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1998

Mondal, M.S., Goodin, D.B., and Armstrong, F.A. (1998) "Simultaneous Voltammetric
Comparisons of Reduction Potentials, Reactivities, and Stabilities of the High-Potential
Catalytic States of Wild-Type and Distal-Pocket Mutant (W51F) Yeast Cytochrome c
Peroxidase,” J. Am. Chem. Soc 120, 6270.
Link to PDF
 
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1998

Liu, K., Williams, J., Lee, H., Fitzgerald, M.M., Jensen, G.M., Goodin, D.B., and
McDermott, A.E. (1998) "Solid-State Deuterium NMR of Imidazole Ligands in CcP,” J.
Am. Chem. Soc 120, 10199.
Link to PDF
 
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1998

Jensen, G.M., Bunte, S.W., Warshel, A., and Goodin, D.B. (1998) "Energetics of Cation
Radical Formation at the Proximal Active Site Trp of CCP and Ascorbate Peroxidase,” J.
Phys. Chem. B 102, 8221.
Link to PDF
 
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1997

Cao, Y., Musah, R.A., Wilcox, S.K., Goodin, D.B., and McRee, D.E. (1998) "Protein
Conformer Selection by Ligand Binding Observed with Crystallography,” Protein
Science 7, 72.
Link to PDF
 
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1997

Sun, J., Fitzgerald, M.M., Goodin, D.B., and Loehr, T.M. (1997) "The Solution and
Crystal Structures of the H175G Mutant of CcP: A Resonance Raman Study,” J. Am.
Chem. Soc 119, 2064.
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1997

Musah, R.A., and Goodin, D.B. (1997) "Introduction of Novel Substrate Oxidation into a
Heme Peroxidase by Cavity Complementation: Oxidation of 2-aminothiazole and
Covalent Modification of the Enzyme,” Biochemistry 36, 11665.
Link to PDF
 
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1997

Musah, R.A., Jensen, G.M., Rosenfeld, R.J., Bunte, S.W., McRee, D.E., and Goodin,
D.B. (1997) “Variation in Strength of a CH to O Hydrogen Bond in an Artificial Cavity,”
J. Am. Chem. Soc 119, 9083.
Link to PDF
 
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1997

Sarma, S., DiGate, R.J., Goodin, D.B., Miller, C.J., and Guiles, R.D. (1997) “Effect of
Axial Ligand Plane Reorientation on Electronic and Electrochemical Properties Observed
in Site Directed Mutants of Rat Cytochrome b5,” Biochemistry 36, 5658.
Link to PDF
 
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1997

Sun, J., Fitzgerald, M.M., Goodin, D.B., and Loehr, T.M. (1997) “The Solution and
Crystal Structures of the H175G Mutant of Cytochrome c Peroxidase: A Resonance
Raman Study,” J. Am. Chem. Soc 119, 2064.
Link to PDF
 
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1996

Goodin, D. B. (1996) “When an Amide is More Like Histidine than Imidazole: the Role
of Axial Ligands in Heme Catalysis,” J. Biol. Inorg. Chem 1, 360.
Link to PDF
 
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1996

Goodin, D. B. (1996) “When an Amide is More Like Histidine than Imidazole: the Role
of Axial Ligands in Heme Catalysis,” J. Biol. Inorg. Chem 1, 360.
Link to PDF
 
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1996

Smulevich, G., Hu, S., Rodgers, K.R., Goodin, D.B., Smith, K.M., and Spiro, T. G.
(1996) “Heme-Protein Interactions in CcP Revealed by Site-Directed Mutagenesis and
Resonance Raman Spectra of Isotopically-Labeled Hemes,” Biospectroscopy 2, 365.
Link to PDF
 
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1996

Fitzgerald, M.M., Musah, R.A., McRee, D. E., and Goodin, D.B. (1996) “A Ligand-
Gated, Hinged Loop Rearrangement Opens a Channel to a Buried Artificial Protein
Cavity,” Nature Structural Biology 3, 626.
Link to PDF
 
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1996

Wilcox, S.K., Jensen, G.M., Fitzgerald, M.M., McRee, D.E., and Goodin, D.B. (1996)
“Altering Substrate Specificity at the Heme Edge of Cytochrome c Peroxidase,”
Biochemistry 35, 4858.

Link to PDF

 
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1996

Jensen, G.M., Goodin, D.B., and Bunte, S.W. (1996) “Density Functional and MP2
Calculations of Spin Densities of Oxidized 3-methyl indole: Models for Tryptophan
Radicals,” J. Phys. Chem 100, 954.
Link to PDF
 
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1995

Huyett, J.E., Doan, P.E., Gurbiel, R., Houseman, A.L.P., Sivaraja, M., Goodin, D.B., and
Hoffman, B.M. (1995) “Compound ES of Cytochrome c Peroxidase Contains a Trp π-
Cation Radical: Characterization by CW and Pulsed Q-Band ENDOR,” J. Am. Chem.
Soc 117, 9033.
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1995

Miller, V.P., Goodin, D.B., Friedman, A.E., Hartmann, C., and Ortiz de Montellano, P.R.
(1995) “Horseradish Peroxidase Phe-172 > Tyr Mutant: Sequential Formation of
Compound I with a Porphyrin Radical Cation and a Protein Radical,” J. Biol. Chem 270,
18413.
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1995

Patterson, W.R., Poulos, T.L., and Goodin, D.B. (1995) "Identification of a Porphyrin π-
Cation Radical in Ascorbate Peroxidase Compound I,” Biochemistry 34, 4342.
Link to PDF
 
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1994

Fitzgerald, M.M., McRee, D.E., Churchill, M.J., and Goodin, D.B. (1994) "Small
Molecule Binding to an Artificially Created Cavity at the Active Site of Cytochrome c
Peroxidase,” Biochemistry 33, 3807.
Link to PDF
 
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1994

Goodin, D.B., and McRee, D.E. (1993) "The Asp-His-Fe Triad of Cytochrome c
Peroxidase Controls the Reduction Potential, Electronic Structure, and Coupling of the
Tryptophan Free Radical to the Heme,” Biochemistry 32, 3313.
Link to PDF
 
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1993

Roe, J.A., and Goodin, D.B. (1993) "Enhanced Oxidation of Aniline Derivatives by Two
Mutants of Cytochrome c Peroxidase at Tryptophan 51,” J. Biol. Chem 268, 20037.
Link to PDF
 
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1993

Goodin, D.B., and McRee, D.E. (1993) "The Asp-His-Fe Triad of Cytochrome c
Peroxidase Controls the Reduction Potential, Electronic Structure, and Coupling of the
Tryptophan Free Radical to the Heme,” Biochemistry 32, 3313.
Link to PDF
 
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1993

Houseman, A.L.P., Doan, P.E., Goodin, D.B., and Hoffman, B.M. (1993)
"Comprehensive Explanation of the Anomalous EPR Spectra of Wild-Type and Mutant
Cytochrome c Peroxidase Compound ES,” Biochemistry 32, 4430.
Link to PDF
 
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1991

Goodin, D.B., Davidson, M.G., Roe, J.A., Mauk, A.G., and Smith, M. (1991) "Amino
Acid Substitutions at Tryptophan-51 of Cytochrome c Peroxidase - Effects on
Coordination, Species Preference for Cytochrome c, and Electron Transfer,”
Biochemistry 30, 4953.
Link to PDF
 
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1990

Watson, W.H., Nagl, A., Marchand, A.P., Vidyasagar, V., and Goodin, D.B. (1990)
"Structure of a Dimer Ketone Formed via Iron Carbonyl-Promoted Coupling of 7-
Phenylnorbornadiene with Carbon Monoxide,” Acta Crystallogr. C46, 1127.
Link to PDF
 
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1989

Sivaraja, M., Goodin, D.B., Smith, M., and Hoffman, B.M. (1989) "Identification by
ENDOR of Trp191 as the Free-Radical Site in Cytochrome C Peroxidase Compound
ES,” Science 245, 738.
Link to PDF
 
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1988

Kroeck, L., Shivanyuk, A., Goodin, D.B., and Rebek, J., Jr. (2004) "Spin Labeling
Monitors Weak Host-Guest Interactions,” Chemical Communications 3, 272.
Link to PDF
 
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1988

Ner, S.S., Goodin, D.B., and Smith, M. (1988) "A Simple and Efficient Procedure for
Generating Random Point Mutations and for Codon Replacements Using Mixed
Oligodeoxynucleotides,” DNA 7, 127.
Link to PDF
 
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1987

Smith, M., Cutler, R.L., Goodin, D.B., Mauk, A.G., and Pielak, G.J. (1987) "Structure-
Function Studies on Yeast Heme Proteins Using Oligonucleotide Mutagenesis,” UCLA
Symp. Mol. Cell. Biol., New Ser 69, 167.
Link to PDF
 
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1987

Goodin, D.B., Mauk, A.G., and Smith, M. (1987) "The Peroxide Complex of Yeast
Cytochrome c Peroxidase Contains Two Distinct Radical Species, Neither of which
Resides at Methionine 172 or Tryptophan 51,” J. Biol. Chem 262, 7719.
Link to PDF
 
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1986

Compound ES of Cytochrome c Peroxidase Altered by Site-Directed Mutagenesis,” Proc.
Natl. Acad. Sci. U.S.A 83, 1295.
Link to PDF
 
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1984

Marchand, A.P., Goodin, D.B., Hossain, M.B., and Van der Helm, D. (1984)
"Stereochemistry of the Reaction of 7-Substituted Norbornadienes with Iron Carbonyls.
2. Reaction of Fe(CO)5 with 7-Phenyl- and 7-o-Anisylnorbornadiene,” J. Org. Chem 49,
2897.
Link to PDF
 
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1984

Goodin, D.B., Yachandra, V.K., Britt, R.D., Sauer, K., and Klein, M.P. (1984) "The State
of Manganese in the Photosynthetic Apparatus. 3. Light-Induced Changes in X-Ray
Absorption (K-Edge) Energies of Manganese in Photosynthetic Membranes,” Biochim.
Biophys. Acta 767, 209.
Link to PDF
 
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1984

Goodin, D.B., Yachandra, V.K., Guiles, R., Britt, R.D., McDermott, A., Sauer, K., and
Klein, M.P. (1984) "Light-Induced Changes in X-Ray Absorption (K-Edge) Energies of
Manganese in Photosynthetic Membranes,” in EXAFS and Near Edge Structure III
(Hodgson, K.O., Hedman, B., and Penner-Hahn, J.E., eds.), pp. 130, Springer-Verlag,
Berlin.
Link to PDF
 
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1982

Acrivos, J.V., Hathaway, K., Reynolds, J., Code, J., Parkin, S., Klein, M.P., Thompson,
A., and Goodin, D.B. (1982) "Measurement of Synchrotron X-Ray Energies and Line
Shapes Using Diffraction Markers,” Rev. Sci. Instrum. 53, 575.
Link to PDF
 
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1981

Kirby, J.A., Goodin, D.B., Wydrzynski, T., Robertson, A.S., and Klein, M.P. (1981)
"State of Manganese in the Photosynthetic Apparatus. 2. X-ray Absorption Edge Studies
on Manganese in Photosynthetic Membranes,” J. Am. Chem. Soc 103, 5537.
Link to PDF
 
       
 
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