Ronald L. Koder Publications
(as
of 2/30/2009)
(25) Koder R.L. and Nanda, V.
Designing enzymes, from intuition
to computation (2009) Nature
Chemistry In Press
(24) Koder
R.L., Anderson, R., Soloman, L.A., Reddy, K.S., Moser, C.M., Dutton, P.L. Design
and Engineering of an O2 transport protein (2009) Nature 458:305-309
(23) Negron, C., Fufezan, C., Koder R.L. Geometric Constraints for
Porphyrin Binding in Helical Protein Binding Sites (2009) Prot. Struct. Func. Bioinform. 74:400-416
(22) Lichtenstein, B.R., Cerda, J.F., Koder, R.L., Dutton, P.L.
Reversible Proton Coupled Electron Transfer in a Peptide-incorporated
Naphthoquinone Amino Acid (2009) Chem.
Comm. 2: 168-170
(21) Anderson,
R., Moser, C.M., Koder, R.L., Dutton, P.L. Controlling complexity and water penetration in
functional de novo protein design (2008)
Biochem. Soc. Trans. 36:1106-1111
(20) Cerda, J.F., Koder, R.L., Lichtenstein, B.R., Moser, C.M.,
Miller, A.-F., Dutton, P.L. Hydrogen Bond-Free Flavin Redox Properties:
Managing Flavins in Extreme Aprotic Solvents (2008) Org. & Biomol. Chem. 6:2204-2212
(19) Koder, R.L., Lichtenstein, B.R., Cerda, J.F., Miller, A.-F., Dutton, P.L. A Benzene
Soluble Flavin Analogue (2007) Tetrahedron Letters 48: 5517-5520
(18) Koder, R. L., Walsh, J.
D., Pometun, M. S.,Dutton, P. L., Wittebort, R. J.,Miller, A.-F. 15N
Solid-State NMR Provides a Sensitive Probe of Oxidized Flavin Reactive Sites
(2006) J. Amer. Chem. Soc. 128:
15200-15208
(17) Koder, R.L., Valentine,
K. G., Cerda, J., Noy, D., Smith, K. M., Wand, A. J., Dutton, P. L. Nativelike
Structure in Designed Four-Helix Bundles Driven by Buried Polar Interactions
(2006) J. Amer. Chem. Soc. 128:
14450-14451
(16) Koder, R.L., Dutton,
P.L. Looking Forward: The de novo Design of Proteins with Specific Function
(2006) Dalt. Trans. 25:
3045-3051
(15) Miller,
A.-F. Koder, R.L., Walsh, J.D., Zhang, P., Haynes, C.A., and Rogers,
D.W. Nitroreductase: Active Site
Structure, Electronics and Thermodynamics (2005) Flavins and Flavoproteins
2005, pp 265-270
(14) Huang, S.L.*,
Koder, R.L.*, Lewis, M.A., Wand A.J. and Dutton, P.L. The HP-1 Maquette: From an Apoprotein Structure to a
Conformationally Specific Hemoprotein Designed to Promote Redox-Coupled Proton
Exchange (2004) Proc. Nat. Acad. Sci. USA
101, 5536-41
(13) Discher, B., Koder,
R.L., Moser, C.C., Dutton, P.L. Hydrophilic to Amphiphilic Design in Redox Protein
Maquettes (2003) Curr. Opin. Chem. Biol. 7, 741-748
(12) Koder,
R.L., Haynes, C.H. Rodgers, M.A. and Miller, A.-F. Flavin Thermodynamics Explain
the Oxygen Insensitivity of Enteric Nitroreductases. (2002) Biochemistry 41, 14197-14205
(11) Koder,
R.L., Haynes, C.H. Rodgers, M.A. and Miller, A.-F. A Spectroscopic Analysis of Inhibitor Binding
to Enterobacter cloacae
Nitroreductase. (2002) Flavins and Flavoproteins 2002, pp 265-270
(10) Miller, A.-F., Koder, R.L., Walsh, J.D.,
(9) Nivinskas, H., Staskeviciene, S. Sarlauskas, J., Koder, R.L.,
Miller, A.-F., Cenas, N. Two-Electron
Reduction of Quinones by Enterobacter cloacae nitroreductase: Quantitative Structure-Activity Relationships
(2002) Arch.
Biochem. Biophys. 403, 249-258
(8) Haynes,
C.A., Koder. R.L., Miller, A.-F., Rodgers, D.W., Structures of
Nitroreductase in Three States: Effects
of Inhibitor Binding and Reduction. (2002) J.
Biol. Chem. 277, 11513-11520
(7) Koder,
R.L., Oyedele, O., Miller, A.-F., Retro-nitroreductase, a Putative Ancestor
of Enterobacter cloacae Nitroreductase.
(2001) Antiox. Redox Cycling 3,
747-756
(6) Nivinskas, H., Koder, R.L., Anusevicius ,Z., Sarlauskas, J.,
Miller, A.-F. Cenas, N., Quantitative structure-activity relationships in
two-electron reduction of nitroaromatic compounds by Enterobacter cloacae NAD(P)H:Nitroreductase (2000) Arch. Biochem. Biophys. 385, 170-178
(5) Schwartz,
A.L., Yikilmaz, E., Vance, C.K., Vathyam, S., Koder, R.L., Miller,
A.-F., Mutational and spectroscopic
studies of the significance of the active site Gln to metal ion specificity in
superoxide dismutases. (2000) J. Inorg.
Biochem. 80, 247-256
(4) Koder,
R.L, Rodgers, M.E. and Miller, A.-F., Flavin binding thermodynamics in Enterobacter cloacae nitroreductase.
(1999) Flavins and Flavoproteins 1999,
pp 45-48
(3) Koder,
R.L. and Miller, A.-F., Steady-state kinetic mechanism, stereospecificity,
substrate and inhibitor specificity of Enterobacter
cloacae nitroreductase. (1998) Biochim.
Biophys. Acta 1387, 395-405.
(2) Koder, R.L. and Miller, A.F., Overexpression, isotopic labelling,
and spectral characterization of Enterobacter
cloacae nitroreductase. (1998) Prot.
Exp. Pur. 13, 53-60.