Biological Design Group

Ronald Koder

Assistant Professor of Physics
B.S. The University of Missouri
Ph.D. The Johns Hopkins University
Post-Doctoral The University of Pennsylvania
Tel. (212) 650-5583
Fax: (212) 650-6940
Email: koder[at]sci.ccny.cuny.edu

(32) Mutter, A.C., Norman, J.C., Tiederman, M.T., Singh, S., Stillman, M.J., Koder, R.L.. Rational Design of a Zinc Phthalocyanine Binding Protein.(2013) J. Struct. Biol. In Press
Link

(31) Brown, M.C., Mutter, A.C., Koder, R.L., JiJi, R.D., Cooley, J.W. Direct quantification of persistent α-helical content and discrete types of backbone disorder during a molten globule to ordered peptide transition. (2013) J. Raman Spect. 44:957-962
Link

(30) Brisendine, J.M., Mutter, A.C., Cerda, J.F., Koder, R.L. A 3D Printed Cell for Rapid, Low Volume Spectroelectrochemistry. (2013) Anal. Biochem. 439:1-3
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(29) Zhang, L., Andersen, E.M.E., Khajo, A., Magliozzo, R.S., Koder, R.L. Dynamic Factors Affecting Gaseous Ligand Binding in an Artificial Oxygen Transport Protein. (2013) Biochemistry 52:447−455
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(28) Punnoose, A., McConnell, L., Liu, W., Mutter, A.C., Koder, R.L. Fundamental Limits on Wavelength, Efficiency and Yield of the Charge Separation Triad. (2012) PLOS One 7:e36065
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(27) Raju, G., Capo, J., Lichtenstein, B.R., Cerda, J.F., Koder, R.L. Manipulating reduction potentials in an artificial safranin cofactor.  (2012)  Tetrahedron Letters 53:1201–1203
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(26) Annavarapu, S., Zhang, L., Koder, R.L., Nanda, V. Computational Design of Thermostabilizing D-Amino Acid Substitutions.  (2011)  J. Amer. Chem. Soc. 133:18750–18759
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(25)Zhang, L., Anderson, J.L.R., Ahmed, I., Norman, J.A., Negron, C., Mutter, A.C., Dutton, P.L., Koder R.L.  Manipulating Heme Binding Thermodynamics in an Artificial Oxygen Transport Protein.  (2011) Biochemistry 50:10254–10261
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(24) Cui, D, Koder, R.L., Dutton, P.L., Miller, A.-F., 15N Solid-State NMR as a Probe of Flavin Hydrogen Bonding. (2011) J. Phys. Chem. B 115:7788–7798
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(23) Braun, P.,  Goldberg, E., Negron, C.,  von Jan, M, Xu, F., Nanda, V., Koder, R.L., Noy, D. Design Principles for Chlorophyll Binding Sites in Helical Proteins. (2011) Prot. Struct. Func. Bioinform.  79:463-476
Link

(22) Xu, F., Zhang, L., Koder, R.L., Nanda, V. De novo self-assembling collagen heterotrimers using explicit positive and negative design (2010) Biochemistry 49:2307-2316
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(21) Nanda, V. and Koder, R.L.  Designing enzymes, from intuition to computation (2010) Nature Chemistry 2:15-24
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(20) Koder R.L.,* Anderson, R.,* Soloman, L.A., Reddy, K.S., Moser, C.M., Dutton, P.L. Design and engineering of an O(2) transport protein (2009) Nature 458:305-309
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From Eric Drexler's Blog: Metamodern. A Revolution in de novo Protein Engineering Methodology. 2009.
Link

(19) 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
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(18) 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
Link

(17) 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
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(16) 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
Link

(15) Koder, R.L.,Lichtenstein, B.R., Cerda, J.F., Miller, A.-F., Dutton, P.L. A flavin analogue with improved solubility in organic solvents (2007) Tetrahedron Letters 48: 5517-5520
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(14) 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
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(13) 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
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(12) Koder, R.L., Dutton, P.L. Intelligent Design: The de novo Design of Proteins with Specific Function (2006) Dalt. Trans. 25: 3045-3051
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(11) 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
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(10) 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
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(9) 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
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(8) 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
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(7) 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
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(6) Koder, R.L., Oyedele, O., Miller, A.-F., Retro-nitroreductase, a Putative Ancestor of Enterobacter cloacae Nitroreductase. (2001)  Antiox. Redox Cycling 3, 747-756
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(5) 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
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(4) 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
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(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.
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(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.
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(1) Beecher,  B.S., Koder,  R.L., Tipton.  P.A.  Tartrate dehydrogenase-oxalate complexes – formation of a stable analog  of a reaction intermediate complex. (1994) Arch. Biochem. Biophys. 315, 255-261
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