Ronald Koder

Associate Professor

Main Affiliation

Chemistry and Biochemistry

Additional Departments/Affiliated Programs

Chemistry and Biochemistry

Biology

Areas of Expertise/Research

  • Synthetic Biology
  • Biodesign

Building

Center for Discovery and Innovation

Office

CDI 1.315

Phone

212-650-5583

Ronald Koder

Profile

 

   
   
 
  • 2012-present Professor            The City College of New York Dept. of Physics
  • 2006-2012     Assistant Professor        The City College of New York Dept. of Physics
  • 2002-2004    Adjunct Professor        Swarthmore College Dept. of Chemistry   
  • 2000-2006    Postdoctoral Fellow        The University of Pennsylvania School of Medicine

Education

B.S.  The University of Missouri
Ph.D.  The Johns Hopkins University
Post-Doctoral  The University of Pennsylvania

Courses Taught

Phys V3800   Biophysics
Phys 422    Biophysics
Phys 315    Medical Physics

Research Interests

experimental biological physics; biodesign; synthetic biology; nuclear magnetic resonance; biosensors; biohybrid metamaterials

Publications

Google Scholar

(41) Schnatz, P.J., Brisendine, J.M., Laing, C.C., Everson, B.H., French, C.A., Koder, R.L. Designing Heterotropically-Activated Allosteric Conformational Switches Using Supercharging   Proc. Nat. Acad. Sci. USA (2020)

(40) Brisendine, J.M., Refaely-Abramson, S., Liu, Z.F., Cui, J., Ng, F., Neaton, J.B., Koder, R.L., Venkataraman, L. Probing Charge Transport Through Peptide Bonds J. Phys. Chem. Lett. (2018) 9:763–767

(39) Greenland, K.N., Carvajal, F.C.A., Preston, J.M., Ekblad, S., Chiang, J.Y., Koder, R.L., Wittebort, R.J. Order, Disorder and Temperature-driven Compaction in a Designed Elastin Protein. J. Phys. Chem. B. (2018) 122(10):2725-2736\

(38) Pitsawong, W., Haynes, C.A., Koder, R.L., Rodgers, D.W., Miller, A.-F. Mechanism-informed refinement reveals altered substrate binding mode for catalytically competent nitroreductase. Structure. (2017) 25:978-987

(37) Gunner, M.R. and Koder, R.L. The design features for how cells build their transmembrane proton gradient. Physical Biology. (2017) 14:013001

(36) Lepak, L.A., Schnatz, P., Bendoym, I., Kosciolek, D., Koder, R.L., Crouse, D.T. Handheld chem/biosensor using extreme conformational changes in designed binding proteins to enhance surface plasmon resonance. (2016) Proc. S.P.I.E. doi:10.1117/12.2222305

(35) Anderson, J.L.R. and Koder, R.L. Biodesign for bioenergetics – the design and engineering of electron transfer cofactors, proteins and protein networks.  Biochim. Biophys. Acta - Bioenergetics (2016) 1857:483-484

(34) Brisendine, J., Koder, R.L. Fast, cheap and out of control - Insights into thermodynamic and informatic constraints on natural protein sequences from de novo protein design. Biochim. Biophys. Acta - Bioenergetics (2016) 1857:485-492

(33) Raju, G., Singh, S., Mutter, A.C., Everson, B.H., Cerda, J., Koder, R.L. Extended Scope Synthesis of an Artificial Safranine Cofactor. (2014) Tetrahedron Letters 55:2487-2491

(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. (2014) J. Struct. Biol. 185:178-185

(31) 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

(30) 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

(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.  Biochemistry (2013) 52:447−455

(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

(27) Raju, G., Capo, G., Lichtenstien, B.R., Cerda, J., Koder, R.L.  Manipulating Reduction Potentials in an Artificial Safranin Cofactor. (2012) Tetrahedron Letters 53:1201–1203

(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

(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

(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

(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

(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

(21) Nanda, V. and Koder, R.L.  Designing enzymes, from intuition to computation (2010) Nature Chemistry 2:15-24

(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

(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

(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

(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

(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

(15) 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

(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

(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

(12) Koder, R.L., Dutton, P.L. Intelligent Design: The de novo Design of Proteins with Specific Function (2006) Dalt. Trans. 25: 3045-3051

(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

(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

(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

(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

(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

(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

(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

(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

(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.

(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