Publications
On the emergence of metabolism: the evolution of proteins that powered life
Nanda, V., Siess, J., Jagilinki, B.P., Hazen, R.M., Kamerlin, S.C.L., Koder, R.L., Noy, D., Silberg, J., Tezcan, F.A., Ulijn, R., Yee, N., Falkowski, P. Phil. Trans. R. Soc. 2025, B38020240090
Quantum defect sensitization via phase-changing supercharged antibody fragments
Kim, M., McCann, J.C., Fortner, J., Ewelina Randall, Chen, C., Chen, Y., Yaari, Z., Wang, H., Koder, R.L, Heller, D.A (2024) J. Amer. Chem. Soc. 2024, 146, 18, 12454–12462
Elastin Recoil is Driven by the Hydrophobic Effect
Jamhawi, N.M., Koder, R.L., Wittebort, R.J. (2024) Proc. Nat. Acad. Sci. USA 121(11):e2304009121
The Energetics and Evolution of Oxidoreductases in Deep Time
Nanda, V., McGuinness, K.N., Fehon, N., Miller, M., Mutter, A.C., Nam, J. AbuSalim, J.E., Atkinson, J.T., Heidari, H., Losada, N., Kim, J.D., Koder, R.L., Lu, Y., Silberg, J., Slusky, J., Falkowski, P.F. (2024) Prot. Struct. Funct. Bioinf. 92(8): 52-59
Protein Dynamics Govern the Oxyferrous State Lifetime of an Artificial Oxygen Transport Protein
Zhang,L., Brown, M.C., Mutter, A.C., Cooley, J.W., Koder R.L. (2023) Biophysical J. 122(22):4440-4450
An expandable, modular de novo protein platform for precision redox engineering
Hutchins, G.H, Noble, C.E.M, Bunzel, H.A., Williams, C., Dubiel, P., Vadiv, S.K.N, Molinaro, P.M., Barringer, R., Blackburn, H., Hardy, B.J., Parnell,, A.E., Koder, R.L., Crump, M., Schaffitzel, C., Oliveira, A.S.F., Mullholland, A.J., Anderson, J.L.R. (2023) Proc. Nat. Acad. Sci. USA 120 (31) e2306046120
Design of a Minimal Di-Nickel Hydrogenase Peptide
Timm, J., Pike, D.H., Mancini, J.A., Tyryshkin, A.M., Poudel, S., Siess, J.A., Molinaro, P.M., McCann, J.J., Walkdie, K.M., Koder, R.L., Falkowski, P.G., Nanda, V. (2023) Science Advances 9, eabq1990
Flavin Charge Redistribution upon Optical Excitation Is Independent of Solvent Polarity
Van Galen, C.J.V., Pauskek, R.F., Koder, R.L., Stanley, R.J. (2023) J. Phys. Chem. B, 127(8):661–672
Liquid to Solid Transition of Elastin Condensates
Ceballos, A.V., Diaz, J.A., Preston, J.M., Vairamon, C., Shen, C., Koder, R.L., Elbaum-Grafinkle, S. (2022) Proc. Nat. Acad. Sci. USA. 119 (37) e2202240119
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ATP-NAD+ Kinases Are Reversible, and NAD+ Product Inhibition is Responsible for the Irreversibility of the Human Enzyme
Willett, E., Jiang, V., Koder, R.L., Banta, S. (2022) Biochemistry 61(17):1862-1873
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Design of a Phase-Changing VX-Sensing Protein
McCann, J.J., Pike, D.L., Brown, M.C., Crouse, D.T., Nanda, V. Koder, R.L. (2022) Science Advances 8, eabh3421
Oxidation/Reduction and Photophysical Properties of Isomeric Forms of Safranin
Andersen, E.M.E., Khoo, J., Wang, H. Koder, R.L. (2022) PLOS One 17(6):e0265105
Thermalization of Fluorescent Protein Exciton-Polaritons at Room Temperature
Satapathy, S., Molinaro, P.M., Koder, R.L., Menon, V.M. (2022) Advanced Materials 34:2109107
Non-Covalent Coatings on Carbon Nanotubes Mediate Photosensitizer Interaction
Horoszko, C.P., Schnatz, P.J., Budhathoki-Uprety, J., Rao-Pothuraju, R., Koder, R.L., Heller, D.A. (2021) ACS Applied Materials & Interfaces 13(43):51343-51350
Dynamics in Natural and Designed Elastins and Their Relation to Elastic Fiber Structure and Recoil
Carvajal, F.C.A., Preston, J.M., Jamhawi, N.M., Sabo, T.M., Aramani, J., Wittebort, R.J., Koder R.L. (2021) Biophysical J 120(20):4623-4634
Designing Heterotropically-Activated Allosteric Conformational Switches Using Supercharging
Schnatz, P.J., Brisendine, J.M., Laing, C.C., Everson, B.H., French, C.A., Koder, R.L. (2020) Proceedings of the National Academy of Sciences USA 117(10):5291-5297
Probing Charge Transport Through Peptide Bonds
Brisendine, J.M., Refaely-Abramson, S., Liu, Z.F., Cui, J., Ng, F., Neaton, J.B., Koder, R.L., Venkataraman, L.J. (2018) The Journal of Physical Chemistry Letters 9:763–767
Order, Disorder and Temperature-driven Compaction in a Designed Elastin Protein
Greenland, K.N., Carvajal, F.C.A., Preston, J.M., Ekblad, S., Chiang, J.Y., Koder, R.L., Wittebort, R.J. (2018) Journal of Physical Chemistry B 122(10):2725-2736
Mechanism-Informed Refinement Reveals Altered Substrate Binding Mode for Catalytically Competent Nitroreductase
Pitsawong, W., Haynes, C.A., Koder, R.L., Rodgers, D.W., Miller, A.-F. (2017) Structure 25:978-987
The Design Features for How Cells Build Their Transmembrane Proton Gradient
Gunner, M.R. and Koder, R.L. (2017) Physical Biology 14:013001
Handheld Chem/Biosensor Using Extreme Conformational Changes in Designed Binding Proteins to Enhance Surface Plasmon Resonance
Lepak, L.A., Schnatz, P., Bendoym, I., Kosciolek, D., Koder, R.L., Crouse, D.T. (2016) Proc. S.P.I.E. 986208
Biodesign for Bioenergetics – The Design and Engineering of Electron Transfer Cofactors, Proteins and Protein Networks
Anderson, J.L.R. and Koder, R.L. (2016) Biochim. Biophys. Acta – Bioenergetics 1857:483-484
Fast, Cheap and Out of Control - Insights Into Thermodynamic and Informatic Constraints on Natural Protein Sequences From De Novo Protein Design
Brisendine, J., Koder, R.L. (2016) Biochim. Biophys. Acta - Bioenergetics 1857:485-492
Extended Scope Synthesis of an Artificial Safranine Cofactor
Raju, G., Singh, S., Mutter, A.C., Everson, B.H., Cerda, J., Koder, R.L. (2014) Tetrahedron Letters 55:2487-2491
Rational Design of a Zinc Phthalocyanine Binding Protein
Mutter, A.C., Norman, J.C., Tiederman, M.T., Singh, S., Stillman, M.J., Koder, R.L. (2014) J. Struct. Biol. 185:178-185
A 3D Printed Cell for Rapid, Low Volume Spectroelectrochemistry
Brisendine, J.M., Mutter, A.C., Cerda, J.F., Koder, R.L. (2013) Anal. Biochem. 439:1-3
Direct Quantification of Persistent α-Helical Content and Discrete Types of Backbone Disorder During a Molten Globule to Ordered Peptide Transition
Brown, M.C., Mutter, A.C., Koder, R.L., JiJi, R.D., Cooley, J.W. (2013) J. Raman Spect. 44:957-962
Dynamic Factors Affecting Gaseous Ligand Binding in an Artificial Oxygen Transport Protein
Zhang, L., Andersen, E.M.E., Khajo, A., Magliozzo, R.S., Koder, R.L. Biochemistry (2013) 52:447−455
Zhang, L., Andersen, E.M.E., Khajo, A., Magliozzo, R.S., Koder, R.L. Biochemistry (2013) 52:447−455
Fundamental Limits on Wavelength, Efficiency and Yield of the Charge Separation Triad
Punnoose, A., McConnell, L., Liu, W., Mutter, A.C., Koder, R.L.. (2012) PLOS One 7(6):e36065
Manipulating Reduction Potentials in an Artificial Safranin Cofactor
Raju, G., Capo, G., Lichtenstien, B.R., Cerda, J., Koder, R.L. (2012) Tetrahedron Letters 53:1201–1203
Computational Design of Thermostabilizing D-Amino Acid Substitutions
Annavarapu, S., Zhang, L., Koder, R.L., Nanda, V. (2011) J. Amer. Chem. Soc. 133:18750-18759
Manipulating Heme Binding Thermodynamics in an Artificial Oxygen Transport Protein
Zhang, L., Anderson, J.L.R., Ahmed, I., Norman, J.A., Negron, C., Mutter, A.C., Dutton, P.L., Koder R.L. (2011) Biochemistry 50:10254-10261
15N Solid-State NMR as a Probe of Flavin Hydrogen Bonding
Cui, D, Koder, R.L., Dutton, P.L., Miller, A.-F. (2011) J. Phys. Chem. B 115:7788-7798
Design Principles for Chlorophyll Binding Sites in Helical Proteins
Braun, P., Goldberg, E., Negron, C., von Jan, M, Xu, F., Nanda, V., Koder, R.L., Noy, D. (2011) Prot. Struct. Func. Bioinform. 79:463-476
De Novo Self-Assembling Collagen Heterotrimers Using Explicit Positive and Negative Design
Xu, F., Zhang, L., Koder, R.L., Nanda, V. (2010) Biochemistry 49:2307-2316
Designing Enzymes, From Intuition to Computation
Nanda, V. and Koder, R.L. (2010) Nature Chemistry 2:15-24
Design and Engineering of an O(2) Transport Protein
Koder R.L.,* Anderson, R.,* Soloman, L.A., Reddy, K.S., Moser, C.M., Dutton, P.L. (2009) Nature 458:305-309
Geometric Constraints for Porphyrin Binding in Helical Protein Binding Sites
Negron, C., Fufezan, C., Koder, R.L. (2009) Prot. Struct. Func. Bioinform. 74:400-416
Reversible Proton Coupled Electron Transfer in a Peptide-Incorporated Naphthoquinone Amino Acid
Lichtenstein, B.R., Cerda, J.F., Koder, R.L., Dutton, P.L. (2009) Chem. Comm. 2:168-170
Controlling Complexity and Water Penetration in Functional De Novo Protein Design
Anderson, R., Moser, C.M., Koder, R.L., Dutton, P.L. (2008) Biochem. Soc. Trans. 36:1106-1111
Hydrogen Bond-Free Flavin Redox Properties: Managing Flavins in Extreme Aprotic Solvents
Cerda, J.F., Koder, R.L., Lichtenstein, B.R., Moser, C.M., Miller, A.-F., Dutton, P.L. (2008) Org. & Biomol. Chem. 6:2204-2212
A Benzene Soluble Flavin Analogue
Koder, R.L., Lichtenstein, B.R., Cerda, J.F., Miller, A.-F., Dutton, P.L. (2007) Tetrahedron Letters 48: 5517-5520
15N Solid-State NMR Provides a Sensitive Probe of Oxidized Flavin Reactive Sites
Koder, R. L., Walsh, J. D., Pometun, M. S., Dutton, P. L., Wittebort, R. J., Miller, A.-F. (2006) J. Amer. Chem. Soc. 128: 15200-15208
Nativelike Structure in Designed Four-Helix Bundles Driven by Buried Polar Interactions
Koder, R.L., Valentine, K. G., Cerda, J., Noy, D., Smith, K. M., Wand, A. J., Dutton, P. L. (2006) J. Amer. Chem. Soc. 128: 14450-14451
Intelligent Design: The De Novo Design of Proteins with Specific Function
Koder, R.L., Dutton, P.L. (2006) Dalt. Trans. 25: 3045-3051
The HP-1 Maquette: From an Apoprotein Structure to a Conformationally Specific Hemoprotein Designed to Promote Redox-Coupled Proton Exchange
Huang, S.L.*, Koder, R.L.*, Lewis, M.A., Wand, A.J. and Dutton, P.L. (2004) Proc. Nat. Acad. Sci. USA 101, 5536-41
Hydrophilic to Amphiphilic Design in Redox Protein Maquettes
Discher, B., Koder, R.L., Moser, C.C., Dutton, P.L. (2003) Curr. Opin. Chem. Biol. 7, 741-748
Flavin Thermodynamics Explain the Oxygen Insensitivity of Enteric Nitroreductases
Koder, R.L., Haynes, C.H. Rodgers, M.A. and Miller, A.-F. (2002) Biochemistry 41, 14197-14205
Two-Electron Reduction of Quinones by Enterobacter cloacae Nitroreductase: Quantitative Structure-Activity Relationships
Nivinskas, H., Staskeviciene, S. Sarlauskas, J., Koder, R.L., Miller, A.-F., Cenas, N. (2002) Arch. Biochem. Biophys. 403, 249-258
Structures of Nitroreductase in Three States: Effects of Inhibitor Binding and Reduction
Haynes, C.A., Koder, R.L., Miller, A.-F., Rodgers, D.W. (2002) J. Biol. Chem. 277, 11513-11520