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Ronald Koder
Title Associate Professor
Faculty Rank Associate Professor
Degree Ph.D.
Institution City College, CUNY
Department Physics
Clusters Cancer
Address
160 Convent Ave CDI11308
City New York
State NY
Postal Code 10031
Telephone 212-650-5583
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Title Associate Professor
Institution The City College of New York
Department Physics
Division Biophysics

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2013 The City College of New York James L. Peace Chair in Physics

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  Work in my laboratory lies at the crossroads of synthetic biology and nanotechnology. Our research projects primarily involve renewable energy production and human health. We use the principles of protein design to create new bioinorganic components, not yet observed in nature, to further extend the possibilities of synthetic biology. These often contain synthetic, non-natural bioinorganic cofactors tailored for their intended purpose. The goal is to fashion protein domains which are clean, modular and ready for assembly into higher order nanostructures with emergent properties. There are a number of related projects underway:

1. Designed proteins for solar energy conversion
The development of artificial photosynthesis – i.e. the production of liquid fuels with only sunlight, water, and CO2 – is the Manhattan Project of our age. We are creating self-assembling artificial reaction centers capable of being modularly attached to a variety of catalysts - protein, synthetic chemical catalysts and nanomaterials, in order to catalyze high-energy fuels with light. Projects include:
-Creating an artificial reaction center
-Creation and optimization of an artificial oxygen evolving protein
-Engineering a photosynthetic E.coli
-Light-driven biofuel generation – solar driven metabolic pathways on hybrid metamaterials
-Single molecule electronics
-Self-assembling antireflective biocoatings

2. Designed protein therapeutics.
Protein design has advanced to the point where several groups are working on therapeutics. My group has been working on several flavors of therapeutics, in particular battlefield blood substitutes and chemotherapeutics. Projects include:
-Designed proteins as optimized oxygen carriers for artificial blood
-An artificial nitric oxide dioxygenase as a chemotherapuetic
-Safranine-based nitroaromatic prodrug-activating enzymes
-Supercharged phase-changing proteins for the detection of cancer


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1. Greenland KN, Carvajal MFCA, Preston JM, Ekblad S, Dean WL, Chiang JY, Koder RL, Wittebort RJ. Order, Disorder, and Temperature-Driven Compaction in a Designed Elastin Protein. J Phys Chem B. 2018 03 15; 122(10):2725-2736.
2. Brisendine JM, Refaely-Abramson S, Liu ZF, Cui J, Ng F, Neaton JB, Koder RL, Venkataraman L. Probing Charge Transport through Peptide Bonds. J Phys Chem Lett. 2018 Feb 15; 9(4):763-767.
3. Pitsawong W, Haynes CA, Koder RL, Rodgers DW, Miller AF. Mechanism-Informed Refinement Reveals Altered Substrate-Binding Mode for Catalytically Competent Nitroreductase. Structure. 2017 07 05; 25(7):978-987.e4.
4. Gunner MR, Koder R. The design features cells use to build their transmembrane proton gradient. Phys Biol. 2017 Feb 07; 14(1):013001.
5. Brisendine JM, Koder RL. Fast, cheap and out of control--Insights into thermodynamic and informatic constraints on natural protein sequences from de novo protein design. Biochim Biophys Acta. 2016 May; 1857(5):485-492.
6. Mutter AC, Norman JA, Tiedemann MT, Singh S, Sha S, Morsi S, Ahmed I, Stillman MJ, Koder RL. Rational design of a zinc phthalocyanine binding protein. J Struct Biol. 2014 Feb; 185(2):178-85.
7. Brown MC, Mutter A, Koder RL, JiJi RD, Cooley JW. Observation of persistent a-helical content and discrete types of backbone disorder during a molten globule to ordered peptide transition via deep-UV resonance Raman spectroscopy. J Raman Spectrosc. 2013 Jul; 44(7):957-962.
8. Brisendine JM, Mutter AC, Cerda JF, Koder RL. A three-dimensional printed cell for rapid, low-volume spectroelectrochemistry. Anal Biochem. 2013 Aug 01; 439(1):1-3.
9. Zhang L, Andersen EM, Khajo A, Magliozzo RS, Koder RL. Dynamic factors affecting gaseous ligand binding in an artificial oxygen transport protein. Biochemistry. 2013 Jan 22; 52(3):447-55.
10. Punnoose A, McConnell LA, McConnell L, Liu W, Mutter AC, Koder RL, Koder R. Fundamental limits on wavelength, efficiency and yield of the charge separation triad. PLoS One. 2012; 7(6):e36065.
11. Raju G, Capo J, Lichtenstein BR, Cerda JF, Koder RL. Manipulating Reduction Potentials in an Artificial Safranin Cofactor. Tetrahedron Lett. 2012 Mar 07; 53(10):1201-1203.
12. Zhang L, Anderson JL, Ahmed I, Norman JA, Negron C, Mutter AC, Dutton PL, Koder RL. Manipulating cofactor binding thermodynamics in an artificial oxygen transport protein. Biochemistry. 2011 Nov 29; 50(47):10254-61.
13. Rodriguez-Granillo A, Annavarapu S, Zhang L, Koder RL, Nanda V. Computational design of thermostabilizing D-amino acid substitutions. J Am Chem Soc. 2011 Nov 23; 133(46):18750-9.
14. Cui D, Koder RL, Dutton PL, Miller AF. 15N solid-state NMR as a probe of flavin H-bonding. J Phys Chem B. 2011 Jun 23; 115(24):7788-98.
15. Braun P, Goldberg E, Negron C, von Jan M, Xu F, Nanda V, Koder RL, Noy D. Design principles for chlorophyll-binding sites in helical proteins. Proteins. 2011 Feb; 79(2):463-76.
16. Xu F, Zhang L, Koder RL, Nanda V. De novo self-assembling collagen heterotrimers using explicit positive and negative design. Biochemistry. 2010 Mar 23; 49(11):2307-16.
17. Nanda V, Koder RL. Designing artificial enzymes by intuition and computation. Nat Chem. 2010 Jan; 2(1):15-24.
18. Koder RL, Anderson JL, Solomon LA, Reddy KS, Moser CC, Dutton PL. Design and engineering of an O(2) transport protein. Nature. 2009 Mar 19; 458(7236):305-9.
19. Negron C, Fufezan C, Koder RL. Geometric constraints for porphyrin binding in helical protein binding sites. Proteins. 2009 Feb 01; 74(2):400-16.
20. Anderson JL, Koder RL, Moser CC, Dutton PL. Controlling complexity and water penetration in functional de novo protein design. Biochem Soc Trans. 2008 Dec; 36(Pt 6):1106-11.
21. Lichtenstein BR, Cerda JF, Koder RL, Dutton PL. Reversible proton coupled electron transfer in a peptide-incorporated naphthoquinone amino acid. Chem Commun (Camb). 2009 Jan 08; (2):168-70.
22. Cerda JF, Koder RL, Lichtenstein BR, Moser CM, Miller AF, Dutton PL. Hydrogen bond-free flavin redox properties: managing flavins in extreme aprotic solvents. Org Biomol Chem. 2008 Jun 21; 6(12):2204-12.
23. Koder RL, Lichtenstein BR, Cerda JF, Miller AF, Dutton PL. A Flavin Analogue with Improved Solubility in Organic Solvents. Tetrahedron Lett. 2007 Jul 30; 48(31):5517-5520.
24. Koder RL, Walsh JD, Pometun MS, Dutton PL, Wittebort RJ, Miller AF. 15N solid-state NMR provides a sensitive probe of oxidized flavin reactive sites. J Am Chem Soc. 2006 Nov 29; 128(47):15200-8.
25. Koder RL, Valentine KG, Cerda J, Noy D, Smith KM, Wand AJ, Dutton PL. Nativelike structure in designed four alpha-helix bundles driven by buried polar interactions. J Am Chem Soc. 2006 Nov 15; 128(45):14450-1.
26. Koder RL, Dutton PL. Intelligent design: the de novo engineering of proteins with specified functions. Dalton Trans. 2006 Jul 07; (25):3045-51.
27. Huang SS, Koder RL, Lewis M, Wand AJ, Dutton PL. The HP-1 maquette: from an apoprotein structure to a structured hemoprotein designed to promote redox-coupled proton exchange. Proc Natl Acad Sci U S A. 2004 Apr 13; 101(15):5536-41.
28. Discher BM, Koder RL, Moser CC, Dutton PL. Hydrophilic to amphiphilic design in redox protein maquettes. Curr Opin Chem Biol. 2003 Dec; 7(6):741-8.
29. Koder RL, Haynes CA, Rodgers ME, Rodgers DW, Miller AF. Flavin thermodynamics explain the oxygen insensitivity of enteric nitroreductases. Biochemistry. 2002 Dec 03; 41(48):14197-205.
30. Nivinskas H, Staskeviciene S, Sarlauskas J, Koder RL, Miller AF, Cenas N. Two-electron reduction of quinones by Enterobacter cloacae NAD(P)H:nitroreductase: quantitative structure-activity relationships. Arch Biochem Biophys. 2002 Jul 15; 403(2):249-58.
31. Haynes CA, Koder RL, Miller AF, Rodgers DW. Structures of nitroreductase in three states: effects of inhibitor binding and reduction. J Biol Chem. 2002 Mar 29; 277(13):11513-20.
32. Koder RL, Oyedele O, Miller AF. Retro-nitroreductase, a putative evolutionary precursor to Enterobacter cloacae strain 96-3 nitroreductase. Antioxid Redox Signal. 2001 Oct; 3(5):747-55.
33. Nivinskas H, Koder RL, Anusevicius Z, Sarlauskas J, Miller AF, Cenas N. Quantitative structure-activity relationships in two-electron reduction of nitroaromatic compounds by Enterobacter cloacae NAD(P)H:nitroreductase. Arch Biochem Biophys. 2001 Jan 01; 385(1):170-8.
34. Schwartz AL, Yikilmaz E, Vance CK, Vathyam S, Koder RL, Miller AF. Mutational and spectroscopic studies of the significance of the active site glutamine to metal ion specificity in superoxide dismutase. J Inorg Biochem. 2000 Jul 01; 80(3-4):247-56.
35. Nivinskas H, Koder RL, Anusevicius Z, Sarlauskas J, Miller AF, Cenas N. Two-electron reduction of nitroaromatic compounds by Enterobacter cloacae NAD(P)H nitroreductase: description of quantitative structure-activity relationships. Acta Biochim Pol. 2000; 47(4):941-9.
36. Koder RL, Miller AF. Steady-state kinetic mechanism, stereospecificity, substrate and inhibitor specificity of Enterobacter cloacae nitroreductase. Biochim Biophys Acta. 1998 Sep 08; 1387(1-2):395-405.
37. Koder RL, Miller AF. Overexpression, isotopic labeling, and spectral characterization of Enterobacter cloacae nitroreductase. Protein Expr Purif. 1998 Jun; 13(1):53-60.
38. Beecher BS, Koder RL, Tipton PA. Tartrate dehydrogenase-oxalate complexes: formation of a stable analog of a reaction intermediate complex. Arch Biochem Biophys. 1994 Dec; 315(2):255-61.

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