Ronald Koder

Assistant Professor

Physics

Tel. (212) 650-5583
Fax: (212) 650-6940
E-mail: koder[at]sci.ccny.cuny.edu

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

Research

Synthetic Biologists are re-imagining the proteins that do the work of living cells as small modular devices, similar to electronic components like resistors and capacitors, that can be reassembled into novel biological functions and systems – much like electrical engineers assemble large numbers of simple electronic components into devices like computers and cellular phones. This is a significant change in the biological paradigm, and it will have as large an effect on people’s everyday lives decades from now as the development of molecular biology twenty years ago is having on our lives today.

Like the physicists of the 40s and 50s, who were focused on the design of simple electronic components like transistors and diodes, my lab uses the principles of protein design to create new biological components, not yet observed in nature, to further extend the possibilities of synthetic biology. Starting from scratch, we create novel proteins that offer new functions or physical properties and then integrate them with natural proteins, other designed proteins or non-protein materials to create new biomaterials with applications in medicine, ‘green’ industrial catalysis and green energy production.

One central idea in our work derives from the knowledge that, as these proteins are non-natural, they can be made to utilize non-natural cofactors specifically tailored for their intended function. Thus a portion of the lab works on designing and synthesizing new protein cofactors. All of the work in my lab is based on NMR analysis: screening designs for structure and stability, solving three-dimensional structures of proteins for the purpose of improving their stability and activity, and analyzing the electronic structures of bound cofactors.

The current thrusts of our research aim at creating new enzyme-based cancer therapies and protein based biological solar energy devices – ‘green’ solar panels. We believe that this novel combination - proteins designed de novo coupled with naturally occurring proteins - will enable us to move beyond the confines of biology and help us to solve many of mankind’s problems.

There are three projects currently underway in my lab:

1) Creating a protein-based photovoltaic device

2) Designed enzymes for the treatment of cancer

3) Methods development for cofactor-binding protein design

Selected Publications (full listing)

Zheng, L., Ahmed, I., Anderson, J.R.L., Norman, J.N., Negron, C., Dutton, P.L., Koder, R.L. Heme-Binding Thermodynamics in an Artificial Neuroglobin (2009) In preparation

Koder, R.L., Nanda, V. Designing Artificial Enzymes by Intuition and Computation (2009) Nature Chemistry In press

Koder, R.L.*, Anderson, J.L.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 link

Good commentary on this paper in the science blog Metamodern.

Negron, C., Fufezon, C., Koder, R.L. Geometric Constraints for Porphyrin Binding in Helical Protein Binding Sites (2009) Proteins: Struct. Func. Bioinf. 74:400-416 PDF

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 PDF

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 PDF

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

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 PDF

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 PDF