☰

Ronald L. Koder - Publications

Affiliations: 
Physics City University of New York, New York, NY, United States 
Area:
General Physics, General Biophysics
Tree Info Similar researchers PubMed Report error

49 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Zhang L, Brown MC, Mutter AC, Greenland KN, Cooley JW, Koder RL. Protein dynamics govern the oxyferrous state lifetime of an artificial oxygen transport protein. Biophysical Journal. PMID 37865818 DOI: 10.1016/j.bpj.2023.10.022  0.759
2023 McGuinness KN, Fehon N, Feehan R, Miller M, Mutter AC, Rybak LA, Nam J, AbuSalim JE, Atkinson JT, Heidari H, Losada N, Kim JD, Koder RL, Lu Y, Silberg JJ, et al. The energetics and evolution of oxidoreductases in deep time. Proteins. PMID 37596815 DOI: 10.1002/prot.26563  0.75
2023 Hutchins GH, Noble CEM, Bunzel HA, Williams C, Dubiel P, Yadav SKN, Molinaro PM, Barringer R, Blackburn H, Hardy BJ, Parnell AE, Landau C, Race PR, Oliver TAA, Koder RL, et al. An expandable, modular de novo protein platform for precision redox engineering. Proceedings of the National Academy of Sciences of the United States of America. 120: e2306046120. PMID 37487099 DOI: 10.1073/pnas.2306046120  0.322
2021 Horoszko CP, Schnatz PJ, Budhathoki-Uprety J, Rao-Pothuraju RV, Koder RL, Heller DA. Non-Covalent Coatings on Carbon Nanotubes Mediate Photosensitizer Interactions. Acs Applied Materials & Interfaces. PMID 34672190 DOI: 10.1021/acsami.1c14266  0.747
2020 Schnatz PJ, Brisendine JM, Laing CC, Everson BH, French CA, Molinaro PM, Koder RL. Designing heterotropically activated allosteric conformational switches using supercharging. Proceedings of the National Academy of Sciences of the United States of America. PMID 32098845 DOI: 10.1073/Pnas.1916046117  0.788
2019 Koder RL, Schnatz PJ, Brisendine J, Liang C, Everson BH, French C. A General Method to Design Allosteric Conformational Switches Biophysical Journal. 116: 164a. DOI: 10.1016/J.Bpj.2018.11.910  0.75
2019 Preston J, Everson B, Giroud F, Vinyard D, Greenland K, Bjerkefeldt E, Minteer S, Brudvig G, Koder R. Engendering Catalytic Activity by Increasing Dynamics in a Designed Enzyme Biophysical Journal. 116: 68a. DOI: 10.1016/J.Bpj.2018.11.411  0.747
2018 Greenland KN, Carvajal MFCA, Preston J, Ekblad S, Dean WL, Chiang JY, Koder RL, Wittebort RJ. Order, Disorder and Temperature-Driven Compaction in a Designed Elastin Protein. The Journal of Physical Chemistry. B. PMID 29461832 DOI: 10.1021/Acs.Jpcb.7B11596  0.374
2018 Schnatz PJ, Brisendine JM, Koder RL. Supercharging as a General Strategy for Making Proteins into Conformational Switches and their Use in Biosensing Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.3218  0.36
2018 Koder RL, Preston JM, Everson BH, Bjerkefeldt E, Macazo FC, Giroud F, Minteer SD, Vinyard DJ, Brudvig GW. Engendering Methane Monooxygenase and Hydrogen Peroxide Oxidase Activity into a Designed Dimetal Protein by Increasing Protein Dynamics Biophysical Journal. 114: 411a. DOI: 10.1016/J.Bpj.2017.11.2276  0.775
2017 Pitsawong W, Haynes CA, Koder RL, Rodgers DW, Miller AF. Mechanism-Informed Refinement Reveals Altered Substrate-Binding Mode for Catalytically Competent Nitroreductase. Structure (London, England : 1993). PMID 28578873 DOI: 10.1016/J.Str.2017.05.002  0.331
2017 Gunner MR, Koder R. The design features cells use to build their transmembrane proton gradient. Physical Biology. 14: 013001. PMID 28169227 DOI: 10.1088/1478-3975/14/1/013001  0.353
2017 Brown MC, Greenland K, Zhang L, Koder RL. Designed Enzymes and the Driving Forces Behind Interdomain Electron Transfer Biophysical Journal. 112: 66. DOI: 10.1016/J.Bpj.2016.11.394  0.409
2017 Schnatz P, Brisendine J, Kosciolek D, Crouse D, Koder R. Design of Supercharged Proteins to Impart Allosteric Behavior and their Use in Biosensing Biophysical Journal. 112: 510a. DOI: 10.1016/J.Bpj.2016.11.2758  0.418
2017 Koder RL, Everson B, Zhang L, Preston J, Bjerkefeldt E. Optimizing Protein Dynamics in Metalloenzyme Design Biophysical Journal. 112: 193a. DOI: 10.1016/J.Bpj.2016.11.1072  0.765
2015 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. Biochimica Et Biophysica Acta. PMID 26498191 DOI: 10.1016/J.Bbabio.2015.10.002  0.472
2015 Andersen EM, Koder RL, Mutter AC. Photosynthesis in a Single Protein Biophysical Journal. 108: 605a. DOI: 10.1016/J.Bpj.2014.11.3297  0.757
2014 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. Journal of Structural Biology. 185: 178-85. PMID 23827257 DOI: 10.1016/J.Bpj.2012.11.3785  0.766
2014 Raju G, Singh S, Mutter AC, Everson BH, Cerda JF, Koder RL. An extended scope synthesis of an artificial safranine cofactor Tetrahedron Letters. 55: 2487-2491. DOI: 10.1016/J.Tetlet.2014.03.010  0.708
2013 Brown MC, Mutter A, Koder RL, JiJi RD, Cooley JW. Observation of persistent α-helical content and discrete types of backbone disorder during a molten globule to ordered peptide transition via deep-UV resonance Raman spectroscopy. Journal of Raman Spectroscopy : Jrs. 44: 957-962. PMID 27795611 DOI: 10.1002/Jrs.4316  0.756
2013 Brisendine JM, Mutter AC, Cerda JF, Koder RL. A three-dimensional printed cell for rapid, low-volume spectroelectrochemistry. Analytical Biochemistry. 439: 1-3. PMID 23583818 DOI: 10.1016/J.Ab.2013.03.036  0.714
2013 Zhang L, Andersen EM, Khajo A, Magliozzo RS, Koder RL. Dynamic factors affecting gaseous ligand binding in an artificial oxygen transport protein. Biochemistry. 52: 447-55. PMID 23249163 DOI: 10.1021/Bi301066Z  0.412
2013 Everson BH, French CA, Mutter AC, Nanda V, Koder RL. Hemoprotein Design using Minimal Sequence Information Biophysical Journal. 104: 661a. DOI: 10.1016/J.Bpj.2012.11.3649  0.734
2013 Koder RL, Raju G, Brisendine J, Nanda V. An Artificial Safranine Enzyme which Activates Chemotherapeutic Prodrugs Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.1155  0.56
2013 Brown MC, Mutter AC, Koder RL, Jiji RD, Cooley JW. Observation of persistent α-helical content and discrete types of backbone disorder during a molten globule to ordered peptide transition via deep-UV resonance Raman spectroscopy Journal of Raman Spectroscopy. 44: 957-962. DOI: 10.1002/jrs.4316  0.695
2012 Raju G, Capo J, Lichtenstein BR, Cerda JF, Koder RL. Manipulating Reduction Potentials in an Artificial Safranin Cofactor. Tetrahedron Letters. 53: 1201-1203. PMID 23335821 DOI: 10.1016/J.Tetlet.2011.12.028  0.56
2012 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. 7: e36065. PMID 22675467 DOI: 10.1371/Journal.Pone.0036065  0.747
2012 Punnoose A, McConnell LA, Liu W, Mutter AC, Koder RL. Correction: Fundamental Limits on Wavelength, Efficiency and Yield of the Charge Separation Triad Plos One. 7. DOI: 10.1371/Annotation/7Db1B9Ef-C93C-4B02-B721-A8473D2Bb4E2  0.704
2012 Brown M, Cooley J, JiJi R, Koder R, Mutter A. Persistent α-Helical Content and Local Helical Structural Fluctuations from a Molten Globule to Ordered Peptide Transition Biophysical Journal. 102: 444a. DOI: 10.1016/J.Bpj.2011.11.2432  0.765
2011 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. 50: 10254-61. PMID 22004125 DOI: 10.1021/Bi201242A  0.763
2011 Rodriguez-Granillo A, Annavarapu S, Zhang L, Koder RL, Nanda V. Computational design of thermostabilizing D-amino acid substitutions. Journal of the American Chemical Society. 133: 18750-9. PMID 21978298 DOI: 10.1021/Ja205609C  0.35
2011 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. 79: 463-76. PMID 21117078 DOI: 10.1002/Prot.22895  0.393
2010 Nanda V, Koder RL. Designing artificial enzymes by intuition and computation. Nature Chemistry. 2: 15-24. PMID 21124375 DOI: 10.1038/Nchem.473  0.384
2010 Xu F, Zhang L, Koder RL, Nanda V. De novo self-assembling collagen heterotrimers using explicit positive and negative design. Biochemistry. 49: 2307-16. PMID 20170197 DOI: 10.1021/Bi902077D  0.367
2009 Koder RL, Anderson JL, Solomon LA, Reddy KS, Moser CC, Dutton PL. Design and engineering of an O(2) transport protein. Nature. 458: 305-9. PMID 19295603 DOI: 10.1038/Nature07841  0.4
2009 Negron C, Fufezan C, Koder RL. Geometric constraints for porphyrin binding in helical protein binding sites. Proteins. 74: 400-16. PMID 18636480 DOI: 10.1002/Prot.22143  0.432
2008 Anderson JL, Koder RL, Moser CC, Dutton PL. Controlling complexity and water penetration in functional de novo protein design. Biochemical Society Transactions. 36: 1106-11. PMID 19021506 DOI: 10.1042/Bst0361106  0.401
2006 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. Journal of the American Chemical Society. 128: 14450-1. PMID 17090015 DOI: 10.1021/ja064883r  0.32
2006 Koder RL, Dutton PL. Intelligent design: the de novo engineering of proteins with specified functions. Dalton Transactions (Cambridge, England : 2003). 3045-51. PMID 16786062 DOI: 10.1039/B514972J  0.406
2004 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. Proceedings of the National Academy of Sciences of the United States of America. 101: 5536-41. PMID 15056758 DOI: 10.1073/Pnas.0306676101  0.442
2003 Discher BM, Koder RL, Moser CC, Dutton PL. Hydrophilic to amphiphilic design in redox protein maquettes. Current Opinion in Chemical Biology. 7: 741-8. PMID 14644184 DOI: 10.1016/J.Cbpa.2003.10.013  0.403
2002 Koder RL, Haynes CA, Rodgers ME, Rodgers DW, Miller AF. Flavin thermodynamics explain the oxygen insensitivity of enteric nitroreductases Biochemistry. 41: 14197-14205. PMID 12450383 DOI: 10.1021/Bi025805T  0.336
2002 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. Archives of Biochemistry and Biophysics. 403: 249-58. PMID 12139974 DOI: 10.1016/S0003-9861(02)00228-X  0.332
2002 Haynes CA, Koder RL, Miller AF, Rodgers DW. Structures of nitroreductase in three states. Effects of inhibitor binding and reduction Journal of Biological Chemistry. 277: 11513-11520. PMID 11805110 DOI: 10.1074/Jbc.M111334200  0.336
2001 Nivinskas H, Koder RL, Anusevičius Z, Šarlauskas J, Miller AF, Čenas N. Quantitative structure-activity relationships in two-electron reduction of nitroaromatic compounds by Enterobacter cloacae NAD(P)H:nitroreductase Archives of Biochemistry and Biophysics. 385: 170-178. PMID 11361014 DOI: 10.1006/Abbi.2000.2127  0.309
2000 Nivinskas H, Koder RL, Anusevičius Z, Šarlauskas J, Miller AF, Čenas N. Two-electron reduction of nitroaromatic compounds by Enterobacter cloacae NAD(P)H nitroreductase: Description of quantitative structure-activity relationships Acta Biochimica Polonica. 47: 941-949. PMID 11996117 DOI: 10.18388/Abp.2000_3949  0.304
1998 Koder RL, Miller AF. Steady-state kinetic mechanism, stereospecificity, substrate and inhibitor specificity of Enterobacter cloacae nitroreductase Biochimica Et Biophysica Acta - Protein Structure and Molecular Enzymology. 1387: 395-405. PMID 9748656 DOI: 10.1016/S0167-4838(98)00151-4  0.313
1998 Koder RL, Miller AF. Overexpression, isotopic labeling, and spectral characterization of Enterobacter cloacae nitroreductase Protein Expression and Purification. 13: 53-60. PMID 9631515 DOI: 10.1006/Prep.1997.0866  0.336
1994 Beecher BS, Koder RL, Tipton PA. Tartrate dehydrogenase-oxalate complexes: formation of a stable analog of a reaction intermediate complex. Archives of Biochemistry and Biophysics. 315: 255-61. PMID 7986065 DOI: 10.1006/Abbi.1994.1497  0.338
Show low-probability matches.