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1

Hydrophilic to amphiphilic design in redox protein maquettes

Bohdana M Discher, Ronald L Koder, Christopher C Moser, P Leslie Dutton

Journal:

Current Opinion in Chemical Biology

Year:

2003

Language:

english

File:

PDF, 236 KB

english, 2003

2

PPARγ Is Required for Placental, Cardiac, and Adipose Tissue Development

Yaacov Barak, Michael C Nelson, Estelita S Ong, Ying Z Jones, Pilar Ruiz-Lozano, Kenneth R Chien, Alan Koder, Ronald M Evans

Journal:

Year:

1999

Language:

english

File:

PDF, 912 KB

english, 1999

3

A General Method to Design Allosteric Conformational Switches

Koder, Ronald L., Schnatz, Peter J., Brisendine, Joseph, Liang, Craig, Everson, Bernard H., French, Cooper

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 46 KB

english, 2019

4

Designing heterotropically activated allosteric conformational switches using supercharging

Schnatz, Peter J., Brisendine, Joseph M., Laing, Craig C., Everson, Bernard H., French, Cooper A., Molinaro, Paul M., Koder, Ronald L.

Journal:

Proceedings of the National Academy of Sciences

Year:

2020

File:

PDF, 1.50 MB

2020

5

A flavin analogue with improved solubility in organic solvents

Ronald L. Koder, Bruce R. Lichtenstein, Jose F. Cerda, Anne-Frances Miller, P. Leslie Dutton

Journal:

Tetrahedron Letters

Year:

2007

Language:

english

File:

PDF, 160 KB

english, 2007

6

Geometric constraints for porphyrin binding in helical protein binding sites

Christopher Negron, Christian Fufezan, Ronald L. Koder

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 433 KB

english, 2009

7

Design principles for chlorophyll-binding sites in helical proteins

Paula Braun, Eran Goldberg, Christopher Negron, Mathias von Jan, Fei Xu, Vikas Nanda, Ronald L. Koder, Dror Noy

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 2.55 MB

english, 2011

8

Corrigendum to: “Mutational and spectroscopic studies of the significance of the active site glutamine to metal ion specificity in superoxide dismutase [Journal of Inorganic Biochemistry 80 (2000) 247]”

Aaron L. Schwartz, Emine Yikilmaz, Carrie K. Vance, Surekha Vathyam, Ronald L. Koder, Anne-Frances Miller

Journal:

Journal of Inorganic Biochemistry

Year:

2008

Language:

english

File:

PDF, 66 KB

english, 2008

9

Mutational and spectroscopic studies of the significance of the active site glutamine to metal ion specificity in superoxide dismutase

Aaron L. Schwartz, Emine Yikilmaz, Carrie K. Vance, Surekha Vathyam, Ronald L. Koder, Anne-Frances Miller

Journal:

Journal of Inorganic Biochemistry

Year:

2000

Language:

english

File:

PDF, 351 KB

english, 2000

10

Design and engineering of an O2 transport protein

Koder, Ronald L., Anderson, J. L. Ross, Solomon, Lee A., Reddy, Konda S., Moser, Christopher C., Dutton, P. Leslie

Journal:

Year:

2009

Language:

english

File:

PDF, 1.15 MB

english, 2009

11

Designing artificial enzymes by intuition and computation

Nanda, Vikas, Koder, Ronald L.

Journal:

Nature Chemistry

Year:

2009

Language:

english

File:

PDF, 1.28 MB

english, 2009

12

Intelligent design: the de novo engineering of proteins with specified functions

Koder, Ronald L., Dutton, P. Leslie

Journal:

Dalton Transactions

Year:

2006

Language:

english

File:

PDF, 358 KB

english, 2006

13

Manipulating reduction potentials in an artificial safranin cofactor

Gheevarghese Raju, Joseph Capo, Bruce R. Lichtenstein, Jose F. Cerda, Ronald L. Koder

Journal:

Tetrahedron Letters

Year:

2012

Language:

english

File:

PDF, 228 KB

english, 2012

14

Steady-state kinetic mechanism, stereospecificity, substrate and inhibitor specificity of Enterobacter cloacae nitroreductase

Ronald L. Koder, Anne-Frances Miller

Journal:

Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology

Year:

1998

Language:

english

File:

PDF, 302 KB

english, 1998

15

Quantitative Structure–Activity Relationships in Two-Electron Reduction of Nitroaromatic Compounds by Enterobacter cloacae NAD(P)H:Nitroreductase

Henrikas Nivinskas, Ronald L. Koder, Žilvinas Anusevičius, Jonas Šarlauskas, Anne-Frances Miller, Narimantas Č≐nas

Journal:

Archives of Biochemistry and Biophysics

Year:

2001

Language:

english

File:

PDF, 117 KB

english, 2001

16

Overexpression, Isotopic Labeling, and Spectral Characterization ofEnterobacter cloacaeNitroreductase

Ronald L. Koder, Anne-Frances Miller

Journal:

Protein Expression and Purification

Year:

1998

Language:

english

File:

PDF, 178 KB

english, 1998

17

Two-electron reduction of quinones by Enterobacter cloacae NAD(P)H:nitroreductase: quantitative structure-activity relationships

Henrikas Nivinskas, Sigita Staškevičien≐, Jonas Šarlauskas, Ronald L. Koder, Anne-Frances Miller, Narimantas Č≐nas

Journal:

Archives of Biochemistry and Biophysics

Year:

2002

Language:

english

File:

PDF, 199 KB

english, 2002

18

Hydrogen bond-free flavin redox properties: managing flavins in extreme aprotic solvents

Cerda, Jose F., Koder, Ronald L., Lichtenstein, Bruce R., Moser, Christopher M., Miller, Anne-Frances, Dutton, P. Leslie

Journal:

Organic & Biomolecular Chemistry

Year:

2008

Language:

english

File:

PDF, 231 KB

english, 2008

19

Rational design of a zinc phthalocyanine binding protein

Mutter, Andrew C., Norman, Jessica A., Tiedemann, Michael T., Singh, Sunaina, Sha, Sha, Morsi, Sara, Ahmed, Ismail, Stillman, Martin J., Koder, Ronald L.

Journal:

Journal of Structural Biology

Year:

2014

Language:

english

File:

PDF, 1.49 MB

english, 2014

20

An extended scope synthesis of an artificial safranine cofactor

Raju, Gheevarghese, Singh, Sunaina, Mutter, Andrew C., Everson, Bernard H., Cerda, Jose F., Koder, Ronald L.

Journal:

Tetrahedron Letters

Year:

2014

Language:

english

File:

PDF, 538 KB

english, 2014

21

Persistent α-Helical Content and Local Helical Structural Fluctuations from a Molten Globule to Ordered Peptide Transition

Brown, Mia, Cooley, Jason, JiJi, Renee, Koder, Ronald, Mutter, Andrew

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 40 KB

english, 2012

22

Rational Design of a Zinc Phthalocyanine Binding Protein

Mutter, Andrew C., Koder, Ronald L., Singh, Sunaina, Norman, Jessica A.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 35 KB

english, 2013

23

A three-dimensional printed cell for rapid, low-volume spectroelectrochemistry

Brisendine, Joseph M., Mutter, Andrew C., Cerda, Jose F., Koder, Ronald L.

Journal:

Analytical Biochemistry

Year:

2013

Language:

english

File:

PDF, 460 KB

english, 2013

24

Hemoprotein Design using Minimal Sequence Information

Everson, Bernard H., French, Cooper A., Mutter, Andrew C., Nanda, Vikas, Koder, Ronald L.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 55 KB

english, 2013

25

An Artificial Safranine Enzyme which Activates Chemotherapeutic Prodrugs

Koder, Ronald L., Raju, Gheevarghese, Brisendine, Joseph, Nanda, Vikas

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 54 KB

english, 2013

26

Nativelike Structure in Designed Four α-Helix Bundles Driven by Buried Polar Interactions

Koder, Ronald L., Valentine, Kathleen G., Cerda, Jose, Noy, Dror, Smith, Kevin M., Wand, A. Joshua, Dutton, P. Leslie

Journal:

Journal of the American Chemical Society

Year:

2006

Language:

english

File:

PDF, 104 KB

english, 2006

27

Flavin Thermodynamics Explain the Oxygen Insensitivity of Enteric Nitroreductases †

Koder, Ronald L., Haynes, Chad A., Rodgers, Michael E., Rodgers, David W., Miller, Anne-Frances

Journal:

Year:

2002

Language:

english

File:

PDF, 198 KB

english, 2002

28

15 N Solid-State NMR as a Probe of Flavin H-Bonding

Cui, Dongtao, Koder, Ronald L., Dutton, P. Leslie, Miller, Anne-Frances

Journal:

Journal of Physical Chemistry B

Year:

2011

Language:

english

File:

PDF, 2.33 MB

english, 2011

29

Computational Design of Thermostabilizing d -Amino Acid Substitutions

Rodriguez-Granillo, Agustina, Annavarapu, Srinivas, Zhang, Lei, Koder, Ronald L., Nanda, Vikas

Journal:

Journal of the American Chemical Society

Year:

2011

Language:

english

File:

PDF, 4.87 MB

english, 2011

30

Manipulating Cofactor Binding Thermodynamics in an Artificial Oxygen Transport Protein

Zhang, Lei, Anderson, J. L. Ross, Ahmed, Ismail, Norman, Jessica A., Negron, Christopher, Mutter, Andrew C., Dutton, P. Leslie, Koder, Ronald L.

Journal:

Year:

2011

Language:

english

File:

PDF, 1.13 MB

english, 2011

31

De Novo Self-Assembling Collagen Heterotrimers Using Explicit Positive and Negative Design

Xu, Fei, Zhang, Lei, Koder, Ronald L., Nanda, Vikas

Journal:

Year:

2010

Language:

english

File:

PDF, 2.22 MB

english, 2010

32

Dynamic Factors Affecting Gaseous Ligand Binding in an Artificial Oxygen Transport Protein

Zhang, Lei, Andersen, Eskil M. E., Khajo, Abdelahad, Magliozzo, Richard S., Koder, Ronald L.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.41 MB

english, 2013

33

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

Brown, Mia C., Mutter, Andrew C., Koder, Ronald L., JiJi, Renee D., Cooley, Jason W.

Journal:

Journal of Raman Spectroscopy

Year:

2013

Language:

english

File:

PDF, 616 KB

english, 2013

34

Retro-Nitroreductase, a Putative Evolutionary Precursor to Enterobacter cloacae Strain 96-3 Nitroreductase

Koder, Ronald L., Oyedele, Omolara, Miller, Anne-Frances

Journal:

Antioxidants & Redox Signaling

Year:

2001

Language:

english

File:

PDF, 332 KB

english, 2001

35

Photosynthesis in a Single Protein

Andersen, Eskil M., Koder, Ronald L., Mutter, Andrew C.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 45 KB

english, 2015

36

Fast, cheap and out of control - insights into thermodynamic and informatic constraints on natural protein sequences from de novo protein design

Brisendine, J.M., Koder, Ronald L.

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2015

Language:

english

File:

PDF, 587 KB

english, 2015

37

SPIE Proceedings [SPIE SPIE Commercial + Scientific Sensing and Imaging - Baltimore, Maryland, United States (Sunday 17 April 2016)] Advanced Environmental, Chemical, and Biological Sensing Technologies XIII - Handheld chem/biosensor using extreme conformational changes in designed binding proteins to enhance surface plasmon resonance (SPR)

Vo-Dinh, Tuan, Lieberman, Robert A., Gauglitz, Günter G., Lepak, Lori A., Schnatz, Peter, Bendoym, Igor, Kosciolek, Derek, Koder, Ronald, Crouse, David T.

Year:

2016

Language:

english

File:

PDF, 946 KB

english, 2016

38

15 N Solid-State NMR Provides a Sensitive Probe of Oxidized Flavin Reactive Sites

Koder,, Ronald L., Walsh, Joseph D., Pometun, Maxim S., Dutton, P. Leslie, Wittebort, Richard J., Miller, Anne-Frances

Journal:

Journal of the American Chemical Society

Year:

2006

Language:

english

File:

PDF, 215 KB

english, 2006

39

ChemInform Abstract: An Extended Scope Synthesis of an Artificial Safranine Cofactor.

Raju, Gheevarghese, Singh, Sunaina, Mutter, Andrew C., Everson, Bernard H., Cerda, Jose F., Koder, Ronald L.

Journal:

Year:

2014

File:

PDF, 15 KB

2014

40

Controlling complexity and water penetration in functional de novo protein design

Anderson, J.L. Ross, Koder, Ronald L., Moser, Christopher C., Dutton, P. Leslie

Journal:

Biochemical Society Transactions

Year:

2008

Language:

english

File:

PDF, 493 KB

english, 2008

41

Designed Enzymes and the Driving Forces Behind Interdomain Electron Transfer

Brown, Mia C., Greenland, Kelly, Zhang, Lei, Koder, Ronald L.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 41 KB

english, 2017

42

Optimizing Protein Dynamics in Metalloenzyme Design

Koder, Ronald L., Everson, Bernard, Zhang, Lei, Preston, Jonathan, Bjerkefeldt, Emma

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 42 KB

english, 2017

43

Design of Supercharged Proteins to Impart Allosteric Behavior and their Use in Biosensing

Schnatz, Peter, Brisendine, Joseph, Kosciolek, Derek, Crouse, David, Koder, Ronald

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 40 KB

english, 2017

44

Mechanism-Informed Refinement Reveals Altered Substrate-Binding Mode for Catalytically Competent Nitroreductase

Pitsawong, Warintra, Haynes, Chad A., Koder, Ronald L., Rodgers, David W., Miller, Anne-Frances

Journal:

Year:

2017

Language:

english

File:

PDF, 2.59 MB

english, 2017

45

Probing Charge Transport through Peptide Bonds

Brisendine, Joseph Murphy, Refaely-Abramson, Sivan, Liu, Zhen-Fei, Cui, Jing, Ng, Fay, Neaton, Jeffrey B., Koder, Ronald L., Venkataraman, Latha

Journal:

The Journal of Physical Chemistry Letters

Year:

2018

Language:

english

File:

PDF, 11.19 MB

english, 2018

46

Order, Disorder and Temperature-Driven Compaction in a Designed Elastin Protein

Greenland, Kelly N., Carvajal, Ma. Faye Charmagne Aquino, Preston, Jonathan, Ekblad, Siri, Dean, William L., Chiang, Jeff Y, Koder, Ronald L, Wittebort, Richard Jules

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 1.16 MB

english, 2018

47

Engendering Methane Monooxygenase and Hydrogen Peroxide Oxidase Activity into a Designed Dimetal Protein by Increasing Protein Dynamics

Koder, Ronald L., Preston, Jonathan M., Everson, Bernard H., Bjerkefeldt, Emma, Macazo, Florika C., Giroud, Fabien, Minteer, Shelly D., Vinyard, David J., Brudvig, Gary W.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 40 KB

english, 2018

48

Fundamental Limits on Wavelength, Efficiency and Yield of the Charge Separation Triad

Punnoose, Alexander, McConnell, Liza, Liu, Wei, Mutter, Andrew C., Koder, Ronald, Bernacchi, Carl J.

Journal:

Year:

2012

Language:

english

File:

PDF, 805 KB

english, 2012

49

The design features cells use to build their transmembrane proton gradient

Gunner, M R, Koder, Ronald

Journal:

Physical Biology

Year:

2017

Language:

english

File:

PDF, 1.55 MB

english, 2017

50

Engendering Catalytic Activity by Increasing Dynamics in a Designed Enzyme

Preston, Jonathan, Everson, Bernard, Giroud, Fabien, Vinyard, David, Greenland, Kelly, Bjerkefeldt, Emma, Minteer, Shelley, Brudvig, Gary, Koder, Ronald

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 45 KB

english, 2019