Impact of Queuosine Modification of Endogenous E. coli tRNAs on Sense Codon Reassignment

Jillyn M. Tittle, David G. Schwark, Wil Biddle, Margaret A. Schmitt, John D. Fisk*

2022, Frontiers in Molecular Biosciences, volume 9, article 938114 (August 31, 2022)

10.3389/fmolb.2022.938114

*Invited contribution to the Special Collection “Exploring and Expanding the Protein Universe with Non-Canonical Amino Acids”

Directed Evolution Pipeline for the Improvement of Orthogonal Translation Machinery for Genetic Code Expansion at Sense Codons

Wil Biddle, David G. Schwark, Margaret A. Schmitt, John D. Fisk*

2022, Frontiers in Chemistry, Volume 10, Article 815788

10.3389/fchem.2022.815788

*Contribution to the Special Collection “Expansion of the Genetic Code: Unnatural Amino Acids and their Applications”

The Influence of Competing tRNA Abundance on Translation: Quantifying the Efficiency of Sense Codon Reassignment at Rarely Used Codons

David G. Schwark, Margaret A. Schmitt, Wil Biddle, John D. Fisk*

2020, ChemBioChem, volume 21, pages 2274-2286

10.1002/cbic.202000052

*Invited contribution to the Special Issue “Xenobiology”

Hyperthermostable Binding Molecules on Phage: Assay Components for Point-of-Care Diagnostics for Active Tuberculosis Infection

Ning Zhao, John S. Spencer, Margaret A. Schmitt, John D. Fisk*

2017, Analytical Biochemistry, volume 521, pages 59-71  

DOI: 10.1016/j.ab.2016.12.021

Modification of Orthogonal tRNAs: Unexpected Consequences for Sense Codon Reassignment

Wil Biddle, Margaret A. Schmitt, John D. Fisk*

2016, Nucleic Acids Research, volume 44, pages 10042-10050

https://doi.org/10.1093/nar/gkw948

Simulation of the M13 Life Cycle I: Assembly of a Genetically-Structured Deterministic Chemical Kinetic Simulation

Steven W. Smeal, Margaret A. Schmitt, Ronnie Rodrigues Pereira, Ashok Prasad, John D. Fisk*

2017, Virology, volume 500, pages 259-274

https://doi.org/10.1016/j.virol.2016.08.017

*Selected by the Editors as a Highlighted article for this issue!

Simulation of the M13 Life Cycle II: Investigation of the Control Mechanisms of M13 Infection and Establishment of the Carrier State

Steven W. Smeal, Margaret A. Schmitt, Ronnie Rodrigues Pereira, Ashok Prasad, John D. Fisk*

2017, Virology, volume 500, pages 275-284

https://doi.org/10.1016/j.virol.2016.08.015

Evaluating sense codon reassignment with a simple fluorescence screen

Wil Biddle, Margaret A. Schmitt, John D. Fisk*

2015, Biochemistry, volume 54, pages 7355-7364

https://doi.org/10.1021/acs.biochem.5b00870

*Selected as An ACS Editors' Choice manuscript!

Earlier Publications

15.       Beatty, K. E.; Szychowski, J.; Fisk, J. D.; Tirrell, D. A., A BODIPY-Cyclooctyne for Protein Imaging in Live Cells. Chembiochem. 2011, 12, 2137-2139.

14.       Freire, F., Almeida, A. M., Fisk, J. D., Steinkruger, J. D. and Gellman, S. H., Impact of Strand Length on the Stability of Parallel-β-Sheet Secondary Structure. Angewandte Chemie Int Ed. 2011, 50, 8735-8738.

13.       Van Deventer, J.A; Fisk, J.D.; Tirrell D.A., Homoisoleucine: A translationally-active leucine surrogate of expanded hydrophobic surface area. Chembiochem 2011, 12, 700-702

12.       Beatty, K. E.; Fisk, J. D.; Smart, B. P.; Lu, Y. Y.; Szychowski, J.; Hangauer, M. J.; Baskin, J. M.; Bertozzi, C. R.; Tirrell, D. A., Live-Cell Imaging of Cellular Proteins by a Strain-Promoted Azide-Alkyne Cycloaddition. Chembiochem 2010, 11 (15), 2092-2095.

11.       Friere-Iribarne, F.; Fisk, J. D.; Peoples, A. J.; Gellman, S. H. “Diacid Linkers that Promote Parallel b-Sheet Secondary Structure in Water” J. Am. Chem. Soc. 2008, 130, 7839-7841.

10.       Fisk, J. D.; Schmitt, M. A.; Gellman, S. H. “Thermodynamic Analysis of Autonomous Parallel b-Sheet Formation in Water.” J. Am. Chem. Soc. 2006, 128, 7148-7149.

9.         Lai, J. R.; Fisk, J. D.; Weisblum, B.; Gellman, S. H. “Hydrophobic Core Repacking in a Coiled-Coil Dimer via Phage Display: Insights into Plasticity and Specificity at a Protein – Protein Interface” J. Am. Chem. Soc. 2004, 126, 10514-10515.

8.         Huck, B. R.; Fisk, J. D.; Guzei, I. A.; Carlson, H. S.;  Gellman, S.H. “Secondary Structural Preferences of 2,2-Disubstituted Pyrrolidine-4-Carboxylic Acid Oligomers: β-Peptide Foldamers that Cannot Form Internal Hydrogen Bonds.” J. Am. Chem. Soc. 2003, 125, 9035-9037.

7.         Syud, F.A.; Stanger, H. E;  Mortell, H. S; Espinosa J. F.; Fisk, J. D.; Fry, C. G.; Gellman S. H.; “Influence of Strand Number on Antiparallel b-Sheet Stability in Designed Three- and Four-stranded b-Sheets.” J. Mol. Biol. 2003, 326, 553-568.

6.         Woll, M. G.; Fisk, J. D.; LePlae, P. R.; Gellman, S. H. “Stereoselective Synthesis of 3-Substituted 2-Aminocyclopropanecarboxylic Acid Derivatives and Their Incorporation into Short 12-Helical b-Peptides that Fold in Water.” J. Am. Chem. Soc. 2002, 124, 12447-12452.

5.         LePlae, P. R.; Fisk, J. D.; Porter, E. A.; Gellman, S. H.  “Tolerance of Acyclic Residues in the Peptide 12-Helix: Access to Diverse Side-Chain Arrays for Biological Applications.” J. Am. Chem. Soc. 2002, 124, 6820-6821.

4.         Langenhan, J. M.; Fisk, J. D.; Gellman, S. H. “Evaluation of Hydrogen Bonding   Complementarity between a Secondary Sulfonamide and an a-Amino Acid Residue.” Org. Lett. 2001; 3, 2559-2562.

3.         Fisk, J. D.; Gellman, S. H. “A Parallel b-Sheet Model System that Folds in Water.” J. Am. Chem. Soc. 2001, 123, 343-344.

2.         Fisk, J. D.; Powell, D. R.; Gellman, S. H. “Control of Hairpin Formation via Proline Configuration in Parallel b-Sheet Model Systems.” J. Am. Chem. Soc. 2000, 122, 5443-5447.

1.         Huck, B. R.; Fisk, J. D.; Gellman, S. H. “Promotion of Sheet Formation in a-Peptide Strands by a b-Peptide Reverse Turn.” Org. Lett. 2000, 2, 2607-2610.  

Fisk Lab Research Publications Keywords:

1) Sense codon reassignment: sense codon reassignment, genetic code expansion, non-canonical amino acids, orthogonal translational machinery, tRNA modification, combinatorial library, aminoacyl tRNA synthetase

2) Phage display: phage display, combinatorial libraries, alternative scaffold, hyperthermophilic protein, molecular recogntion, directed evolution

3) M13 computational model: bacteriophage, M13, virus life cycle, computational simulation, genetically-structured simulation, systems biology, synthetic biology