Phage-based tuberculosis diagnostics

 

 

 

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*

In press, Analytical Biochemistry  

DOI: 10.1016/j.ab/2016.12.021

Accepted December 23, 2016


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

DOI: 10.1093/nar/gkw948

Sense codon reassignment


Computational simulation of the M13 life cycle

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

http://dx.doi.org/10.1016/j.virol.2016.08.017

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


Computational simulation of the M13 life cycle

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

http://dx.doi.org/10.1016/j.virol.2016.08.015


Phage display scaffolds

 

 

 

Phage display selection of tight specific binding variants from a hyperthermostable Sso7d scaffold protein library

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

2016, FEBS J, volume 283, pages 1351-1367

doi:10.1111/febs.1367


Sense codon reassignment

 

 

 

 

Evaluating sense codon reassignment with a simple fluorescence screen

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

2015, Biochemistry, volume 54, pages 7355-7364

doi: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