scholarly journals Engineered unnatural ubiquitin for optimal detection of deubiquitinating enzymes

2020 ◽  
Vol 11 (23) ◽  
pp. 6058-6069
Author(s):  
Wioletta Rut ◽  
Mikolaj Zmudzinski ◽  
Scott J. Snipas ◽  
Miklos Bekes ◽  
Tony T. Huang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Unnatural Amino Acids ◽  
Optimal Detection ◽  
Deubiquitinating Enzymes ◽  
Design And Synthesis

Herein we present a workflow for design and synthesis of novel selective Ub-based tools for DUBs. Selectivity is achieved by incorporation of unnatural amino acids into the Ub C-terminal epitope.

scholarly journals Engineered unnatural ubiquitin for optimal detection of deubiquitinating enzymes

2020 ◽  
Author(s):  
Wioletta Rut ◽  
Mikołaj Żmudziński ◽  
Scott J. Snipas ◽  
Miklos Bekes ◽  
Tony T. Huang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Neurodegenerative Disorders ◽  
Unnatural Amino Acids ◽  
Biochemical Analysis ◽  
Deubiquitinating Enzymes ◽  
Fluorogenic Substrates ◽  
Protein Conjugates ◽  
Highly Active ◽  
Selective Chemical

AbstractDeubiquitinating enzymes (DUBs) are responsible for removing ubiquitin (Ub) from its protein conjugates. DUBs have been implicated as attractive therapeutic targets in the treatment of viral diseases, neurodegenerative disorders and cancer. The lack of selective chemical tools for the exploration of these enzymes significantly impairs the determination of their roles in both normal and pathological states. Commercially available fluorogenic substrates are based on the C-terminal Ub motif or contain Ub coupled to a fluorophore (Z-LRGG-AMC, Ub-AMC); therefore, these substrates suffer from lack of selectivity. By using a hybrid combinatorial substrate library (HyCoSuL) and a defined P2 library containing a wide variety of nonproteinogenic amino acids, we established a full substrate specificity profile for two DUBs—MERS PLpro and human UCH-L3. Based on these results, we designed and synthesized Ub-based substrates and activity-based probes (ABPs) containing selected unnatural amino acids located in the C-terminal Ub motif. Biochemical analysis and cell-based experiments confirmed the activity and selectivity of engineered Ub-based substrates and probes. Using this approach, we propose that for any protease that recognizes Ub and Ub-like substrates, a highly active and selective unnatural substrate or probe can be engineered.

Molecular Design and Synthesis of Artificial Ion Channels Based on Cyclic Peptides Containing Unnatural Amino Acids

2001 ◽  
Vol 66 (9) ◽  
pp. 2978-2989 ◽  
Author(s):  
Hitoshi Ishida ◽  
Zhi Qi ◽  
Masahiro Sokabe ◽  
Kiyoshi Donowaki ◽  
Yoshihisa Inoue
Keyword(s):  
Amino Acids ◽  
Ion Channels ◽  
Unnatural Amino Acids ◽  
Cyclic Peptides ◽  
Molecular Design ◽  
Design And Synthesis

ChemInform Abstract: Molecular Design and Synthesis of Artificial Ion Channels Based on Cyclic Peptides Containing Unnatural Amino Acids.

ChemInform ◽  
2010 ◽  
Vol 32 (34) ◽  
pp. no-no
Author(s):  
Hitoshi Ishida ◽  
Zhi Qi ◽  
Masahiro Sokabe ◽  
Kiyoshi Donowaki ◽  
Yoshihisa Inoue
Keyword(s):  
Amino Acids ◽  
Ion Channels ◽  
Unnatural Amino Acids ◽  
Cyclic Peptides ◽  
Molecular Design ◽  
Design And Synthesis

scholarly journals Enzymatic aminoacylation of tRNA with unnatural amino acids

2006 ◽  
Vol 103 (12) ◽  
pp. 4356-4361 ◽  
Author(s):  
M. C. T. Hartman ◽  
K. Josephson ◽  
J. W. Szostak
Keyword(s):  
Amino Acids ◽  
Unnatural Amino Acids

scholarly journals Transferability of N-terminal mutations of pyrrolysyl-tRNA synthetase in one species to that in another species on unnatural amino acid incorporation efficiency

Amino Acids ◽  
2020 ◽  
Author(s):  
Thomas L. Williams ◽  
Debra J. Iskandar ◽  
Alexander R. Nödling ◽  
Yurong Tan ◽  
Louis Y. P. Luk ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Unnatural Amino Acids ◽  
Trna Synthetase ◽  
Unnatural Amino Acid ◽  
Amino Acid Incorporation ◽  
Acid Incorporation ◽  
Genetic Code Expansion ◽  
Incorporation Efficiency

AbstractGenetic code expansion is a powerful technique for site-specific incorporation of an unnatural amino acid into a protein of interest. This technique relies on an orthogonal aminoacyl-tRNA synthetase/tRNA pair and has enabled incorporation of over 100 different unnatural amino acids into ribosomally synthesized proteins in cells. Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA from Methanosarcina species are arguably the most widely used orthogonal pair. Here, we investigated whether beneficial effect in unnatural amino acid incorporation caused by N-terminal mutations in PylRS of one species is transferable to PylRS of another species. It was shown that conserved mutations on the N-terminal domain of MmPylRS improved the unnatural amino acid incorporation efficiency up to five folds. As MbPylRS shares high sequence identity to MmPylRS, and the two homologs are often used interchangeably, we examined incorporation of five unnatural amino acids by four MbPylRS variants at two temperatures. Our results indicate that the beneficial N-terminal mutations in MmPylRS did not improve unnatural amino acid incorporation efficiency by MbPylRS. Knowledge from this work contributes to our understanding of PylRS homologs which are needed to improve the technique of genetic code expansion in the future.

Sign in / Sign up

Export Citation Format

Share Document