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1. Genetically Encoded 2-Aryl-5-carboxytetrazoles for Site-Selective Protein Photo-Cross-Linking

Author:
Liu, Wenshe R.,   et al.   ; Tian, Yulin; Jacinto, Marco Paolo; Zeng, Yu; Yu, Zhipeng; Qu, Jun; Lin, Qing;     Show all 7 Authors
Source:
Journal of the American Chemical Society 2017 v.139 no.17 pp. 6078-6081
ISSN:
1520-5126
Subject:
Escherichia coli; aminoacyl tRNA ligases; mammals; protein-protein interactions; proteins; stop codon
Abstract:
... The genetically encoded photo-cross-linkers promise to offer a temporally controlled tool to map transient and dynamic protein–protein interaction complexes in living cells. Here we report the synthesis of a panel of 2-aryl-5-carboxytetrazole-lysine analogs (ACTKs) and their site-specific incorporation into proteins via amber codon suppression in Escherichia coli and mammalian cells. Among five AC ...
DOI:
10.1021/jacs.7b02615
PubMed:
28422494
PubMed Central:
PMC5423124

2. Pyrrolysyl-tRNA synthetase: An ordinary enzyme but an outstanding genetic code expansion tool

Author:
Liu, Wenshe R.,   et al.   ; Wan, Wei; Tharp, Jeffery M.;     Show all 3 Authors
Source:
BBA - Proteins and Proteomics 2014 v.1844 pp. 1059-1070
ISSN:
1570-9639
Subject:
acids; amino acids; aminoacyl tRNA ligases; genetic code; proteins; stop codon
Abstract:
... The genetic incorporation of the 22nd proteinogenic amino acid, pyrrolysine (Pyl) at amber codon is achieved by the action of pyrrolysyl-tRNA synthetase (PylRS) together with its cognate tRNAPyl. Unlike most aminoacyl-tRNA synthetases, PylRS displays high substrate side chain promiscuity, low selectivity toward its substrate α-amine, and low selectivity toward the anticodon of tRNAPyl. These uniqu ...
DOI:
10.1016/j.bbapap.2014.03.002
PubMed:
24631543
PubMed Central:
PMC4016821

3. Time-Resolved Analysis Reveals Rapid Dynamics and Broad Scope of the CBP/p300 Acetylome

Author:
Liu, Wenshe R.,   et al.   ; Weinert, Brian T.; Narita, Takeo; Satpathy, Shankha; Srinivasan, Balaji; Hansen, Bogi K.; Schölz, Christian; Hamilton, William B.; Zucconi, Beth E.; Wang, Wesley W.; Brickman, Joshua M.; Kesicki, Edward A.; Lai, Albert; Bromberg, Kenneth D.; Cole, Philip A.; Choudhary, Chunaram;     Show all 16 Authors
Source:
Cell 2018 v.174 no.1 pp. 231-244.e12
ISSN:
0092-8674
Subject:
acetylation; acetyltransferases; data collection; gene targeting; histones; messenger RNA; proteomics; transcription (genetics); transcription factors
Abstract:
... The acetyltransferases CBP and p300 are multifunctional transcriptional co-activators. Here, we combined quantitative proteomics with CBP/p300-specific catalytic inhibitors, bromodomain inhibitor, and gene knockout to reveal a comprehensive map of regulated acetylation sites and their dynamic turnover rates. CBP/p300 acetylates thousands of sites, including signature histone sites and a multitude ...
DOI:
10.1016/j.cell.2018.04.033

4. Facile Removal of Leader Peptides from Lanthipeptides by Incorporation of a Hydroxy Acid

Author:
Liu, Wenshe R.,   et al.   ; Bindman, Noah A.; Bobeica, Silvia C.; van der Donk, Wilfred A.;     Show all 4 Authors
Source:
Journal of the American Chemical Society 2015 v.137 no.22 pp. 6975-6978
ISSN:
1520-5126
Subject:
Escherichia coli; acids; bacteriocins; biosynthesis; genome mining; hydrolysis; peptides; proteinases; signal peptide
Abstract:
... The biosynthesis of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products typically involves a precursor peptide which contains a leader peptide that is important for the modification process, and that is removed in the final step by a protease. Genome mining efforts for new RiPPs are often hampered by the lack of a general method to remove the leader peptides. ...
DOI:
10.1021/jacs.5b04681
PubMed:
26006047
PubMed Central:
PMC4505723

5. Genetically encoded fluorophenylalanines enable insights into the recognition of lysine trimethylation by an epigenetic reader

Author:
Liu, Wenshe R.,   et al.   ; Lee, Yan-Jiun; Schmidt, M. J.; Tharp, Jeffery M.; Weber, Annemarie; Koenig, Amber L.; Zheng, Hong; Gao, Jianmin; Waters, Marcey L.; Summerer, Daniel;     Show all 10 Authors
Source:
Chemical communications 2016 v.52 no.85 pp. 12606-12609
ISSN:
1364-548X
Subject:
chemical compounds; chemical reactions; epigenetics; fluorine; histones; lysine; peptides; phenylalanine; stop codon
Abstract:
... Fluorophenylalanines bearing 2–5 fluorine atoms at the phenyl ring have been genetically encoded by amber codon. Replacement of F59, a phenylalanine residue that is directly involved in interactions with trimethylated K9 of histone H3, in the Mpp8 chromodomain recombinantly with fluorophenylalanines significantly impairs the binding to a K9-trimethylated H3 peptide. ...
DOI:
10.1039/c6cc05959g

6. Near-cognate suppression of amber, opal and quadruplet codons competes with aminoacyl-tRNAᴾʸˡ for genetic code expansion

Author:
Liu, Wenshe R.,   et al.   ; O’Donoghue, Patrick; Prat, Laure; Heinemann, Ilka U.; Ling, Jiqiang; Odoi, Keturah; Söll, Dieter;     Show all 7 Authors
Source:
FEBS letters 2012 v.586 no.21 pp. 3931-3937
ISSN:
0014-5793
Subject:
Escherichia coli; amino acids; genetic code; proteins; stop codon
Abstract:
... Over 300 amino acids are found in proteins in nature, yet typically only 20 are genetically encoded. Reassigning stop codons and use of quadruplet codons emerged as the main avenues for genetically encoding non-canonical amino acids (NCAAs). Canonical aminoacyl-tRNAs with near-cognate anticodons also read these codons to some extent. This background suppression leads to ‘statistical protein’ that ...
DOI:
10.1016/j.febslet.2012.09.033
PubMed:
23036644
PubMed Central:
PMC3488457

7. A Rationally Designed Pyrrolysyl-tRNA Synthetase Mutant with a Broad Substrate Spectrum

Author:
Liu, Wenshe R.,   et al.   ; Wang, Yane-Shih; Fang, Xinqiang; Wallace, Ashley L.; Wu, Bo;     Show all 5 Authors
Source:
Journal of the American Chemical Society 2012 v.134 no.6 pp. 2950-2953
ISSN:
1520-5126
Subject:
Escherichia coli; green fluorescent protein; mutants; nonsense mutation; phenylalanine
Abstract:
... Together with tRNACUAᴾʸˡ, a rationally designed pyrrolysyl-tRNA synthetase mutant N346A/C348A has been successfully used for the genetic incorporation of a variety of phenylalanine derivatives with large para substituents into superfolder green fluorescent protein at an amber mutation site in Escherichia coli. This discovery greatly expands the genetically encoded noncanonical amino acid inventory ...
DOI:
10.1021/ja211972x
PubMed:
22289053
PubMed Central:
PMC3288562

8. A Facile Method to Synthesize Histones with Posttranslational Modification Mimics

Author:
Liu, Wenshe R.,   et al.   ; Wang, Zhiyong U.; Wang, Yane-Shih; Pai, Pei-Jing; Russell, William K.; Russell, David H.;     Show all 6 Authors
Source:
Biochemistry 2012 v.51 no.26 pp. 5232-5234
ISSN:
1520-4995
Subject:
acetylation; histones; lysine; methylation; phosphorylation; post-translational modification; serine; thiols
Abstract:
... Using an evolved pyrrolysyl-tRNA synthetase-tRNAᴾʸˡ pair, a Se-alkylselenocysteine was genetically incorporated into histone H3 with a high protein expression yield. Quantitative oxidative elimination of Se-alkylselenocysteine followed by Michael addition reactions with various thiol nucleophiles generated biologically active mimics of H3 with posttranslational modifications including lysine methy ...
DOI:
10.1021/bi300535a
PubMed:
22697363
PubMed Central:
PMC3448024

9. Reversal of the Hofmeister Series: Specific Ion Effects on Peptides B

Author:
Liu, Wenshe R.,   et al.   ; Paterová, Jana; Rembert, Kelvin B.; Heyda, Jan; Kurra, Yadagiri; Okur, Halil I.; Hilty, Christian; Cremer, Paul S.; Jungwirth, Pavel;     Show all 9 Authors
Source:
The Journal of physical chemistry 2013 v.117 no.27 pp. 8150-8158
ISSN:
1520-5207
Subject:
amino acids; anions; enzyme activity; iodides; models; molecular dynamics; mutation; nuclear magnetic resonance spectroscopy; peptides; physical properties; protein denaturation; proteins; sulfates; thiocyanates; titration
Abstract:
... Ion-specific effects on salting-in and salting-out of proteins, protein denaturation, as well as enzymatic activity are typically rationalized in terms of the Hofmeister series. Here, we demonstrate by means of NMR spectroscopy and molecular dynamics simulations that the traditional explanation of the Hofmeister ordering of ions in terms of their bulk hydration properties is inadequate. Using trig ...
DOI:
10.1021/jp405683s