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Peptides

  • 1.
    Juarez R, Jiang Y, Tremblay M, Shao Q, Link J, Yang Z. LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling. J Chem Inf Model. 2023;63(2):522–530. PMID: 36594886
    Reference Link
  • 1.
    Carson D, Patiño M, Elashal H, Cartagena A, Zhang Y, Whitley M, So L, Kayser-Browne A, Earl A, Bhattacharyya R, Link J. Cloacaenodin, an Antimicrobial Lasso Peptide with Activity against . ACS Infect Dis. 2023;9(1):111–121. PMCID: PMC10038104
    Reference Link
  • 1.
    Clark K, Covington B, Seyedsayamdost M. Biosynthesis-guided discovery reveals enteropeptins as alternative sactipeptides containing N-methylornithine. Nat Chem. 2022;14(12):1390–1398. PMID: 36316408
    Reference Link
  • 1.
    Clark K, Seyedsayamdost M. Bioinformatic Atlas of Radical SAM Enzyme-Modified RiPP Natural Products Reveals an Isoleucine-Tryptophan Crosslink. J Am Chem Soc. 2022;144(39):17876–17888. PMID: 36128669
    Reference Link
  • 1.
    Chen H, Zhan M, Liu J, Liu Z, Shen M, Yang F, Kang Y, Yin F, Li Z. Structure-Based Design, Optimization, and Evaluation of Potent Stabilized Peptide Inhibitors Disrupting MTDH and SND1 Interaction. J Med Chem. 2022;65(18):12188–12199. PMID: 36044768
    Reference Link
  • 1.
    Bushin L, Covington B, Clark K, Caruso A, Seyedsayamdost M. Bicyclostreptins are radical SAM enzyme-modified peptides with unique cyclization motifs. Nat Chem Biol. 2022;18(10):1135–1143. PMCID: 6686864
    Reference Link
  • 1.
    Covington B, Seyedsayamdost M. Vitamin B3 Triggers Biosynthesis of Secondary Metabolite Dormancy Signals in . J Am Chem Soc. 2022;144(33):14997–15001. PMID: 35969232
    Reference Link
  • 1.
    Elashal H, Koos J, Cheung-Lee W, Choi B, Cao L, Richardson M, White H, Link J. Biosynthesis and characterization of fuscimiditide, an aspartimidylated graspetide. Nat Chem. 2022;14(11):1325–1334. PMCID: PMC10078976
    Reference Link
  • 1.
    Tomer D, Arriagada C, Munshi S, Alexander B, French B, Vedula P, Caorsi V, House A, Guvendiren M, Kashina A, Schwarzbauer J, Astrof S. A new mechanism of fibronectin fibril assembly revealed by live imaging and super-resolution microscopy. J Cell Sci. 2022;135(16). PMCID: PMC9481930
    Reference Link
  • 1.
    Do T, Link J. Protein Engineering in Ribosomally Synthesized and Post-translationally Modified Peptides (RiPPs). Biochemistry. 2023;62(2):201–209. PMCID: PMC9454058
    Reference Link
  • 1.
    Schröder H, Stadlmeier M, Wühr M, Link J. The Shuttling Cascade in Lasso Peptide Benenodin-1 is Controlled by Non-Covalent Interactions. Chemistry. 2022;28(5):e202103615. PMCID: PMC8792204
    Reference Link
  • 1.
    Etzion-Fuchs A, Todd D, Singh M. dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. Nucleic Acids Res. 2021;49(13):e78. PMCID: PMC8287948
    Reference Link
  • 1.
    Caruso A, Seyedsayamdost M. Radical SAM Enzyme QmpB Installs Two 9-Membered Ring Sactionine Macrocycles during Biogenesis of a Ribosomal Peptide Natural Product. J Org Chem. 2021;86(16):11284–11289. PMID: 34351169
    Reference Link
  • 1.
    Song H, Burton A, Shirran S, Fahrig-Kamarauskaitė J, Kaspar H, Muir T, Künzler M, Naismith J. Engineering of a Peptide α-N-Methyltransferase to Methylate Non-Proteinogenic Amino Acids. Angew Chem Int Ed Engl. 2021;60(26):14319–14323. PMCID: PMC8251615
    Reference Link
  • 1.
    Schröder H, Zhang Y, Link J. Dynamic covalent self-assembly of mechanically interlocked molecules solely made from peptides. Nat Chem. 2021;13(9):850–857. PMCID: PMC8446321
    Reference Link
  • 1.
    Cao L, Beiser M, Koos J, Orlova M, Elashal H, Schröder H, Link J. Cellulonodin-2 and Lihuanodin: Lasso Peptides with an Aspartimide Post-Translational Modification. J Am Chem Soc. 2021;143(30):11690–11702. PMCID: PMC9206484
    Reference Link
  • 1.
    Cao L, Do T, Link J. Mechanisms of action of ribosomally synthesized and posttranslationally modified peptides (RiPPs). J Ind Microbiol Biotechnol. 2021;48(3-4). PMCID: PMC8183687
    Reference Link
  • 1.
    Johnson A, Stadlmeier M, Wühr M. TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level. J Proteome Res. 2021;20(6):3043–3052. PMCID: PMC8330405
    Reference Link
  • 1.
    Rued B, Covington B, Bushin L, Szewczyk G, Laczkovich I, Seyedsayamdost M, Federle M. Quorum Sensing in Streptococcus mutans Regulates Production of Tryglysin, a Novel RaS-RiPP Antimicrobial Compound. mBio. 2021;12(2). PMCID: PMC8092268
    Reference Link
  • 1.
    Kloosterman A, Cimermancic P, Elsayed S, Du C, Hadjithomas M, Donia M, Fischbach M, van Wezel G, Medema M. Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides. PLoS Biol. 2020;18(12):e3001026. PMCID: PMC7794033
    Reference Link
  • 1.
    Montalbán-López M, Scott T, Ramesh S, Rahman I, van Heel A, Viel J, Bandarian V, Dittmann E, Genilloud O, Goto Y, Burgos M, Hill C, Kim S, Koehnke J, Latham J, Link J, Martínez B, Nair S, Nicolet Y, Rebuffat S, Sahl H-G, Sareen D, Schmidt E, Schmitt L, Severinov K, Süssmuth R, Truman A, Wang H, Weng J-K, van Wezel G, Zhang Q, Zhong J, Piel J, Mitchell D, Kuipers O, van der Donk W. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep. 2021;38(1):130–239. PMCID: PMC7864896
    Reference Link
  • 1.
    Xie Q, Wiedmann M, Zhao A, Pagan I, Novick R, Suga H, Muir T. Discovery of quorum quenchers targeting the membrane-embedded sensor domain of the receptor histidine kinase, AgrC. Chem Commun (Camb). 2020;56(76):11223–11226. PMCID: PMC7530097
    Reference Link
  • 1.
    Caruso A, Bushin L, Clark K, Martinie R, Seyedsayamdost M. Radical Approach to Enzymatic β-Thioether Bond Formation. J Am Chem Soc. 2019;141(2):990–997. PMID: 30521328
    Reference Link
  • 1.
    Cheung-Lee W, Cao L, Link J. Pandonodin: A Proteobacterial Lasso Peptide with an Exceptionally Long C-Terminal Tail. ACS Chem Biol. 2019;14(12):2783–2792. PMCID: PMC7010350
    Reference Link
  • 1.
    Zhang C, Seyedsayamdost M. CanE, an Iron/2-Oxoglutarate-Dependent Lasso Peptide Hydroxylase from . ACS Chem Biol. 2020;15(4):890–894. PMID: 32191027
    Reference Link
  • 1.
    Mao D, Yoshimura A, Wang R, Seyedsayamdost M. Reporter-Guided Transposon Mutant Selection for Activation of Silent Gene Clusters in Burkholderia thailandensis. Chembiochem. 2020;21(13):1826–1831. PMCID: PMC7493819
    Reference Link
  • 1.
    Peshkin L, Gupta M, Ryazanova L, Wühr M. Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance. Mol Cell Proteomics. 2019;18(10):2108–2120. PMCID: PMC6773559
    Reference Link
  • 1.
    Shi C, Booth L, Murphy C. Insulin-like peptides and the mTOR-TFEB pathway protect hermaphrodites from mating-induced death. Elife. 2019;8. PMCID: PMC6697448
    Reference Link
  • 1.
    Clark K, Bushin L, Seyedsayamdost M. Aliphatic Ether Bond Formation Expands the Scope of Radical SAM Enzymes in Natural Product Biosynthesis. J Am Chem Soc. 2019;141(27):10610–10615. PMID: 31246011
    Reference Link
  • 1.
    Cheung-Lee W, Link J. Genome mining for lasso peptides: past, present, and future. J Ind Microbiol Biotechnol. 2019;46(9-10):1371–1379. PMCID: PMC6989040
    Reference Link
  • 1.
    Cheung-Lee W, Parry M, Cartagena A, Darst S, Link J. Discovery and structure of the antimicrobial lasso peptide citrocin. J Biol Chem. 2019;294(17):6822–6830. PMCID: PMC6497930
    Reference Link
  • 1.
    Shen H, Liu D, Wu K, Lei J, Yan N. Structures of human Na1.7 channel in complex with auxiliary subunits and animal toxins. Science. 2019;363(6433):1303–1308. PMID: 30765606
    Reference Link
  • 1.
    Braffman N, Piscotta F, Hauver J, Campbell E, Link J, Darst S. Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin. Proc Natl Acad Sci U S A. 2019;116(4):1273–1278. PMCID: PMC6347699
    Reference Link
  • 1.
    Gupta M, Sonnett M, Ryazanova L, Presler M, Wühr M. Quantitative Proteomics of Xenopus Embryos I, Sample Preparation. Methods Mol Biol. 2018;1865:175–194. PMCID: PMC6564683
    Reference Link
  • 1.
    Sonnett M, Gupta M, Nguyen T, Wühr M. Quantitative Proteomics for Xenopus Embryos II, Data Analysis. Methods Mol Biol. 2018;1865:195–215. PMCID: PMC6534117
    Reference Link
  • 1.
    Bushin L, Seyedsayamdost M. Guidelines for Determining the Structures of Radical SAM Enzyme-Catalyzed Modifications in the Biosynthesis of RiPP Natural Products. Methods Enzymol. 2018;606:439–460. PMID: 30097102
    Reference Link
  • 1.
    Gramespacher J, Stevens A, Nguyen D, Chin J, Muir T. Intein Zymogens: Conditional Assembly and Splicing of Split Inteins via Targeted Proteolysis. J Am Chem Soc. 2017;139(24):8074–8077. PMCID: PMC5533455
    Reference Link
  • 1.
    Elashal H, Cohen R, Elashal H, Zong C, Link J, Raj M. Cyclic and Lasso Peptides: Sequence Determination, Topology Analysis, and Rotaxane Formation. Angew Chem Int Ed Engl. 2018;57(21):6150–6154. PMCID: PMC6080247
    Reference Link
  • 1.
    Schramma K, Seyedsayamdost M. Lysine-Tryptophan-Crosslinked Peptides Produced by Radical SAM Enzymes in Pathogenic Streptococci. ACS Chem Biol. 2017;12(4):922–927. PMID: 28191919
    Reference Link
  • 1.
    Metelev M, Arseniev A ii, Bushin L, Kuznedelov K, Artamonova T, Kondratenko R, Khodorkovskii M, Seyedsayamdost M, Severinov K. Acinetodin and Klebsidin, RNA Polymerase Targeting Lasso Peptides Produced by Human Isolates of Acinetobacter gyllenbergii and Klebsiella pneumoniae. ACS Chem Biol. 2017;12(3):814–824. PMID: 28106375
    Reference Link
  • 1.
    Jenness C, Giunta S, Müller M, Kimura H, Muir T, Funabiki H. HELLS and CDCA7 comprise a bipartite nucleosome remodeling complex defective in ICF syndrome. Proc Natl Acad Sci U S A. 2018;115(5):E876-E885. PMCID: PMC5798369
    Reference Link
  • 1.
    Zong C, Wu M, Qin J, Link J. Lasso Peptide Benenodin-1 Is a Thermally Actuated [1]Rotaxane Switch. J Am Chem Soc. 2017;139(30):10403–10409. PMCID: PMC5576865
    Reference Link
  • 1.
    Allen C, Chen M, Trick A, Le D, Ferguson A, Link J. Thermal Unthreading of the Lasso Peptides Astexin-2 and Astexin-3. ACS Chem Biol. 2016;11(11):3043–3051. PMCID: PMC5148663
    Reference Link
  • 1.
    Allen C, Link J. Self-Assembly of Catenanes from Lasso Peptides. J Am Chem Soc. 2016;138(43):14214–14217. PMCID: PMC5245162
    Reference Link
  • 1.
    Chekan J, Koos J, Zong C, Maksimov M, Link J, Nair S. Structure of the Lasso Peptide Isopeptidase Identifies a Topology for Processing Threaded Substrates. J Am Chem Soc. 2016;138(50):16452–16458. PMCID: PMC5245167
    Reference Link
  • 1.
    Link J. Biosynthesis: Leading the way to RiPPs. Nat Chem Biol. 2015;11(8):551–2. PMCID: PMC4794250
    Reference Link
  • 1.
    Zong C, Maksimov M, Link J. Construction of Lasso Peptide Fusion Proteins. ACS Chem Biol. 2016;11(1):61–8. PMCID: PMC4795474
    Reference Link
  • 1.
    Maksimov M, Koos J, Zong C, Lisko B, Link J. Elucidating the Specificity Determinants of the AtxE2 Lasso Peptide Isopeptidase. J Biol Chem. 2015;290(52):30806–12. PMCID: PMC4692210
    Reference Link
  • 1.
    Zhang H, Elbaum-Garfinkle S, Langdon E, Taylor N, Occhipinti P, Bridges A, Brangwynne C, Gladfelter A. RNA Controls PolyQ Protein Phase Transitions. Mol Cell. 2015;60(2):220–30. PMCID: PMC5221516
    Reference Link
  • 1.
    Cosgrove M, Bever K, Avalos J, Muhammad S, Zhang X, Wolberger C. The structural basis of sirtuin substrate affinity. Biochemistry. 2006;45(24):7511–21. PMID: 16768447
    Reference Link

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