Fluorescent Probes for Studying Thioamide Positional Effects on Proteolysis Reveal Insight into Resistance to Cysteine Proteases

Chunxiao Liu, Taylor Barrett, Xing Chen, John Ferrie, E. James Petersson
ChemBioChem In Press DOI:10.1002/cbic.201900115

Cyclized NDGA modifies dynamic α-synuclein monomers preventing aggregation and toxicity

Malcolm J. Daniels, J. Brucker Nourse Jr., Hanna Kim, Valerio Sainati, Marco Schiavina, Maria Grazia Murrali, Buyan Pan, John J. Ferrie, Conor M. Haney, Rani Moons, Neal S. Gould, Antonino Natalello, Rita Grandori, Frank Sobott, E. James Petersson, Elizabeth Rhoades, Roberta Pierattelli, Isabella Felli, Vladimir N. Uversky, Kim A. Caldwell, Guy A. Caldwell, Edward S. Krol and Harry Ischiropoulos
Nature Sci. Rep. 9 Article 2937 (2019) DOI:10.1038/s41598-019-39480-z

Biosynthesis and Chemical Applications of Thioamides

Nilkamal Mahanta,* D. Miklos Szantai-Kis,* E. James Petersson, and Douglas A. Mitchell
ACS Chemical Biology 14 142-163 (2019) DOI:10.1021/acschembio.8b01022

A “Clickable” Photoconvertible Small Fluorescent Molecule as a Minimalist Probe for Tracking Individual Biomolecule Complexes

Joomyung V. Jun, Conor M. Haney, Richard J. Karpowicz, Jr., Sam Giannakoulias, Virginia M.-Y. Lee, E. James Petersson, and David M. Chenoweth
J. Am. Chem. Soc. 141 1893-1897 (2019) DOI:10.1021/jacs.8b13094
Spotlighted by J. Am. Chem. Soc. and highlighted in C&E News.

A PARP-1 Feed-Forward Mechanism To Accelerate α-Synuclein Toxicity in Parkinson’s Disease

Buyan Pan and E. James Petersson
Biochemistry 58 859-860 (2019) DOI:10.1021/acs.biochem.8b01311

Optimization of Second Window Indocyanine Green for Intraoperative Near-Infrared Imaging of Thoracic Malignancy

Andrew D. Newton, Jarrod D. Predina, Christopher J. Corbett, Lydia G. Frenzel-Sulyok, Leilei Xia, E. James Petersson, Andrew Tsourkas, Shuming Nie, Edward J. Delikatny, Sunil Singhal
J. Am. Coll. Surg. 228 188-197 (2018) DOI:10.1016/j.jamcollsurg.2018.11.003

Systematic Evaluation of Soluble Protein Expression Using a Fluorescent Unnatural Amino Acid Reveals No Reliable Predictors of Tolerability

Zachary M. Hostetler, John J. Ferrie, Marc R. Bornstein, Itthipol Sungwienwong, E. James Petersson, and Rahul M. Kohli
ACS Chem. Biol. 13 2855-2861 (2018) DOI:10.1021/acschembio.8b00696
Highlighted by Science Translational Medicine's "In the Pipeline."

Rational Design and Facile Synthesis of a Highly Tunable Quinoline-Based Fluorescent Small-Molecule Scaffold for Live Cell Imaging

Joomyung V. Jun, E. James Petersson, and David M. Chenoweth
J. Am. Chem. Soc. 140 9486-9493 (2018) DOI:10.1021/jacs.8b03738

Alpha Synuclein Fibrils Contain Multiple Binding Sites for Small Molecules

Chia-Ju Hsieh, John J. Ferrie, Kuiying Xu, Iljung Lee, Thomas J. A. Graham, Zhude Tu, Jennifer Yu, Dhruva Dhaval∥, Paul Kotzbauer, E. James Petersson, Robert H. Mach
ACS Chem. Neurosci. 9 2521-2527 (2018) DOI:10.1021/acschemneuro.8b00177
Chosen as one of the "Best of 2018" by ACS Chem. Neurosci.

Improving the fluorescent probe acridonylalanine through a combination of theory and experiment

Itthipol Sungwienwong,* John J. Ferrie,* Joomyung V. Jun, Chunxiao Liu, Taylor M. Barrett, Zachary M. Hostetler, Naoya Ieda, Amara Hendricks, Anand K. Muthusamy, Rahul M. Kohli, David M. Chenoweth, George A. Petersson, E. James Petersson
J. Phys. Org. Chem. 31 e3813 (2018) DOI:10.1002/poc.3813
Part of a special issue in honor of John D. Roberts.

Dithioamide Substitutions in Proteins: Effects on thermostability, peptide binding, and fluorescence quenching in calmodulin

Christopher R. Walters, John J. Ferrie, and E. James Petersson
Chem. Commun. 54 1766-1769 (2018) DOI:10.1039/C8CC00104A

Using a FRET Library with Multiple Probe Pairs To Drive Monte Carlo Simulations of α-Synuclein

John J. Ferrie, Conor M. Haney, Jimin Yoon, Buyan Pan, Yi-Chih Lin, Zahra Fakhraai, Elizabeth Rhoades, Abhinav Nath, and E. James Petersson
Biophys. J. 114 53-64 (2018) DOI:10.1016/j.bpj.2017.11.006
Highlighted on the Biophys. J. website and on the NSF Science360 News website.

Scalable thioarylation of unprotected peptides and biomolecules under Ni/photoredox catalysis

Brandon A. Vara, Xingpin Li, Simon Berritt, Christopher R. Walters, E. James Petersson, and Gary A. Molander
Chem. Sci. 9 336-344 (2018) DOI:10.1039/C7SC04292B

Fluorescence spectroscopy reveals N-terminal order in fibrillar forms of α-synuclein

Conor M. Haney and E. James Petersson
Chem. Commun. 54 833–836 (2018) DOI:10.1039/C7CC08601F

Thioamide Substitution Selectively Modulates Proteolysis and Receptor Activity of Therapeutic Peptide Hormones

Xing Chen, Elizabeth G. Mietlicki-Baase, Taylor M. Barrett, Lauren E. McGrath, Kieran Koch-Laskowski, John J. Ferrie, Matthew R. Hayes, and E. James Petersson
J. Am. Chem. Soc. 139 16688–16695 (2017) DOI:10.1021/jacs.7b08417
Highlighted in Nature.

A cryptophane-based “turn-on” 129Xe NMR biosensor for monitoring calmodulin

Brittany A. Riggle,  Mara Greenberg,  Yanfei Wang,  Rebecca F. Wissner,  Serge Zemerov,  E. James Petersson,  and  Ivan Dmochowski 
Org. Biomol. Chem. 15 8883-8887 (2017) DOI:10.1039/C7OB02391J

Multicolor Protein FRET with Tryptophan, Selective Coumarin-Cysteine Labeling, and Genetic Acridonylalanine Encoding

John J. Ferrie,* Naoya Ieda,* Conor M. Haney, Christopher R. Walters, Itthipol Sungwienwong, Jimin Yoon, and E. James Petersson
Chem. Commun. 53 11072-11075 (2017) DOI:10.1039/c7cc05492k

Selective imaging of internalized proteopathic α-synuclein seeds in primary neurons reveals mechanistic insight into transmission of synucleinopathies

Richard J. Karpowicz Jr., Conor M. Haney, Tiberiu S. Mihaila, Raizel M. Sandler, E. James Petersson and Virginia M.-Y. Lee
J. Biol. Chem. 292 13482-13497 (2017) DOI:10.1074/jbc.M117.780296
Selected as an Editor's Pick and highlighted by EurekAlert! and ALZForum.

Thioamide Labeling of Proteins through a Combination of Semisynthetic Methods

Christopher R. Walters, John J. Ferrie, E. James Petersson
in Chemical Ligation: Tools for Biomolecule Synthesis and Modification, John Wiley & Sons, Inc., Hoboken, NJ, USA. (2017) DOI:10.1002/9781119044116.ch10

Thieme Chemistry Journals Awardees – Where Are They Now? Special Issue

Improved Fmoc Deprotection Methods for the Synthesis of Thioamide-Containing Peptides and Proteins

D. Miklos Szantai-Kis,* Christopher R. Walters,* Taylor M. Barrett, Eileen M. Hoang, E. James Petersson
SYNLETT 28 1789–1794 (2017) DOI:10.1055/s-0036-1589027

Featured in Synform!


Effect of nascent peptide steric bulk on elongation kinetics in the ribosome exit tunnel

Pengse Po, Erin Delaney, Howard Gamper, Miklos Szanti-Kis, Lee Speight, LiWei Tu, Andrey Kosolapov, E. James Petersson, Ya-Ming Hou, Carol Deutsch
J. Mol. Biol. 429 1873–1888 (2017) DOI:10.1016/j.jmb.2017.04.019

Improving target amino acid selectivity in a permissive aminoacyl tRNA synthetase through counter-selection

Itthipol Sungwienwong,* Zachary M. Hostetler,* Robert J. Blizzard, Joseph J. Porter, Camden M. Driggers, Lea Z. Mbengi, José A. Villegas, Lee C. Speight, Jeffery G. Saven, John J. Perona, Rahul M. Kohli, Ryan A. Mehl, and E. James Petersson
Org. Biomol. Chem. 15 3603-3610 (2017) DOI:10.1039/C7OB00582B
Selected as a Hot Article for 2017!

Potential Artifacts in Sample Preparation Methods Used for Imaging Amyloid Oligomers and Protofibrils due to Surface-Mediated Fibril Formation

Yi-Chih Lin, Milton H. Repollet-Pedrosa, John J. Ferrie, E. James Petersson, and Zahra Fakhraai
J. Phys. Chem. B 121 2534–2542 (2017) DOI:10.1021/acs.jpcb.6b12560

The Effects of Thioamide Backbone Substitution on Protein Stability: A study in α-helical, β-sheet, and polyproline II helical contexts

Christopher R. Walters, D. Miklos Szantai-Kis, Yitao Zhang, Zachary E. Reinert, W. Seth Horne David M. Chenoweth, and E. James Petersson
Chem. Sci. 8 2868-2877 (2017) DOI:10.1039/C6SC05580J

Site-Specific Fluorescence Polarization for Studying the Disaggregation of α-Synuclein Fibrils by Small Molecules

Conor M. Haney,* Christina L. Cleveland,* Rebecca F. Wissner,* Lily Owei, Jaclyn Robustell, Malcolm J. Daniels, Merve Canyurt, Priscilla Rodriguez, Harry Ischiropoulos, Tobias Baumgart, and E. James Petersson
Biochemistry 56 683–691(2017) DOI:10.1021/acs.biochem.6b01060
Highlighted in Biochemistry Newsflash!

Chemoselective modifications for the traceless ligation of thioamide-containing peptides and proteins

Yanxin J. Wang, D. Miklos Szantai-Kis, and E. James Petersson
Org. Biomol. Chem. 14 6262-6269 (2016) DOI:10.1039/C6OB01020B

Electronic interactions of i, i + 1 dithioamides: increased fluorescence quenching and evidence for n-to-π* interactions

Yun Huang, John J. Ferrie, Xing Chen, Yitao Zhang, D. Miklos Szantai-Kis, David M. Chenoweth, and E. James Petersson
Chem. Commun. 52 7798-7801 (2016) DOI:10.1039/C6CC00105J

Comparison of strategies for non-perturbing labeling of α-synuclein to study amyloidogenesis

Conor M. Haney,* Rebecca F. Wissner,* John B. Warner, Yanxin J. Wang, John J. Ferrie, Dustin J. Covell, Richard J. Karpowicz, Jr., Virginia M.-Y. Lee, and E. James Petersson
Org. Biomol. Chem. 14 1584-1592 (2016) DOI:10.1039/C5OB02329G

Transferase-Mediated Labeling of Protein N-Termini with Click Chemistry Handles

Anne M. Wagner, John B. Warner, Haviva E. Garrett, Christopher R. Walters, and E. James Petersson
Methods Mol. Biol. 1337 109-127 (2015) DOI:10.1007/978-1-4939-2935-1_15

Multiply labeling proteins for studies of folding and stability

Conor M. Haney. Rebecca F. Wissner, and E. James Petersson
Curr. Opin. Chem. Biol. 28 123-130 (2015) DOI:10.1016/j.cbpa.2015.07.007

Semi-synthesis of thioamide containing proteins

Yanxin J. Wang, D. Miklos Szantai-Kis, and E. James Petersson
Org. Biomol. Chem. 13 5074-5081 (2015) DOI:10.1039/C5OB00224A
Selected as a Hot Article for 2015!

Inteins as Traceless Purification Tags for Unnatural Amino Acid Proteins

Solongo Batjargal, Christopher R. Walters, and E. James Petersson
J. Am. Chem. Soc. 137 1734-1737 (2015) DOI:10.1021/ja5103019

Specific Modulation of Protein Activity by Using a Bioorthogonal Reaction

John B. Warner, Anand K. Muthusamy, and E. James Petersson
ChemBioChem 15 2508-2514 (2014) DOI:10.1002/cbic.201402423

Surface Effects Mediate Self-Assembly of Amyloid-β Peptides

Yi-Chih Lin, E. James Petersson, and Zahra Fakhraai
ACS Nano 8 10178–10186 (2014) DOI:10.1021/nn5031669

Characterization of the Lipid Binding Properties of Otoferlin Reveal Specific Interactions Between PI(4,5)P2 and the C2C and C2F Domains

Murugesh Padmanarayana, Nicole Hams, Lee C. Speight, E. James Petersson, Ryan A. Mehl, and Colin P. Johnson
Biochemistry 53 5023-5033 (2014) DOI:10.1021/bi5004469

Two-for-one designer labels

E. James Petersson and John B. Warner
Nat. Chem. 6 379-381 (2014) DOI:10.1038/nchem.1935

On the use of thioamides as fluorescence quenching probes for tracking protein folding and stability

E. James Petersson, Jacob M. Goldberg, and Rebecca F. Wissner
Phys. Chem. Chem. Phys. 16 6827-6837 (2014) DOI:10.1039/C3CP55525A

Thioamide-Based Fluorescent Protease Sensors

Jacob M. Goldberg, Xing Chen, Nataline Meinhardt, Doron C. Greenbaum, and E. James Petersson
J. Am. Chem. Soc. 136 2086–2093 (2014) DOI:10.1021/ja412297x

Minimalist Approaches to Protein Labelling: Getting the Most Fluorescent Bang for Your Steric Buck

Lee C. Speight,* Moumita Samanta,* and E. James Petersson
Aust. J. Chem. 67 686-700 (2014) DOI:10.1071/CH13554

Included in Aust. J. Chem. 2013 Physical Organic Chemistry Gordon Research Conference Issue.


Synthesis of thioester peptides for the incorporation of thioamides into proteins by native chemical ligation

Solongo Batjargal, Yun Huang, Yanxin J. Wang, and E. James Petersson
J. Peptide Sci. 20 87-91 (2014) DOI:10.1002/psc.2589
Included in J. Peptide Sci. 2013 Chemical Protein Synthesis Meeting Issue.

Efficient Synthesis and In Vivo Incorporation of Acridon-2-ylalanine, a Fluorescent Amino Acid for Lifetime and Förster Resonance Energy Transfer/Luminescence Resonance Energy Transfer Studies

Lee C. Speight, Anand K. Muthusamy, Jacob M. Goldberg, John B. Warner, Rebecca F. Wissner, Taylor S. Willi, Bradley F. Woodman, Ryan A. Mehl, and E. James Petersson
J. Am. Chem. Soc. 135 18806-18814 (2013) DOI:10.1021/ja403247j

Thioamide Quenching of Fluorescent Probes through Photoinduced Electron Transfer: Mechanistic Studies and Applications

Jacob M. Goldberg, Solongo Batjargal, Benson S. Chen, and E. James Petersson
J. Am. Chem. Soc. 135 18651-18658 (2013) DOI:10.1021/ja409709x

Efficient, Traceless Semi-Synthesis of α-Synuclein Labeled with a Fluorophore/Thioamide FRET Pair

Rebecca F. Wissner, Anne M. Wagner, John B. Warner, and E. James Petersson
Synlett 24 2454-2458 (2013) DOI:10.1055/s-0033-1339853

Included in Synlett 2013 EuCheMS Young Investigator Workshop Issue.


Molecular basis for N-terminal acetylation by the heterodimeric NatA complex

Glen Liszczak, Jacob M. Goldberg, Håvard Foyn, E. James Petersson, Thomas Arnesen, and Ronen Marmorstein
Nat. Struct. Mol. Biol. 20 1098-1105 (2013) DOI:10.1038/nsmb.2636

Labeling Proteins with Fluorophore/Thioamide Förster Resonant Energy Transfer Pairs by Combining Unnatural Amino Acid Mutagenesis and Native Chemical Ligation

Rebecca F. Wissner, Solongo Batjargal, Colin M. Fadzen, and E. James Petersson
J. Am. Chem. Soc. 135 6529-6540 (2013) DOI:10.1021/ja4005943

Expressed Protein Ligation at Methionine: N-Terminal Attachment of Homocysteine, Ligation, and Masking

Tomohiro Tanaka, Anne M. Wagner, John B. Warner, Yanxin J. Wang, and E. James Petersson
Angew. Chem. Int. Ed. 52 6210-6213 (2013) DOI:10.1002/anie.201302065

Native Chemical Ligation of Thioamide-Containing Peptides: Development and Application to the Synthesis of Labeled α-Synuclein for Misfolding Studies

Solongo Batjargal, Yanxin J. Wang, Jacob M. Goldberg, Rebecca F. Wissner, and E. James Petersson
J. Am. Chem. Soc. 134 9172-9182 (2012) DOI:10.1021/ja2113245

Highlighted in C&E News: Chem. Eng. News 90 34 (2012).

Spotlighted in JACS: J. Am. Chem. Soc. 134 6499 (2012).


Minimalist Probes for Studying Protein Dynamics: Thioamide Quenching of Selectively Excitable Fluorescent Amino Acids

Jacob M. Goldberg, Lee C. Speight, Mark W. Fegley, and E. James Petersson
J. Am. Chem. Soc. 134 6088-6091 (2012) DOI: 10.1021/ja3005094

Highlighted in C&E News: Chem. Eng. News 90 34 (2012).


Thioamide Quenching of Intrinsic Protein Fluorescence

Jacob M. Goldberg, Rebecca F. Wissner, Alyssa M. Klein, and E. James Petersson
Chem. Commun. 48 1550-1552 (2012) DOI:10.1039/C1CC14708K
Included in Chem. Commun. 2012 Emerging Investigator Issue.

N-Terminal Protein Modification Using Simple Aminoacyl Transferase Substrates

Anne M. Wagner, Mark W. Fegley, John B. Warner, Christina L. J. Grindley, Nicholas P. Marotta, and E. James Petersson
J. Am. Chem. Soc. 133 15139-15147 (2011) DOI:10.1021/ja2055098

Thioamides as Fluorescence Quenching Probes: Minimalist Chromophores to Monitor Protein Dynamics

Jacob M. Goldberg, Solongo Batjargal, and E. James Petersson
J. Am. Chem. Soc. 132 14718-14720 (2010) DOI:10.1021/ja1044924
* These authors contributed equally to this manuscript.
For Professor Petersson's publications from Yale University or Caltech, click here.