John Ferrie
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Thioamide substitution selectively modulates proteolysis and receptor activity of therapeutic peptide hormones
X Chen, EG Mietlicki-Baase, TM Barrett, LE McGrath, K Koch-Laskowski, ...
Journal of the American Chemical Society 139 (46), 16688-16695, 2017
A comparative protease stability study of synthetic macrocyclic peptides that mimic two endocrine hormones
JJ Ferrie, JJ Gruskos, AL Goldwaser, ME Decker, DA Guarracino
Bioorganic & medicinal chemistry letters 23 (4), 989-995, 2013
Electronic interactions of i, i+ 1 dithioamides: increased fluorescence quenching and evidence for n-to-π* interactions
Y Huang, JJ Ferrie, X Chen, Y Zhang, DM Szantai-Kis, DM Chenoweth, ...
Chemical Communications 52 (50), 7798-7801, 2016
Alpha synuclein fibrils contain multiple binding sites for small molecules
CJ Hsieh, JJ Ferrie, K Xu, I Lee, TJA Graham, Z Tu, J Yu, D Dhavale, ...
ACS chemical neuroscience 9 (11), 2521-2527, 2018
Comparison of strategies for non-perturbing labeling of α-synuclein to study amyloidogenesis
CM Haney, RF Wissner, JB Warner, YJ Wang, JJ Ferrie, DJ Covell, ...
Organic & biomolecular chemistry 14 (5), 1584-1592, 2016
Cyclized NDGA modifies dynamic α-synuclein monomers preventing aggregation and toxicity
MJ Daniels, JB Nourse, H Kim, V Sainati, M Schiavina, MG Murrali, B Pan, ...
Scientific reports 9 (1), 1-17, 2019
Using a FRET library with multiple probe pairs to drive monte carlo simulations of α-synuclein
JJ Ferrie, CM Haney, J Yoon, B Pan, YC Lin, Z Fakhraai, E Rhoades, ...
Biophysical journal 114 (1), 53-64, 2018
Multicolor protein FRET with tryptophan, selective coumarin-cysteine labeling, and genetic acridonylalanine encoding
JJ Ferrie, N Ieda, CM Haney, CR Walters, I Sungwienwong, J Yoon, ...
Chemical Communications 53 (80), 11072-11075, 2017
Systematic evaluation of soluble protein expression using a fluorescent unnatural amino acid reveals no reliable predictors of tolerability
ZM Hostetler, JJ Ferrie, MR Bornstein, I Sungwienwong, EJ Petersson, ...
ACS chemical biology 13 (10), 2855-2861, 2018
Dithioamide substitutions in proteins: effects on thermostability, peptide binding, and fluorescence quenching in calmodulin
CR Walters, JJ Ferrie, EJ Petersson
Chemical Communications 54 (14), 1766-1769, 2018
Synthesis and characterization of high affinity fluorogenic α-synuclein probes
Z Lengyel-Zhand, JJ Ferrie, B Janssen, CJ Hsieh, T Graham, K Xu, ...
Chemical Communications 56 (24), 3567-3570, 2020
Improving the fluorescent probe acridonylalanine through a combination of theory and experiment
I Sungwienwong, JJ Ferrie, JV Jun, C Liu, TM Barrett, ZM Hostetler, ...
Journal of physical organic chemistry 31 (8), e3813, 2018
Potential artifacts in sample preparation methods used for imaging amyloid oligomers and protofibrils due to surface-mediated fibril formation
YC Lin, MH Repollet-Pedrosa, JJ Ferrie, EJ Petersson, Z Fakhraai
The Journal of Physical Chemistry B 121 (12), 2534-2542, 2017
Identification of a nanomolar affinity α-synuclein fibril imaging probe by ultra-high throughput in silico screening
JJ Ferrie, Z Lengyel-Zhand, B Janssen, MG Lougee, S Giannakoulias, ...
Chemical science 11 (47), 12746-12754, 2020
The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer–promoter communication
JP Karr, JJ Ferrie, R Tjian, X Darzacq
Genes & Development 36 (1-2), 7-16, 2022
Fluorescent probes for studying thioamide positional effects on proteolysis reveal insight into resistance to cysteine proteases
C Liu, TM Barrett, X Chen, JJ Ferrie, EJ Petersson
ChemBioChem 20 (16), 2059-2062, 2019
A unified de novo approach for predicting the structures of ordered and disordered proteins
JJ Ferrie, EJ Petersson
The Journal of Physical Chemistry B 124 (27), 5538-5548, 2020
Rosetta machine learning models accurately classify positional effects of thioamides on proteolysis
S Giannakoulias, SR Shringari, C Liu, HAT Phan, TM Barrett, JJ Ferrie, ...
The Journal of Physical Chemistry B 124 (37), 8032-8041, 2020
Rosetta custom score functions accurately predict ΔΔ G of mutations at protein–protein interfaces using machine learning
SR Shringari, S Giannakoulias, JJ Ferrie, EJ Petersson
Chemical Communications 56 (50), 6774-6777, 2020
Thioamide labeling of proteins through a combination of semisynthetic methods
CR Walters, JJ Ferrie, EJ Petersson
Chemical ligation: Tools for biomolecule synthesis and modification, 355, 2017
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