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John Ferrie
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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
802022
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
782017
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
512018
“Structure”-function relationships in eukaryotic transcription factors: The role of intrinsically disordered regions in gene regulation
JJ Ferrie, JP Karr, R Tjian, X Darzacq
Molecular Cell 82 (21), 3970-3984, 2022
382022
Cyclized NDGA modifies dynamic α-synuclein monomers preventing aggregation and toxicity
MJ Daniels, JB Nourse Jr, H Kim, V Sainati, M Schiavina, MG Murrali, ...
Scientific reports 9 (1), 2937, 2019
382019
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
372016
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
362016
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
342013
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
322020
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
322020
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
282018
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
262018
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
242017
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
222018
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
192018
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
192017
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
172020
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
142019
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
122020
Detecting molecular interactions in live-cell single-molecule imaging with proximity-assisted photoactivation (PAPA)
TGW Graham, JJ Ferrie, GM Dailey, R Tjian, X Darzacq
Elife 11, e76870, 2022
112022
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Articles 1–20