John J. Ferrie

University of California, Berkeley

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E. James Petersson

California University of Pennsylvania

Sam Giannakoulias

University of Pennsylvania

Robert Tjian

Howard Hughes Medical Institute

Xavier Darzacq

University of California, Berkeley

Conor M. Haney

Philadelphia University

Thomas G.W. Graham

University of California, Berkeley

Gina M. Dailey

University of California, Berkeley

Sumant R. Shringari

University of Pennsylvania

Virginia M.‐Y. Lee

University of Pennsylvania

Robert H. Mach

University of Pennsylvania

Cooperative Institutions

University of Pennsylvania

California University of Pennsylvania

Philadelphia University

College of New Jersey

Washington University in St. Louis

University of California, Berkeley

Institute on Aging

University of Wisconsin–Madison

Howard Hughes Medical Institute

Institute for Neurodegenerative Disorders

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The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer–promoter communication

Genes & Development (2021)

Jonathan P. Karr John J. Ferrie Robert Tjian Xavier Darzacq

How distal cis -regulatory elements (e.g., enhancers) communicate with promoters remains an unresolved question of fundamental importance. Although transcription factors and cofactors are known to mediate this communication, the mechanism by which diffusible molecules relay regulatory information from one position to another along the chromosome is a biophysical puzzle—one that needs to be revisited in light of recent data that cannot easily fit into previous solutions. Here we propose a new model that diverges from the textbook enhancer–promoter looping paradigm and offer a synthesis of the literature to make a case for its plausibility, focusing on the coactivator p300.

Transcription

10.1101/gad.349160.121

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Citations (111)

Synthesis and characterization of high affinity fluorogenic α-synuclein probes

Chemical Communications (2020)

Zsofia Lengyel‐Zhand John J. Ferrie Bieneke Janssen Chia‐Ju Hsieh Thomas J. A. Graham

Fluorescent molecules are powerful tools for imaging α-synuclein pathology. Here, we demonstrate that benzofuranone derivatives have high affinity for α-synuclein and display different binding to α-synucleinopathies in post-mortem brain tissue.

Synucleinopathies

Characterization

10.1039/c9cc09849f

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Citations (29)

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

The Journal of Physical Chemistry (2017)

Yi‐Chih Lin Milton H. Repollet-Pedrosa John J. Ferrie E. James Petersson Zahra Fakhraai

Accurate imaging of nanometer-sized structures and morphologies is essential to characterizing amyloid species formed at various stages of amyloid aggregation. In this article, we examine the effect of different drying procedures on the final morphology of surface-mediated fibrils formed during the incubation period, which may then be mistaken as oligomers or protofibrils intentionally formed in solution for a particular study. Atomic force microscopy results show that some artifacts, such as globules, flakelike structures, and even micrometer-long fibrils, can be produced under various drying conditions. We also demonstrate that one can prevent drying artifacts by using an appropriate spin-coating procedure to dry amyloid samples. This procedure can bypass the wetting/dewetting transition of the liquid layer during the drying process and preserve the structure of interest on the substrate without generating drying artifacts.

Dewetting

Micrometer

Amyloid (mycology)

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The Nature of Peptidomimetics: Synthetic Peptide Macrocycles as Potential Therapeutics and Artificial Peptide Helices

Danielle A. Guarracino John J. Ferrie Jessica J. Gruskos Ari L. Goldwaser Megan E. Decker

Peptidomimetic

10.17952/24aps.2015.012

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Identification of a nanomolar affinity α-synuclein fibril imaging probe by ultra-high throughput in silico screening

Chemical Science (2020)

John J. Ferrie Zsofia Lengyel‐Zhand Bieneke Janssen Marshall G. Lougee Sam Giannakoulias

Ultra-high throughput in silico screening identified molecules that bind to α-synuclein fibrils, which were analyzed by photo-crosslinking, structure-activity studies, and radioligand binding to validate this approach for finding imaging probes.

Identification

10.1039/d0sc02159h

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Citations (38)

Thioamide Labeling of Proteins through a Combination of Semisynthetic Methods

Christopher R. Walters John J. Ferrie E. James Petersson

Backbone thioamide substitutions in peptides and proteins provide a nearly isosteric substitution for their oxoamide counterparts with distinct spectroscopic and electrostatic properties that may be harnessed for biophysical studies. In this review, we discuss thiopeptide synthesis and the important advances made toward achieving thioamide replacements in larger, structurally defined proteins through native chemical ligation. Finally, we examine some of the protein systems that have been studied with thioamide substitutions to highlight their versatility and potential as biophysical probes.

Thioamide

10.1002/9781119044116.ch10

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Citations (3)

Publisher's Note: “Photo-induced refractive index and topographical surface gratings in functionalized nanocarbon solid film” [Appl. Phys. Lett. 107, 181102 (2015)]

Applied Physics Letters (2015)

David J. McGee John J. Ferrie Aljoscha Plachy Yongho Joo Jonathan W. Choi

First Page

Solid surface

10.1063/1.4937143

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

Scientific Reports (2019)

Malcolm J. Daniels J. Brucker Nourse Hanna Kim Valerio Sainati Marco Schiavina

Growing evidence implicates α-synuclein aggregation as a key driver of neurodegeneration in Parkinson's disease (PD) and other neurodegenerative disorders. Herein, the molecular and structural mechanisms of inhibiting α-synuclein aggregation by novel analogs of nordihydroguaiaretic acid (NDGA), a phenolic dibenzenediol lignan, were explored using an array of biochemical and biophysical methodologies. NDGA analogs induced modest, progressive compaction of monomeric α-synuclein, preventing aggregation into amyloid-like fibrils. This conformational remodeling preserved the dynamic adoption of α-helical conformations, which are essential for physiological membrane interactions. Oxidation-dependent NDGA cyclization was required for the interaction with monomeric α-synuclein. NDGA analog-pretreated α-synuclein did not aggregate even without NDGA-analogs in the aggregation mixture. Strikingly, NDGA-pretreated α-synuclein suppressed aggregation of naïve untreated aggregation-competent monomeric α-synuclein. Further, cyclized NDGA reduced α-synuclein-driven neurodegeneration in Caenorhabditis elegans. The cyclized NDGA analogs may serve as a platform for the development of small molecules that stabilize aggregation-resistant α-synuclein monomers without interfering with functional conformations yielding potential therapies for PD and related disorders.

Nordihydroguaiaretic acid

10.1038/s41598-019-39480-z

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Citations (39)

The development of process models : executive summary

John J. Ferrie

Executive summary

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Investigating the Trimethylamine N-Oxide (TMAO) Induced Structure of α-Synuclein

Biophysical Journal (2015)