A5037552980- Parkinson's Disease Mechanisms and Treatments
- Protein Structure and Dynamics
- Chemical Synthesis and Analysis
- Click Chemistry and Applications
- Alzheimer's disease research and treatments
- RNA and protein synthesis mechanisms
- Biotin and Related Studies
- Advanced Fluorescence Microscopy Techniques
- Enzyme Structure and Function
- Genomics and Chromatin Dynamics
- Neurological disorders and treatments
- Protein Degradation and Inhibitors
- RNA Research and Splicing
- Receptor Mechanisms and Signaling
- Biofuel production and bioconversion
- DNA and Nucleic Acid Chemistry
- Bioinformatics and Genomic Networks
- Biochemical and biochemical processes
- Advanced Biosensing Techniques and Applications
- Genetic Neurodegenerative Diseases
- Synthesis and Reactivity of Sulfur-Containing Compounds
- Electron Spin Resonance Studies
- Computational Drug Discovery Methods
- RNA modifications and cancer
- Photochromic and Fluorescence Chemistry
University of California, Berkeley
2021-2023
Howard Hughes Medical Institute
2021-2023
University of Pennsylvania
2015-2023
Philadelphia University
2015-2020
California University of Pennsylvania
2015-2020
College of New Jersey
2012-2015
Peptide hormones are attractive as injectable therapeutics and imaging agents, but they often require extensive modification by mutagenesis and/or chemical synthesis to prevent rapid in vivo degradation. Alternatively, the single-atom, O-to-S of peptide backbone thioamidation has potential selectively perturb interactions with proteases while preserving other proteins, such target receptors. Here, we use validated diabetes therapeutic, glucagon-like peptide-1 (GLP-1), clinical investigation,...
Transcription coactivators are proteins or protein complexes that mediate transcription factor (TF) function. However, they lack DNA-binding capacity, prompting the question of how engage target loci. Three non-exclusive hypotheses have been posited: recruited by complexing with TFs, binding histones through epigenetic reader domains, partitioning into condensates their extensive intrinsically disordered regions. Using p300 as a prototypical coactivator, we systematically mutated its...
The fibrillary aggregation of the protein alpha synuclein (Asyn) is a hallmark Parkinson's disease, and identification small molecule binding sites on fibrils essential to development diagnostic imaging probes. A series molecular modeling, photoaffinity labeling, mass spectrometry, radioligand studies were conducted Asyn fibrils. results these revealed presence three different within fibrillar capable molecules with moderate high affinity. knowledge amino acid residues in will be important...
Single-molecule imaging provides a powerful way to study biochemical processes in live cells, yet it remains challenging track single molecules while simultaneously detecting their interactions. Here, we describe novel property of rhodamine dyes, proximity-assisted photoactivation (PAPA), which one fluorophore (the ‘sender’) can reactivate second ‘receiver’) from dark state. PAPA requires proximity between the two fluorophores, operates at longer average intermolecular distance than Förster...
Growing evidence implicates α-synuclein aggregation as a key driver of neurodegeneration in Parkinson's disease (PD) and other neurodegenerative disorders. Herein, the molecular structural mechanisms inhibiting by novel analogs nordihydroguaiaretic acid (NDGA), phenolic dibenzenediol lignan, were explored using an array biochemical biophysical methodologies. NDGA induced modest, progressive compaction monomeric α-synuclein, preventing into amyloid-like fibrils. This conformational remodeling...
Ultra-high throughput <italic>in silico</italic> screening identified molecules that bind to α-synuclein fibrils, which were analyzed by photo-crosslinking, structure-activity studies, and radioligand binding validate this approach for finding imaging probes.
Complementary methods for site-specific protein labeling are used to introduce fluorescent probes into the Parkinson's Disease α-synuclein examine fibril formation and cellular uptake.
Adjacent thioamides can have electronic interactions that alter spectral properties and fluorescence quenching.
Fluorescent molecules are powerful tools for imaging α-synuclein pathology. Here, we demonstrate that benzofuranone derivatives have high affinity and display different binding to α-synucleinopathies in post-mortem brain tissue.
Improvements in genetic code expansion have made preparing proteins with diverse functional groups almost routine. Nonetheless, unnatural amino acids (Uaas) pose theoretical burdens on protein solubility, and determinants of position-specific tolerability to Uaas remain underexplored. To broadly examine associations, we systematically assessed the effect substituting fluorescent Uaa, acridonylalanine, at more than 50 chemically, evolutionarily, structurally residues two bacterial proteins:...
As recognition of the abundance and relevance intrinsically disordered proteins (IDPs) continues to grow, demand increases for methods that can rapidly predict conformational ensembles populated by these proteins. To date, IDP simulations have largely been dominated molecular dynamics (MD) simulations, which require significant compute times and/or complex hardware. Recent developments in MD afforded capable simulating both ordered proteins, yet accurate fold prediction from a sequence has...
A combination of labeling techniques enables site-specific installation fluorescent probes for measuring distances within proteins by Förster resonance energy transfer (FRET).
Combinations of thioamide modifications can enhance protein stability or fluorescence quenching.
Reweighting Rosetta energy terms <italic>via</italic> machine learning improves prediction of ΔΔ<italic>G</italic> values for mutations at protein interfaces, providing insight into biological processes and guiding development therapeutic molecules targeted these interfaces.
Accurate imaging of nanometer-sized structures and morphologies is essential to characterizing amyloid species formed at various stages aggregation. In this article, we examine the effect different drying procedures on final morphology surface-mediated fibrils during incubation period, which may then be mistaken as oligomers or protofibrils intentionally in solution for a particular study. Atomic force microscopy results show that some artifacts, such globules, flakelike structures, even...
Acridonylalanine (Acd) is a useful fluorophore for studying proteins by fluorescence spectroscopy, but it can potentially be improved being made longer wavelength or brighter. Here, we report the synthesis of Acd core derivatives and their photophysical characterization. We also performed ab initio calculations absorption emission spectra derivatives, which agree well with experimental measurements. The amino acid aminoacridonylalanine (Aad) was synthesized in forms appropriate genetic...
Abstract Thioamide substitutions of the peptide backbone have been shown to reduce proteolytic degradation, and this property can be used generate competitive protease inhibitors stabilize peptides toward degradation in vivo. Here, we present a straightforward sensor design that allows systematic study positional effects thioamide substitution by using real‐time fluorescence. scanning substrates five papain family cysteine proteases demonstrates at or near scissile bond slow proteolysis all...
Thioamide substitutions of the peptide backbone have been shown to stabilize therapeutic and imaging peptides toward proteolysis. In order rationally design thioamide modifications, we developed a novel Rosetta custom score function classify positional effects on proteolysis in substrates serine cysteine proteases. Peptides interest were docked into proteases using FlexPepDock application Rosetta. Docked complexes modified contain thioamides parametrized through creation atom types based ab...
Transcription coactivators are proteins or protein complexes that mediate transcription factor (TF) function. However, they lack DNA binding capacity, prompting the question of how engage target loci. Three non-exclusive hypotheses have been posited: recruited by complexing with TFs, histones through epigenetic reader domains, partitioning into phase-separated compartments their extensive intrinsically disordered regions (IDRs). Using p300 as a prototypical coactivator, we systematically...
Abstract The incorporation of unnatural amino acids (Uaas) has provided an avenue for novel chemistries to be explored in biological systems. However, the successful application Uaas is often hampered by site-specific impacts on protein yield and solubility. Although previous efforts identify features which accurately capture these effects have been unsuccessful, we developed a set Rosetta Custom Score Functions alternative Empirical that predict acridon-2-yl-alanine (Acd) Acd-containing...