A5078916441- Cellular Mechanics and Interactions
- RNA and protein synthesis mechanisms
- Microbial Natural Products and Biosynthesis
- Chromosomal and Genetic Variations
- DNA Repair Mechanisms
- Plant biochemistry and biosynthesis
- Heat shock proteins research
- RNA modifications and cancer
- Photosynthetic Processes and Mechanisms
- Genomics and Chromatin Dynamics
- DNA and Nucleic Acid Chemistry
- RNA Research and Splicing
- Nuclear Structure and Function
- Enzyme Structure and Function
- Cardiomyopathy and Myosin Studies
- Advanced Electron Microscopy Techniques and Applications
- Enzyme Production and Characterization
- 14-3-3 protein interactions
- Bacterial Genetics and Biotechnology
- ATP Synthase and ATPases Research
- Photoreceptor and optogenetics research
- Graphite, nuclear technology, radiation studies
- Genomics and Phylogenetic Studies
- Advanced Proteomics Techniques and Applications
- Metalloenzymes and iron-sulfur proteins
University of Pennsylvania
2017-2024
Rockefeller University
2021-2024
California University of Pennsylvania
2020-2021
Abstract The LINE-1 (L1) retrotransposon is an ancient genetic parasite that has written around one-third of the human genome through a ‘copy and paste’ mechanism catalysed by its multifunctional enzyme, open reading frame 2 protein (ORF2p) 1 . ORF2p reverse transcriptase (RT) endonuclease activities have been implicated in pathophysiology cancer 2,3 , autoimmunity 4,5 ageing 6,7 making potential therapeutic target. However, lack structural mechanistic knowledge hampered efforts to...
The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, peripheral regions can exhibit considerable variation within and between species. One such structure cage-like basket. crucial roles mRNA surveillance chromatin organization, an architectural has remained elusive. Using in-cell cryo-electron tomography subtomogram analysis, we explored NPC's structural variations basket across fungi...
Actin-related protein (Arp) 2/3 complex nucleates branched actin networks that drive cell motility. It consists of seven proteins, including two actin-related subunits (Arp2 and Arp3). Two nucleation-promoting factors (NPFs) bind Arp2/3 during activation, but the order, specific interactions, contribution each NPF to activation are unresolved. Here, we report cryo-electron microscopy structure recombinantly expressed human with WASP family NPFs bound address mechanism activation. A...
Abstract Nuclear pore complexes (NPCs) mediate nucleocytoplasmic transport of specific macromolecules while impeding the exchange unsolicited material. However, key aspects this gating mechanism remain controversial. To address issue, we determined nanoscopic behavior permeability barrier directly within yeast S. cerevisiae NPCs at transport-relevant timescales. We show that large intrinsically disordered domains phenylalanine-glycine repeat nucleoporins (FG Nups) exhibit highly dynamic...
Abstract The versatile nucleotide excision repair (NER) pathway initiates as the XPC–RAD23B–CETN2 complex first recognizes DNA lesions from genomic and recruits general transcription factor complex, TFIIH, for subsequent lesion verification. Here, we present a cryo-EM structure of an NER initiation containing Rad4–Rad23-Rad33 (yeast homologue XPC–RAD23B–CETN2) 7-subunit coreTFIIH assembled on carcinogen-DNA adduct at 3.9–9.2 Å resolution. A ~30-bp duplex could be mapped it straddles between...
Abstract Fusicoccadiene synthase from Phomopsis amygdali (PaFS) is a unique bifunctional terpenoid that catalyzes the first two steps in biosynthesis of diterpene glycoside Fusicoccin A, mediator 14-3-3 protein interactions. The prenyltransferase domain PaFS generates geranylgeranyl diphosphate, which cyclase then utilizes to generate fusicoccadiene, tricyclic hydrocarbon skeleton A. Here, we use cryo-electron microscopy show structure full-length consists central octameric core domains,...
Abstract Positive feedback loops involving signaling and actin assembly factors mediate the formation remodeling of branched networks in processes ranging from cell organelle motility to mechanosensation. The Arp2/3 complex inhibitor Arpin controls directional persistence migration by interrupting a loop Rac-WAVE-Arp2/3 complex, but Arpin’s mechanism inhibition is unknown. Here, we describe cryo-EM structure bound at 3.24-Å resolution. Unexpectedly, binds similarly WASP-family...
The nuclear pore complex (NPC) physically interacts with chromatin and regulates gene expression. Saccharomyces cerevisiae inner ring nucleoporin Nup170 has been implicated in organization the maintenance of silencing subtelomeric regions. To gain insight into how this process, we used protein-protein interactions, genetic transcriptome correlation analyses to identify Ctf18-RFC complex, an alternative proliferating cell antigen (PCNA) loader, as a facilitator regulatory functions Nup170. is...
The evolutionarily conserved HIRA/Hir histone chaperone complex and ASF1a/Asf1 co-chaperone cooperate to deposit (H3/H4)
Abstract Cortactin coactivates Arp2/3 complex synergistically with WASP-family nucleation-promoting factors (NPFs) and stabilizes branched networks by linking to F-actin. It is poorly understood how cortactin performs these functions. We describe the 2.89 Å resolution cryo-EM structure of cortactin’s N-terminal domain (Cort 1-76 ) bound complex. binds through an inverted Acidic (D20-V29), which targets same site on Arp3 as NPFs but opposite polarity. Sequences N- C-terminal do not increase...
The loss and mutation of Topoisomerase 3β (TOP3B), the only known eukaryotic topoisomerase with ability to catalyze RNA strand passage reactions, is linked schizophrenia, autism, intellectual disability. Uniquely, TOP3B primarily localizes cytoplasm has been shown regulate mRNA translation stability a subset transcripts. Three neurological disease-linked de novo point mutations outside active site have identified but their impact on activity in cells remains poorly understood. Upon...
Abstract Respiratory electron transport complexes are organized as individual entities or combined large supercomplexes (SC). Gram-negative bacteria deploy a mitochondrial-like cytochrome (cyt) bc 1 (Complex III, CIII 2 ), and may have specific cbb 3 -type cyt c oxidases IV, CIV) instead of the canonical aa CIV. Electron transfer between these is mediated by soluble ( ) membrane-anchored y cyts. Here, we report structure an engineered - type SC (CIII CIV, 5.2 Å resolution) three conformers...
The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, peripheral regions can exhibit considerable variation within and between species. One such structure cage-like basket. crucial roles mRNA surveillance chromatin organization, an architectural has remained elusive. Using in-cell cryo-electron tomography subtomogram analysis, we explored NPC's structural variations basket across fungi (yeast;
Arp2/3 complex generates branched actin networks that drive fundamental processes such as cell motility and cytokinesis. The comprises seven proteins, including actin-related proteins (Arps) 2 3 five scaffolding (ArpC1–ArpC5) mediate interactions with a pre-existing (mother) filament at the branch junction. exists in two main conformations, inactive Arps interacting end-to-end active side-by-side like subunits of short-pitch helix filament. Several cofactors transition toward state, ATP...
Direct methods for determining the fidelity of DNA polymerases are robust, with relatively little sample manipulation before sequencing. In contrast, measuring RNA polymerase and reverse transcriptase fidelities complicated by additional preparation steps that introduce ambiguity error. Here, we describe a sequencing method, termed Roll-Seq, simultaneously individual transcriptases (RT) using Pacific Biosciences single molecule real-time By high rolling-circle activity, Roll-Seq generates...
Cryo-EM structure of TFIIK provides insight into CTD phosphorylation RNA polymerase II in the preinitiation-Mediator complex.
Significance All eukaryotes respond to DNA damage by polyubiquitylation and degradation of the largest subunit RNA polymerase II (pol II), facilitated Elongin-Cullin ubiquitin ligase. In yeast, recruitment ligase pol is dependent on Def1. We report a finding made in course isolating TFIIH-Def1 from yeast that suggests potential novel function Def1 as transcription regulator response cellular stress. The regulation demonstrably separable its role coordinating stability
Fusicoccadiene synthase from the fungus
The mechanisms that regulate the physical properties of cell interior remain poorly understood, especially at mesoscale (10nm-100nm). Changes in these have been suggested to be crucial for both normal physiology and disease. Many macromolecules molecular assemblies such as ribosomes, RNA polymerase, biomolecular condensates span size range. Therefore, we need better tools study cellular environment this scale. A recent approach has use genetically encoded multimeric nanoparticles (GEMs),...
Abstract The versatile nucleotide excision repair (NER) pathway initiates as the XPC-RAD23B-CETN2 complex first recognizes DNA lesions from genomic and recruits general transcription factor complex, TFIIH, for subsequent lesion verification. Here, we present a cryo-EM structure of an NER initiation containing Rad4-Rad23-Rad33 (yeast homologue XPC-RAD23B-CETN2) 7-subunit core TFIIH assembled on carcinogen-DNA adduct at 3.9–9.2 Å resolution. A ~30-bp duplex could be mapped it straddles between...
I will showcase some of our latest research on LINE-1 (L1) retrotransposons. L1 is the only active, autonomous (protein coding) retrotransposon in humans; non-autonomous SINEs, such as Alu, hijack for their own mobilization. proliferates genomes through a 'copy-and-paste' mechanism that involves viral-like ribonucleoprotein intermediate, imbued with immunogenic pathogen associated molecular patterns. proteins (ORF1p, ORF2p) preferentially assemble RNA encodes them (a property termed cis...