Understanding the chemical mechanisms at play in atomic layer deposition (ALD) is critical for effective process development and expansion of ALD into more complex classes of materials. In this work, a mechanistic study of iron oxide deposited by ALD using
Targeted protein oxidation using a chromophore-modified rapamycin analog
Chemically induced dimerization of FKBP and FRB using rapamycin and rapamycin analogs has been utilized in a variety of biological applications. Formation of the FKBP-rapamycin-FRB ternary complex is typically used to activate a biological process and this interaction has proven to be essentially irreversible. In many cases, it would be beneficial to also have temporal control over deactivating a biological process once it has been initiated. Thus, we developed the first reactive oxygen species-generating rapamycin analog toward this goal. The BODIPY-rapamycin analog BORap is capable of dimerizing FKBP and FRB to form a ternary complex, and upon irradiation with 530 nm light, generates singlet oxygen to oxidize and inactivate proteins of interest fused to FKBP/FRB.
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- Award ID(s):
- 1904972
- NSF-PAR ID:
- 10344451
- Date Published:
- Journal Name:
- Chemical Science
- Volume:
- 12
- Issue:
- 40
- ISSN:
- 2041-6520
- Page Range / eLocation ID:
- 13425 to 13433
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract tert ‐butylferrocene and ozone as reactants is performed. Iron oxide ALD using ozone is a useful model system for mechanistic studies due to the prevalence of ozone‐based ALD processes and the uses of iron oxide in ternary and quaternary metal oxides. Results show that saturation conditions require significantly greater exposures of both reactants than is typically reported in the literature, and growths per cycle of greater than one monolayer of Fe2O3per cycle are observed and explained. A growth mechanism is proposed whereby increased ozone exposure results in uptake of superstoichiometric oxygen into the film. X‐ray characterizations reveal the presence of excess oxygen stored near the surface of films deposited with larger ozone exposures and show that increased ozone exposures cause crystalline domain rearrangement and conversion of the film from the γ‐maghemite phase to the α‐hematite phase. The mechanism described here has implications for the wider class of ozone‐based ALD processes, and potential applications of this growth phenomenon are discussed. -
INTRODUCTION Eukaryotes contain a highly conserved signaling pathway that becomes rapidly activated when adenosine triphosphate (ATP) levels decrease, as happens during conditions of nutrient shortage or mitochondrial dysfunction. The adenosine monophosphate (AMP)–activated protein kinase (AMPK) is activated within minutes of energetic stress and phosphorylates a limited number of substrates to biochemically rewire metabolism from an anabolic state to a catabolic state to restore metabolic homeostasis. AMPK also promotes prolonged metabolic adaptation through transcriptional changes, decreasing biosynthetic genes while increasing expression of genes promoting lysosomal and mitochondrial biogenesis. The transcription factor EB (TFEB) is a well-appreciated effector of AMPK-dependent signals, but many of the molecular details of how AMPK controls these processes remain unknown. RATIONALE The requirement of AMPK and its specific downstream targets that control aspects of the transcriptional adaptation of metabolism remain largely undefined. We performed time courses examining gene expression changes after various mitochondrial stresses in wild-type (WT) or AMPK knockout cells. We hypothesized that a previously described interacting protein of AMPK, folliculin-interacting protein 1 (FNIP1), may be involved in how AMPK promotes increases in gene expression after metabolic stress. FNIP1 forms a complex with the protein folliculin (FLCN), together acting as a guanosine triphosphate (GTP)–activating protein (GAP) for RagC. The FNIP1-FLCN complex has emerged as an amino acid sensor to the mechanistic target of rapamycin complex 1 (mTORC1), involved in how amino acids control TFEB activation. We therefore examined whether AMPK may regulate FNIP1 to dominantly control TFEB independently of amino acids. RESULTS AMPK was found to govern expression of a core set of genes after various mitochondrial stresses. Hallmark features of this response were activation of TFEB and increases in the transcription of genes specifying lysosomal and mitochondrial biogenesis. AMPK directly phosphorylated five conserved serine residues in FNIP1, suppressing the function of the FLCN-FNIP1 GAP complex, which resulted in dissociation of RagC and mTOR from the lysosome, promoting nuclear translocation of TFEB even in the presence of amino acids. FNIP1 phosphorylation was required for AMPK to activate TFEB and for subsequent increases in peroxisome proliferation–activated receptor gamma coactivator 1-alpha (PGC1α) and estrogen-related receptor alpha (ERRα) mRNAs. Cells in which the five serines in FNIP1 were mutated to alanine were unable to increase lysosomal and mitochondrial gene expression programs after treatment with mitochondrial poisons or AMPK activators despite the presence and normal regulation of all other substrates of AMPK. By contrast, neither AMPK nor its control of FNIP1 were needed for activation of TFEB after amino acid withdrawal, illustrating the specificity to energy-limited conditions. CONCLUSION Our data establish FNIP1 as the long-sought substrate of AMPK that controls TFEB translocation to the nucleus, defining AMPK phosphorylation of FNIP1 as a singular event required for increased lysosomal and mitochondrial gene expression programs after metabolic stresses. This study also illuminates the larger biological question of how mitochondrial damage triggers a temporal response of repair and replacement of damaged mitochondria: Within early hours, AMPK-FNIP1–activated TFEB induces a wave of lysosome and autophagy genes to promote degradation of damaged mitochondria, and a few hours later, TFEB–up-regulated PGC1⍺ and ERR⍺ promote expression of a second wave of genes specifying mitochondrial biogenesis. These insights open therapeutic avenues for several common diseases associated with mitochondrial dysfunction, ranging from neurodegeneration to type 2 diabetes to cancer. Mitochondrial damage activates AMPK to phosphorylate FNIP1, stimulating TFEB translocation to the nucleus and sequential waves of lysosomal and mitochondrial biogenesis. After mitochondrial damage, activated AMPK phosphorylates FNIP1 (1), causing inhibition of FLCN-FNIP1 GAP activity (2). This leads to accumulation of RagC in its GTP-bound form, causing dissociation of RagC, mTORC1, and TFEB from the lysosome (3). TFEB is therefore not phosphorylated and translocates to the nucleus, inducing transcription of lysosomal or autophagy genes, with parallel increases in NT-PGC1α mRNA (4), which, in concert with ERRα (5), subsequently induces mitochondrial biogenesis (6). CCCP, carbonyl cyanide m-chlorophenylhydrazone; CLEAR, coordinated lysosomal expression and regulation; GDP, guanosine diphosphate; P, phosphorylation. [Figure created using BioRender]more » « less
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Nanoscale complex metal oxides have transformed how technology is used around the world. A ubiquitous example is the class of electroreactive cathodes used in Li-ion batteries, found in portable electronics and electric cars. Lack of recycling infrastructure and financial drivers contribute to improper disposal, and ultimately, introduction of these materials into the environment. Outside of sealed operational conditions, it has been demonstrated that complex metal oxides can transform in the environment, and cause negative biological impact through leaching of cations into aqueous phases. Using a combined DFT and thermodynamics methodology, insights into the mechanism and driving forces of cation release can be studied at the molecular-level. Here, we describe design principles that can be drawn from previous collaborative research on complex metal oxide dissolution of the Li(Ni y Mn z Co 1−y−z )O 2 family of materials, and go on to posit ternary complex metal oxides in the delafossite structure type with controlled release behavior. Using equistoichiometric formulations in the delfossite structure, we use DFT and thermodynamics to model cation release. The release trends are discussed in terms of lattice stability, solution chemistry/solubility limits, and electronic/magnetic properties. Intercalation voltages are calculated and discussed as a predictive metric for potential functionality of the model materials.more » « less
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Fe is a critical nutrient to the marine biological pump, which is the process that exports photosynthetically fixed carbon in the upper ocean to the deep ocean. Fe limitation controls photosynthetic activity in major regions of the oceans, and the subsequent degradation of exported photosynthetic material is facilitated particularly by marine heterotrophic bacteria. Despite their importance in the carbon cycle and the scarcity of Fe in seawater, the Fe requirements, storage and cytosolic utilization of these marine heterotrophs has been less studied. Here, we characterized the Fe metallome of Pseudoalteromonas (BB2-AT2). We found that with two copies of bacterioferritin (Bfr), Pseudoalteromonas possesses substantial capacity for luxury uptake of Fe. Fe : C in the whole cell metallome was estimated (assuming C : P stoichiometry ∼51 : 1) to be between ∼83 μmol : mol Fe : C, ∼11 fold higher than prior marine bacteria surveys. Under these replete conditions, other major cytosolic Fe-associated proteins were observed including superoxide dismutase (SodA; with other metal SOD isoforms absent under Fe replete conditions) and catalase (KatG) involved in reactive oxygen stress mitigation and aconitase (AcnB), succinate dehydrogenase (FrdB) and cytochromes (QcrA and Cyt1) involved in respiration. With the aid of singular value decomposition (SVD), we were able to computationally attribute peaks within the metallome to specific metalloprotein contributors. A putative Fe complex TonB transporter associated with the closely related Alteromonas bacterium was found to be abundant within the Pacific Ocean mesopelagic environment. Despite the extreme scarcity of Fe in seawater, the marine heterotroph Pseudoalteromonas has expansive Fe storage capacity and utilization strategies, implying that within detritus and sinking particles environments, there is significant opportunity for Fe acquisition. Together these results imply an evolved dedication of marine Pseudoalteromonas to maintaining an Fe metalloproteome, likely due to its dependence on Fe-based respiratory metabolism.more » « less
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Latest algorithmic development has brought competitive classification accuracy for neural networks despite constraining the network parameters to ternary or binary representations. These findings show significant optimization opportunities to replace computationally-intensive convolution operations (based on multiplication) with more efficient and less complex operations such as addition. In hardware implementation domain, processing-in-memory architecture is becoming a promising solution to alleviate enormous energy-hungry data communication between memory and processing units, bringing considerable improvement for system performance and energy efficiency while running such large networks. In this paper, we review several of our recent works regarding Processing-in-Memory (PIM) accelerator based on Magnetic Random Access Memory computational sub-arrays to accelerate the inference mode of quantized neural networks using digital non-volatile memory rather than using analog crossbar operation. In this way, we investigate the performance of two distinct in-memory addition schemes compared to other digital methods based on processing-in-DRAM/GPU/ASIC design to tackle DNN power and memory wall bottleneck.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/D1SC04464H
