The voltage-dependent anion channel (VDAC) mediates trafficking of small molecules and ions across the eukaryotic outer mitochondrial membrane. VDAC also interacts with antiapoptotic proteins from ...the Bcl-2 family, and this interaction inhibits release of apoptogenic proteins from the mitochondrion. We present the nuclear magnetic resonance (NMR) solution structure of recombinant human VDAC-1 reconstituted in detergent micelles. It forms a 19-stranded β barrel with the first and last strand parallel. The hydrophobic outside perimeter of the barrel is covered by detergent molecules in a beltlike fashion. In the presence of cholesterol, recombinant VDAC-1 can form voltage-gated channels in phospholipid bilayers similar to those of the native protein. NMR measurements revealed the binding sites of VDAC-1 for the Bcl-2 protein Bcl-xL, for reduced β-nicotinamide adenine dinucleotide, and for cholesterol. Bcl-xL interacts with the VDAC barrel laterally at strands 17 and 18.
Programmed Cell Death 4 (PDCD4) is a protein known to bind eukaryotic initiation factor 4A (eIF4A), inhibit translation initiation, and act as a tumor suppressor. PDCD4 contains two C-terminal MA3 ...domains, which are thought to be responsible for its inhibitory function. Here, we analyze the structures and inhibitory functions of these two PDCD4 MA3 domains by x-ray crystallography, NMR, and surface plasmon resonance. We show that both MA3 domains are structurally and functionally very similar and bind specifically to the eIF4A N-terminal domain (eIF4A-NTD) using similar binding interfaces. We found that the PDCD4 MA3 domains compete with the eIF4G MA3 domain and RNA for eIF4A binding. Our data provide evidence that PDCD4 inhibits translation initiation by displacing eIF4G and RNA from eIF4A. The PDCD4 MA3 domains act synergistically to form a tighter and more stable complex with eIF4A, which explains the need for two tandem MA3 domains.
Abstract
Abrupt warming events recorded in Greenland ice cores known as Dansgaard-Oeschger (DO) interstadials are linked to changes in tropical circulation during the last glacial cycle. ...Corresponding variations in South American summer monsoon (SASM) strength are documented, most commonly, in isotopic records from speleothems, but less is known about how these changes affected precipitation and Andean glacier mass balance. Here we present a sediment record spanning the last ~50 ka from Lake Junín (Peru) in the tropical Andes that has sufficient chronologic precision to document abrupt climatic events on a centennial-millennial time scale. DO events involved the near-complete disappearance of glaciers below 4700 masl in the eastern Andean cordillera and major reductions in the level of Peru’s second largest lake. Our results reveal the magnitude of the hydroclimatic disruptions in the highest reaches of the Amazon Basin that were caused by a weakening of the SASM during abrupt arctic warming. Accentuated warming in the Arctic could lead to significant reductions in the precipitation-evaporation balance of the southern tropical Andes with deleterious effects on this densely populated region of South America.
The cyanobacterial clock proteins KaiA and KaiB are proposed as regulators of the circadian rhythm in cyanobacteria. Mutations in both proteins have been reported to alter or abolish circadian ...rhythmicity. Here, we present molecular models of both KaiA and KaiB from the cyanobacteria Anabaena sp PCC7120 deduced by crystal structure analysis, and we discuss how clock‐changing or abolishing mutations may cause their resulting circadian phenotype. The overall fold of the KaiA monomer is that of a four‐helix bundle. KaiB, on the other hand, adopts an alpha–beta meander motif. Both proteins purify and crystallize as dimers. While the folds of the two proteins are clearly different, their size and some surface features of the physiologically relevant dimers are very similar. Notably, the functionally relevant residues Arg 69 of KaiA and Arg 23 of KaiB align well in space. The apparent structural similarities suggest that KaiA and KaiB may compete for a potential common binding site on KaiC.
Rcd‐1, a protein highly conserved across eukaryotes, was initially identified as a factor essential for nitrogen starvation‐invoked differentiation in fission yeast, and its Saccharomyces cerevisiae ...homolog, CAF40, has been identified as part of the CCR4–NOT transcription complex, where it interacts with the NOT1 protein. Mammalian homologs are involved in various cellular differentiation processes including retinoic acid‐induced differentiation and hematopoetic cell development. Here, we present the 2.2 Å X‐ray structure of the highly conserved region of human Rcd‐1 and investigate possible functional abilities of this and the full‐length protein. The monomer is made up of six armadillo repeats forming a solvent‐accessible, positively‐charged cleft 21–22 Å wide that, in contrast to other armadillo proteins, stays fully exposed in the dimer. Prompted by this finding, we established that Rcd‐1 can bind to single‐ and double‐stranded oligonucleotides in vitro with the affinity of G/C/T ≫ A. Mutation of an arginine residue within the cleft strongly reduced or abolished oligonucleotide binding. Rcd‐1's ability to bind to nucleic acids, in addition to the previously reported protein–protein interaction with NOT1, suggests a new feature in Rcd‐1's role in regulation of overall cellular differentiation processes.
We employ a combination of 13C/15N magic angle spinning (MAS) NMR and 2H NMR to study the structural and functional consequences of different membrane environments on VDAC1 and, conversely, the ...effect of VDAC1 on the structure of the lipid bilayer. MAS spectra reveal a well-structured VDAC1 in 2D crystals of dimyristoylphosphatidylcholine (DMPC) and diphytanoylphosphatidylcholine (DPhPC), and their temperature dependence suggests that the VDAC structure does not change conformation above and below the lipid phase transition temperature. The same data show that the N-terminus remains structured at both low and high temperatures. Importantly, functional studies based on electrophysiological measurements on these same samples show fully functional channels, even without the presence of Triton X-100 that has been found necessary for in vitro-refolded channels. 2H solid-state NMR and differential scanning calorimetry were used to investigate the dynamics and phase behavior of the lipids within the VDAC1 2D crystals. 2H NMR spectra indicate that the presence of protein in DMPC results in a broad lipid phase transition that is shifted from 19 to ∼27 °C and show the existence of different lipid populations, consistent with the presence of both annular and bulk lipids in the functionally and structurally homogeneous samples.
Deep sediment cores from long-lived lake basins are fundamental records of paleoenvironmental history, but the power of these reconstructions has been often limited by poor age control. ...Uranium-thorium (U-Th) dating has the potential to fill a gap in current geochronological tools available for such sediment archives. We present our systematic approach to U-Th date carbonate-rich sediments from the ∼100 m drill core from Lake Junín, Peru. The results form the foundation of an age-depth model spanning ∼700 kyrs. High uranium concentrations (0.3–4 ppm) of these sediments allow us to date smaller amounts of material, giving us the opportunity to improve sample selection by avoiding detrital contamination, the greatest factor limiting the success of previous U-Th dating efforts in other lake basins. Despite this advantage, the dates from 174 analyses on 55 bulk carbonate samples reveal significant scatter that cannot be resolved with traditional isochrons, suggesting that at least some of the sediments have not remained closed systems. To understand the source of noise in the geochronological data, we first apply threshold criteria that screen samples by their U/Th ratio, reproducibility, and δ234Uinitial value. We then compare these results with facies types, trace element concentrations, carbonate and total organic carbon content, color reflectance, mineralogy, and ostracode shell color to investigate the causes of open system behavior. Alongside simulations of the isotopic evolution of our samples, we find that the greatest impediment to U-Th dating of these sediments is not detrital contamination, but rather post-depositional remobilization of uranium. Examining U-Th data in these contexts, we identify samples that have likely experienced the least amount of alteration, and use dates from those samples as constraints for the age-depth model. Our work has several lessons for future attempts to U-Th date lake sediments, namely that geologic context is equally as important as the accuracy and precision of analytical measurements. In addition, we caution that significant geologic scatter may remain undetected if not for labor intensive tests of reproducibility achieved through replication. As a result of this work, the deep sediment core from Lake Junín is the only continuous record in the tropical Andes spanning multiple glacial cycles that is constrained entirely by independent radiometric dates.
•An exploration of mechanisms driving scatter in 174 U-Th dates on lake sediments.•Uranium remobilization, not detrital contamination, is greatest barrier to success.•Single, unreplicated U-Th dates from lake sediments must be considered with caution.•Geologic context is critical for interpretation of geochronological data.•The 700 ka Lake Junín record is constrained entirely by independent radiometric dates.
•In this real-world PACIFIC experience, the rate of grade 2+ pneumonitis is 26.3%.•The rate of grade 3+ and grade 5 pneumonitis is 8.9% and 2.1%, respectively.•Multiple lung and heart dosimetric ...parameters are predictive of pneumonitis.•Overall survival at 1- and 3-years is 87.4% and 60.3%, respectively.
The incidence and predictors of pneumonitis for patients with unresectable, locally advanced non-small cell lung cancer (NSCLC) in the era of consolidation durvalumab have yet to be fully elucidated. In this large single institution analysis, we report the incidence of and factors associated with grade 2 + pneumonitis in NSCLC patients treated with the PACIFIC regimen.
We identified all patients treated at our institution with definitive CRT followed by durvalumab from 2018 to 2021. Clinical documentation and imaging studies were reviewed to determine grade 2 + pneumonitis events, which required the following: 1) pulmonary symptoms warranting prolonged steroid taper, oxygen dependence, and/or hospital admission and 2) radiographic findings consistent with pneumonitis.
One-hundred ninety patients were included. The majority received 60 Gray (Gy) in 30 fractions with concurrent carboplatin and paclitaxel. Median number of durvalumab cycles received was 12 (IQR: 4–22). At a median follow-up of 14.8 months, 50 (26.3%) patients experienced grade 2 + pneumonitis with a 1-year cumulative incidence of 27.8% (95% CI: 21.9–35.4). Seventeen (8.9%) patients experienced grade 3 + pneumonitis and 4 grade 5 (2.1%). Dosimetric predictors of pneumonitis included ipsilateral and total lung volume receiving 5 Gy or greater (V5Gy), V10Gy, V20Gy, V40Gy, and mean dose and contralateral V40Gy. Heart V5Gy, V10Gy, and mean dose were also significant variables. Overall survival estimates at 1 and 3 years were 87.4% (95% CI: 82.4–92.8) and 60.3% (95% CI: 47.9–74.4), respectively.
We report a risk of pneumonitis higher than that seen on RTOG 0617 and comparable to the PACIFIC study. Multiple lung and heart dosimetric factors were predictive of pneumonitis.
The voltage dependent anion channel (VDAC) forms a channel for metabolites and nutrients in the outer membrane of mitochondria, and it is also involved in apoptotic pathways. Here, we report ...sequence-specific NMR assignments for the isoform 1 of human VDAC reconstituted in lauryldimethylamine oxide (LDAO) detergent micelles. The assignments were deposited in the BMRB data base with accession number 16381.
To evaluate the dosimetry, clinical outcomes, and toxicity of patients treated with stereotactic body radiotherapy (SBRT) for adrenal metastases.
From February 2009 to February 2011, a total of 13 ...patients were treated with SBRT for metastases to the adrenal glands. Median age was 71 years (range, 60.8 to 83.2). Primary sites included lung (n=6), kidney (n=2), skin (n=2), bladder (n=1), colon (n=1), and liver (n=1). Nine patients had metastases to the left adrenal gland and 4 to the right. The median prescribed total dose was 45 Gy (range, 33.75 to 60 Gy), all in 5 fractions.
Median follow-up for living patients was 12.3 months (range, 3.1 to 18 mo). Twelve of the 13 patients (92.3%) were evaluable for local control (LC). The crude LC rate was 100%, with no cases of local or marginal failure. Two patients had a complete response to treatment, 9 patients had a partial response, and 1 patient displayed stable disease. One-year overall survival and distant control were 62.9% and 55%, respectively. Median OS was 7.2 months (range, 2 to 18 mo). Grade 2 nausea was noted in 2 patients.
SBRT seems to be a safe and effective measure to achieve LC for adrenal metastases.
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