Computed structures of core eukaryotic protein complexes Humphreys, Ian R; Pei, Jimin; Baek, Minkyung ...
Science (American Association for the Advancement of Science),
2021-Dec-10, 2021-12-10, 20211210, Letnik:
374, Številka:
6573
Journal Article
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Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take ...advantage of advances in proteome-wide amino acid coevolution analysis and deep-learning–based structure modeling to systematically identify and build accurate models of core eukaryotic protein complexes within the
proteome. We use a combination of RoseTTAFold and AlphaFold to screen through paired multiple sequence alignments for 8.3 million pairs of yeast proteins, identify 1505 likely to interact, and build structure models for 106 previously unidentified assemblies and 806 that have not been structurally characterized. These complexes, which have as many as five subunits, play roles in almost all key processes in eukaryotic cells and provide broad insights into biological function.
The role of osteoclast‐mediated resorption during fracture healing was assessed. The impact of two osteoclast inhibitors with different mechanisms of action, alendronate (ALN) and denosumab (DMAB), ...were examined during fracture healing. Male human RANKL knock‐in mice that express a chimeric (human/murine) form of RANKL received unilateral transverse femur fractures. Mice were treated biweekly with ALN 0.1 mg/kg, DMAB 10 mg/kg, or PBS (control) 0.1 ml until death at 21 and 42 days after fracture. Treatment efficacy assessed by serum levels of TRACP 5b showed almost a complete elimination of TRACP 5b levels in the DMAB‐treated animals but only ∼25% reduction of serum levels in the ALN‐treated mice. Mechanical testing showed that fractured femurs from both ALN and DMAB groups had significantly increased mechanical properties at day 42 compared with controls. μCT analysis showed that callus tissues from DMAB‐treated mice had significantly greater percent bone volume and BMD than did both control and ALN‐treated tissues at both 21 and 42 days, whereas ALN‐treated bones only had greater percent bone volume and BMC than control at 42 days. Qualitative histological analysis showed that the 21‐and 42‐day ALN and DMAB groups had greater amounts of unresorbed cartilage or mineralized cartilage matrix compared with the controls, whereas unresorbed cartilage could still be seen in the DMAB groups at 42 days after fracture. Although ALN and DMAB delayed the removal of cartilage and the remodeling of the fracture callus, this did not diminish the mechanical integrity of the healing fractures in mice receiving these treatments. In contrast, strength and stiffness were enhanced in these treatment groups compared with control bones.
The initiation of reverse transcription in human immunodeficiency virus-1 is a key early step in the virus replication cycle. During this process, the viral enzyme reverse transcriptase (RT) copies ...the single-stranded viral RNA (vRNA) genome into double-stranded DNA using human tRNALys3 as a primer for initiation. The tRNA primer and vRNA genome contain several complementary sequences that are important for regulating reverse transcription initiation kinetics. Using single-molecule Förster resonance energy transfer spectroscopy, we demonstrate that the vRNA–tRNA initiation complex is conformationally heterogeneous and dynamic in the absence of RT. As shown previously, nucleic acid–RT interaction is characterized by rapid dissociation constants. We show that extension of the vRNA–tRNA primer binding site helix from 18 base pairs to 22 base pairs stabilizes RT binding to the complex and that the tRNA 5′ end has a role in modulating RT binding. RT occupancy on the complex stabilizes helix 1 formation and reduces global structural heterogeneity. The stabilization of helix 1 upon RT binding may serve to destabilize helix 2, the first pause site for RT during initiation, during later steps of reverse transcription initiation.
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•RNA and protein together dynamically modulate reverse transcription initiation.•Formation of an extended RNA PBS helix stabilizes reverse transcriptase binding.•The initiation complex is structurally dynamic when reverse transcriptase is absent.•Reverse transcriptase binding stabilizes RNA elements within the initiation complex.
Pathogenic hemizygous or heterozygous mutations in the IQSEC2 gene cause X-linked intellectual developmental disorder-1 (XLID1), characterized by a variable phenotype including developmental delay, ...intellectual disability, epilepsy, hypotonia, autism, microcephaly and stereotypies. It affects both males and females typically through loss of function in males and haploinsufficiency in heterozygous females. Females are generally less affected than males. Two novel unrelated cases, one male and one female, with de novo IQSEC2 variants were detected by trio-based whole exome sequencing. The female case had a previously undescribed frameshift mutation (NM_001111125:c.3300dup; p.Met1101Tyrfs*5), and the male showed an intronic variant in intron 6, with a previously unknown effect (NM_001111125:c.2459+21C>T). IQSEC2 gene expression study revealed that this intronic variant created an alternative donor splicing site and an aberrant product, with the inclusion of 19bp, confirming the pathogenic effect of the intron variant. Moreover, a strong reduction in the expression of the long, but also the short IQSEC2 isoforms, was detected in the male correlating with a more severe phenotype, while the female case showed no decreased expression of the short isoform, and milder effects of the disease. This suggests that the abnormal expression levels of the different IQSEC2 transcripts could be implicated in the severity of disease manifestations.
•Vocal Activity Rate (VAR) is an index used for monitoring wildlife using automated recorders.•VAR can be used for estimating wildlife abundance or assess population changes over time and ...sites.•Estimate a low-error VAR is desirable to obtain adequate results and recommendations.•Coefficient of variation of VAR was close to 100% when recording a single day.•Coefficient of variation decreased up to 20% after nine days of monitoring.
Indices based on singing activity have often been used in wildlife surveys conducted with passive acoustic monitoring. For instance, the Vocal Activity Rate index (VAR) has been employed to estimate animal populations and detect changes in abundance between years or sites. VAR may differ greatly between days due to environmental and biological factors, therefore leading to inadequate population size estimations and recommendations. However, there is still little information about the minimum number of monitoring days required for estimating a reliable VAR to assess changes over time or sites. We describe, for first time for a terrestrial bird species, the pattern of variation of VAR as a function of the number of monitoring days. Coefficient of variation sharply decreased with the number of monitoring days, and this pattern was similar during the breeding and post-breeding period. Coefficient of variation was close to 100% when a single monitoring day was surveyed, but decreased up to 30% and 20% after six or seven and nine monitoring days, depending on the monitoring period. Mean VAR was significantly related to bird abundance, but no relationship was found between bird abundance and number of days needed to reach a CV lower than 20%. Our results highlight that prior assessment of effort needed to estimate a reliable VAR should be a prerequisite for future monitoring programmes using singing activity indices. We found large differences in the number of monitoring days needed to obtain a reliable VAR in comparison to prior research on seabirds, suggesting that further research should be developed in different taxa and situations.
Monitoring temporal dynamics in genetic diversity is of great importance for conservation, especially for threatened species that are suffering a rapid population decline and increased fragmentation. ...Here, we investigate temporal variation in genetic diversity, structure, and gene flow in the Dupont’s lark (Chersophilus duponti) across most of its range. This species shows increasing levels of population fragmentation, substantial population declines, and severe range contraction, so temporal losses of genetic diversity, increasing differentiation, and decreasing gene flow are expected when comparing present day data with previous situations. To address this, we resampled sites (nine regions in two countries) after 12–15 years (five-to-seven generations) and assessed changes in genetic parameters using 11 microsatellite markers. We found no substantial loss in genetic diversity over time at the species level, but we detected considerable variation among regions in the amount of allelic diversity and heterozygosity lost over time. Temporal variation in allele frequencies (common, rare, and private alleles), and changes in genetic differentiation and gene flow over time suggest a major role of connectivity for the stability of the overall metapopulation. Our results agree with the hypothesis that connectivity rescues genetic diversity via immigration and gene flow. However, evidence of recent genetic bottleneck and the substantial changes detected in some regions are clear signs of genetic erosion and may be signalling a rapid decline of the populations. Urgent actions must be carried out to stop and reverse human impacts on this threatened lark and its habitat.
Mitochondrial Ca2+ Uniporter (MCU)-dependent mitochondrial Ca2+ uptake is the primary mechanism for increasing matrix Ca2+ in most cell types. However, a limited understanding of the MCU complex ...assembly impedes the comprehension of the precise mechanisms underlying MCU activity. Here, we report that mouse cardiomyocytes and endothelial cells lacking MCU regulator 1 (MCUR1) have severely impaired Ca2+m uptake and IMCU current. MCUR1 binds to MCU and EMRE and function as a scaffold factor. Our protein binding analyses identified the minimal, highly conserved regions of coiled-coil domain of both MCU and MCUR1 that are necessary for heterooligomeric complex formation. Loss of MCUR1 perturbed MCU heterooligomeric complex and functions as a scaffold factor for the assembly of MCU complex. Vascular endothelial deletion of MCU and MCUR1 impaired mitochondrial bioenergetics, cell proliferation, and migration but elicited autophagy. These studies establish the existence of a MCU complex that assembles at the mitochondrial integral membrane and regulates Ca2+-dependent mitochondrial metabolism.
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•MCUR1 binds to MCU and EMRE and functions as a scaffold factor•The coiled-coil domains of both MCU and MCUR1 are essential for MCU complex assembly•Genetic deletion of MCUR1 severely impairs Ca2+m uptake and IMCU current•MCUR1 deletion impairs bioenergetics and cell migration and elicits autophagy
Tomar et al. show that genetic ablation of the MCU complex component MCUR1 perturbs MCU heterooligomeric complex and impairs mitochondrial Ca2+ uptake. MCUR1 binds to MCU and EMRE and functions as a scaffold factor that is necessary for proper Ca2+-dependent mitochondrial bioenergetics.
Stress in birds has been widely studied through the measurement of heterophil-to-lymphocyte ratio (H/L ratio). In this study we aimed to assess for the first time the potential variation of stress, ...measured as H/L ratio, associated to geography (between-country variation) and seasonality (between seasons and within the breeding season), as well as the leukocyte profiles, in the threatened Dupont’s Lark (
Chersophilus duponti
), using samples from Spain and Morocco. Furthermore, we tested whether variation in H/L ratio was associated with variables such as population density, presence of blood parasites and individual body condition. We found that H/L ratio did not vary between countries, but individuals captured during the breeding season showed higher values of H/L compared to non-breeding ones. Neither male density, nor date within the breeding season had an effect on the H/L ratio. In Spain, individuals with higher body condition showed lower H/L ratio regardless of whether they were malaria-infected. In Morocco, malaria-infected individuals showed higher values of H/L ratio than the non-infected birds. Moreover, we found that our average values of H/L ratio in Morocco were within the ranges of other passerines, but not in Spain. Individuals with higher H/L ratios may be more stressed or present higher capability to face stressful situations. Although H/L ratio is a useful and relatively easy way to obtain measure of stress, the impact that the environment might have on stress and the way it is explained by H/L ratio must be addressed carefully. This study provides new insight for this species’ biology and provides useful reference information to test the status and survival of other populations.
Multiphase machines are complex multi-variable electro-mechanical systems that are receiving special attention from industry due to their better fault tolerance and power-per-phase splitting ...characteristics compared with conventional three-phase machines. Their utility and interest are restricted to the definition of high-performance controllers, which strongly depends on the knowledge of the electrical parameters used in the multiphase machine model. This work presents the proof-of-concept of a new method based on particle swarm optimization and standstill time-domain tests. This proposed method is tested to estimate the electrical parameters of a five-phase induction machine. A reduction of the estimation error higher than 2.5% is obtained compared with gradient-based approaches.
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