Integrative structure determination is a powerful approach to modeling the structures of biological systems based on data produced by multiple experimental and theoretical methods, with implications ...for our understanding of cellular biology and drug discovery. This Primer introduces the theory and methods of integrative approaches, emphasizing the kinds of data that can be effectively included in developing models and using the nuclear pore complex as an example to illustrate the practice and challenges involved. These guidelines are intended to aid the researcher in understanding and applying integrative structural methods to systems of their interest and thus take advantage of this rapidly evolving field.
Integrative structure determination is a powerful approach to modeling the structures of biological systems based on data produced by multiple experimental and theoretical methods, with implications for our understanding of cellular biology and drug discovery. This Primer introduces the theory and methods of integrative approaches, emphasizing the kinds of data that can be effectively included in developing models and using the nuclear pore complex as an example to illustrate the practice and challenges involved. These guidelines are intended to aid the researcher in understanding and applying integrative structural methods to systems of their interest and thus take advantage of this rapidly evolving field.
The nuclear pore complex (NPC) is the massive protein assembly that regulates the transport of macromolecules between the nucleus and the cytoplasm. Recent breakthroughs have provided major insights ...into the structure of the NPC in different eukaryotes, revealing a previously unsuspected diversity of NPC architectures. In parallel, the NPC has been shown to be a key player in regulating essential nuclear processes such as chromatin organization, gene expression, and DNA repair. However, our knowledge of the NPC structure has not been able to address the molecular mechanisms underlying its regulatory roles. We discuss potential explanations, including the coexistence of alternative NPC architectures with specific functional roles.
The NPC is a large protein assembly that regulates macromolecular transport between the nucleus and the cytoplasm, and acts as a regulatory platform for many other essential nuclear processes.NPC structural characterization has been challenging, but recent technical and methodological advances are advancing our understanding of NPC architecture.Structural analyses of the NPC in different organisms revealed that, although there is a common bauplan, a significant degree of variability is observed in the peripheral modules that build these NPCs.The multiple regulatory roles shown for the NPC suggest an even greater degree of NPC architectural diversity that has not yet been unveiled.
Nuclear processing and quality control of eukaryotic RNA is mediated by the RNA exosome, which is regulated by accessory factors. However, the mechanism of exosome recruitment to its ...ribonucleoprotein (RNP) targets remains poorly understood. Here we report a physical link between the human exosome and the cap-binding complex (CBC). The CBC associates with the ARS2 protein to form CBC-ARS2 (CBCA) and then further connects, together with the ZC3H18 protein, to the nuclear exosome targeting (NEXT) complex, thus forming CBC-NEXT (CBCN). RNA immunoprecipitation using CBCN factors as well as the analysis of combinatorial depletion of CBCN and exosome components underscore the functional relevance of CBC-exosome bridging at the level of target RNA. Specifically, CBCA suppresses read-through products of several RNA families by promoting their transcriptional termination. We suggest that the RNP 5' cap links transcription termination to exosomal RNA degradation through CBCN.
Heat shock proteins regulate the physiological mechanism of heat stress adaptation at cellular level. The present investigation was carried out to analyse the HSP70 gene regulation in various growth ...stage in ruminants in peripheral blood mononuclear cells (PBMCs). The relationship between HSP gene expression and thermotolerance in age-specific manner in ruminants has not been analysed. Therefore m-RNA HSP70 expression level was examined in different age groups of Jamunpari goat during hot climatic conditions. The experiment was carried out in 32 animals of Jamunapari goat belonging to the age groups of 3-months, 9-months, 12-months, and adults (2-3 year). Total RNA was isolated from peripheral blood mononuclear cells. The physiological response such as rectal temperature (RT), respiration rate (RR) and heart rate (HR) was used as indicator to heat stress. Temperature Humidity Index (THI) was used as an indicator of severity of environmental stress. The THI range varied from 82.00-92.08 during experimental period. The m-RNA HSP70 expression level at 9-month age of animals was up-regulated and significantly higher than other age groups. It was observed that the level of HSP70 transcripts in PBMCs was highest at 9-month age group, and age-related decline in HSP70 expression was observed in adult age. Based on the physiological response, the contrasting heat-stress phenotypes were recognised as heat stress susceptible (HSS) and heat stress tolerant (HST) individuals and the expression of m-RNA HSP70 was analysed at different ages in response to chronic heat stress. The differential mRNA expression of HSS individuals at 3 and 9-month of age showed the highest fold expression than HST. Age and phenotype had significant effect (p < 0.01) on the crossing point (CP) value. The m-RNA HSP70 gene expression in different age groups was correlated with heat stress tolerance and this could be used as biomarker for breeders to analyse the HSP response in -vivo in ruminants.
Internal membrane bound structures sequester all genetic material in eukaryotic cells. The most prominent of these structures is the nucleus, which is bounded by a double membrane termed the nuclear ...envelope (NE). Though this NE separates the nucleoplasm and genetic material within the nucleus from the surrounding cytoplasm, it is studded throughout with portals called nuclear pore complexes (NPCs). The NPC is a highly selective, bidirectional transporter for a tremendous range of protein and ribonucleoprotein cargoes. All the while the NPC must prevent the passage of nonspecific macromolecules, yet allow the free diffusion of water, sugars, and ions. These many types of nuclear transport are regulated at multiple stages, and the NPC carries binding sites for many of the proteins that modulate and modify the cargoes as they pass across the NE. Assembly, maintenance, and repair of the NPC must somehow occur while maintaining the integrity of the NE. Finally, the NPC appears to be an anchor for localization of many nuclear processes, including gene activation and cell cycle regulation. All these requirements demonstrate the complex design of the NPC and the integral role it plays in key cellular processes.
LINE-1s are active human DNA parasites that are agents of genome dynamics in evolution and disease. These streamlined elements require host factors to complete their life cycles, whereas hosts have ...developed mechanisms to combat retrotransposition’s mutagenic effects. As such, endogenous L1 expression levels are extremely low, creating a roadblock for detailed interactomic analyses. Here, we describe a system to express and purify highly active L1 RNP complexes from human suspension cell culture and characterize the copurified proteome, identifying 37 high-confidence candidate interactors. These data sets include known interactors PABPC1 and MOV10 and, with in-cell imaging studies, suggest existence of at least three types of compositionally and functionally distinct L1 RNPs. Among the findings, UPF1, a key nonsense-mediated decay factor, and PCNA, the polymerase-delta-associated sliding DNA clamp, were identified and validated. PCNA interacts with ORF2p via a PIP box motif; mechanistic studies suggest that this occurs during or immediately after target-primed reverse transcription.
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•Isolated highly active LINE-1 ribonucleoprotein particle complexes from human cells•37 identified interactors comprise known and novel factors, notably UPF1 and PCNA•L1 RNP is linked by a both protein-protein (PCNA) and protein-RNA (UPF1) interactions•PCNA binds to ORF2p via a PIP box and is critical for retrotransposition
Affinity proteomics of retrotransposons with human host cells identifies high-confidence protein interactors and reveals at least three types of compositionally and functionally distinct transposon ribonucleoprotein complexes.
Goat milk is a source of nutrition in difficult areas and has lesser allerginicity than cow milk. It is leading in the area for nutraceutical formulation and drug development using goat mammary gland ...as a bioreactor. Post translational modifications of a protein regulate protein function, biological activity, stabilization and interactions. The protein variants of goat milk from 10 breeds were studied for the post translational modifications by combining highly sensitive 2DE and Q-Exactive LC-MS/MS. Here we observed high levels of post translational modifications in 201 peptides of 120 goat milk proteins. The phosphosites observed for CSN2, CSN1S1, CSN1S2, CSN3 were 11P, 13P, 17P and 6P, respectively in 105 casein phosphopeptides. Whey proteins BLG and LALBA showed 19 and 4 phosphosites respectively. Post translational modification was observed in 45 low abundant non-casein milk proteins mainly associated with signal transduction, immune system, developmental biology and metabolism pathways. P
is reported for the first time in 47 sites. The rare conserved peptide sequence of (SSSEE) was observed in αS1 and αS2 casein. The functional roles of identified phosphopeptides included anti-microbial, DPP-IV inhibitory, anti-inflammatory and ACE inhibitory. This is first report from tropics, investigating post translational modifications in casein and non-casein goat milk proteins and studies their interactions.
Passive macromolecular diffusion through nuclear pore complexes (NPCs) is thought to decrease dramatically beyond a 30-60-kD size threshold. Using thousands of independent time-resolved fluorescence ...microscopy measurements in vivo, we show that the NPC lacks such a firm size threshold; instead, it forms a soft barrier to passive diffusion that intensifies gradually with increasing molecular mass in both the wild-type and mutant strains with various subsets of phenylalanine-glycine (FG) domains and different levels of baseline passive permeability. Brownian dynamics simulations replicate these findings and indicate that the soft barrier results from the highly dynamic FG repeat domains and the diffusing macromolecules mutually constraining and competing for available volume in the interior of the NPC, setting up entropic repulsion forces. We found that FG domains with exceptionally high net charge and low hydropathy near the cytoplasmic end of the central channel contribute more strongly to obstruction of passive diffusion than to facilitated transport, revealing a compartmentalized functional arrangement within the NPC.
The nuclear pore complex (NPC) is responsible for nucleocytoplasmic transport and constitutes a hub for control of gene expression. The components of NPCs from several eukaryotic lineages have been ...determined, but only the yeast and vertebrate NPCs have been extensively characterized at the quaternary level. Significantly, recent evidence indicates that compositional similarity does not necessarily correspond to homologous architecture between NPCs from different taxa. To address this, we describe the interactome of the trypanosome NPC, a representative, highly divergent eukaryote. We identify numerous new NPC components and report an exhaustive interactome, allowing assignment of trypanosome nucleoporins to discrete NPC substructures. Remarkably, despite retaining similar protein composition, there are exceptional architectural dissimilarities between opisthokont (yeast and vertebrates) and excavate (trypanosomes) NPCs. Whilst elements of the inner core are conserved, numerous peripheral structures are highly divergent, perhaps reflecting requirements to interface with divergent nuclear and cytoplasmic functions. Moreover, the trypanosome NPC has almost complete nucleocytoplasmic symmetry, in contrast to the opisthokont NPC; this may reflect divergence in RNA export processes at the NPC cytoplasmic face, as we find evidence supporting Ran-dependent mRNA export in trypanosomes, similar to protein transport. We propose a model of stepwise acquisition of nucleocytoplasmic mechanistic complexity and demonstrate that detailed dissection of macromolecular complexes provides fuller understanding of evolutionary processes.
This paper reports the effect of sintering temperature on ferroelectric properties of GdMnO3 (GMO) bulk ceramics at room temperature prepared by the conventional solid state reaction route following ...slow step sintering schedule. Ferroelectric hysteresis loop as well as sharp dielectric anomaly in pure (99.999%) GMO sintered ceramics has been clearly observed. Samples sintered at 1350°C become orthorhombic with Pbnm space group and showed frequency independent sharp dielectric anomalies at 373K and a square type of novel ferroelectric hysteresis loop was observed at room temperature. Interestingly, dielectric anomalies and ferroelectric behavior were observed to be dependent upon sintering temperature of GdMnO3. Room temperature dielectric constant (εr) value at different frequencies is observed to be abnormally high. The magnetic field and temperature dependent magnetization show antiferromagnetic behavior at 40K for both 1350°C and 1700°C sintered GMO. Present findings showed the possibility of application of GdMnO3 at room temperature as multifunctional materials.
• Preparation of single-phasic polycrystalline GdMnO3 sample by the solid state sintering route.• Observation of square type P–E hysteresis loop with higher saturation and remnant polarization.• Observation of antiferromagnetic behavior at 40K in polycrystalline GdMnO3.• Possibility of room temperature application of GdMnO3 as multifunctional material.
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