Co‐translational folding and molecular chaperone action are crucial for productive protein folding in the cell, but how these processes shape folding pathways remains largely unknown. We have ...utilized translation arrest peptides (APs) to monitor co‐translational folding in live bacterial cells, combined with single‐molecule optical tweezers experiments, to define the co‐translational folding pathway of the GTPase domain (G‐domain) from E. coli elongation factor G (EF‐G). Surprisingly, the 293 amino acid long domain remains unfolded, without forming stable intermediate structures, until it is fully extruded from the ribosome. The full‐length G‐domain transitions to its stable native structure via obligate folding intermediates both in isolation and while bound to the ribosome. Folding therefore follows a strictly sequential pathway that initiates at the very C‐terminus, which is likely imposed by the structure and topology of the G‐domain from EF‐G. Consequently, folding and synthesis proceed in opposite directions. G‐domains represent a common element in a number of multi‐domain proteins. To determine whether their folding pathways are conserved, we have combined our AP approach with cell sorting and deep sequencing into a method that we term “AP profiling”. Homologous G‐domains exhibited distinct folding patterns that are conserved across distant bacterial species. Individual deletion of the primary nascent chain‐binding chaperones, trigger factor and DnaK (Hsp70), resulted in numerous localized changes to co‐translational folding while preserving overall G‐domain folding, highlighting the functional redundancy of cellular chaperone systems. In summary, we have developed AP profiling as a technique for monitoring co‐translational folding in the native cellular environment with high throughput. Combined with single‐molecule force spectroscopy, AP profiling yields a unique view of co‐translational folding and chaperone function.
Mermin–Wagner fluctuations in 2D amorphous solids Illing, Bernd; Fritschi, Sebastian; Kaiser, Herbert ...
Proceedings of the National Academy of Sciences - PNAS,
02/2017, Letnik:
114, Številka:
8
Journal Article
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In a recent commentary, J. M. Kosterlitz described how D. Thouless and he got motivated to investigate melting and suprafluidity in two dimensions Kosterlitz JM (2016) J Phys Condens Matter ...28:481001. It was due to the lack of broken translational symmetry in two dimensions—doubting the existence of 2D crystals—and the first computer simulations foretelling 2D crystals (at least in tiny systems). The lack of broken symmetries proposed by D. Mermin and H. Wagner is caused by long wavelength density fluctuations. Those fluctuations do not only have structural impact, but additionally a dynamical one: They cause the Lindemann criterion to fail in 2D in the sense that the mean squared displacement of atoms is not limited. Comparing experimental data from 3D and 2D amorphous solids with 2D crystals, we disentangle Mermin–Wagner fluctuations from glassy structural relaxations. Furthermore, we demonstrate with computer simulations the logarithmic increase of displacements with system size: Periodicity is not a requirement for Mermin–Wagner fluctuations, which conserve the homogeneity of space on long scales.
Purpose: Biologically-based mechanistic models that are used in combining current understanding of human carcinogenesis with epidemiological studies were reviewed. Assessment was made of how well ...they fit the data, whether they account for non-linear radiobiological low-dose effects, and whether they suggest any implications for the dose response at low doses and dose rates. However, the present paper does not make an attempt to provide a complete review of the existing literature on biologically-based models and their application to epidemiological data.
Conclusion: In most studies the two-stage clonal expansion (TSCE) model of carcinogenesis was used. The model provided robust estimates of identifiable parameters and radiation risk. While relatively simple, it is flexible, so that more stages can easily be added, and tests made of various types of radiation action. In general, the model performed similarly or better than descriptive excess absolute and excess relative risk models, in terms of quality of fit and number of parameters. Only very rarely the shape of dose-response predicted by the models was investigated. For some tumors, when more detailed biological information was known, additional pathways were included in the model. The future development of these models will benefit from growing knowledge on carcinogenesis processes, and in particular from use of biobank tissue samples and advances in omics technologies. Their use appears a promising approach to investigate the radiation risk at low doses and low dose rates. However, the uncertainties involved are still considerable, and the models provide only a simplified description of the underlying complexity of carcinogenesis. Current assumptions in radiation protection including the linear-non-threshold (LNT) model are not in contradiction to what is presently known on the process of cancer development.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Dense fluorophore labeling without compromising the biological target is crucial for genuine super-resolution microscopy. Here we introduce a broadly applicable labeling strategy for fixed and living ...cells utilizing a short peptide tag-specific nanobody (BC2-tag/bivBC2-Nb). BC2-tagging of ectopically introduced or endogenous proteins does not interfere with the examined structures and bivBC2-Nb staining results in a close-grained fluorophore labeling with minimal linkage errors. This allowed us to perform high-quality dSTORM imaging of various targets in mammalian and yeast cells. We expect that this versatile strategy will render many more demanding cellular targets amenable to dSTORM imaging.
The modulation of protein–protein interactions (PPIs) has been recognized as one of the most challenging tasks in drug discovery. While their systematic development has long been considered as ...intractable, this view has changed over the last years, with the first drug candidates undergoing clinical studies. To date, the vast majority of PPI modulators are interaction inhibitors. However, in many biological contexts a prolonged lifespan of a PPI might be desirable, calling for the complementary approach of PPI stabilization. In fact, nature offers impressive examples of this concept and some PPI‐stabilizing natural products have already found application as important drugs. Moreover, directed small‐molecule stabilization has recently been demonstrated. Therefore, it is time to take a closer look at the constructive side of modulating PPIs.
Doing it the other way round: The modulation of protein–protein interactions (PPIs) by small molecules has become increasingly popular over the last few decades. However, “modulation” has mainly been perceived as “inhibition” of protein–protein interactions, omitting the complementary strategy of stabilizing such macromolecular complexes. This Minireview highlights amazing examples and the potential of this constructive side of modulating PPIs.
Mutations in the leucine-rich repeat kinase 2 gene (LRRK2) are associated with familial and sporadic Parkinson's disease (PD). LRRK2 is a complex protein that consists of multiple domains, including ...predicted C-terminal WD40 repeats. In this study, we analyzed functional and molecular features conferred by the WD40 domain. Electron microscopic analysis of the purified LRRK2 C-terminal domain revealed doughnut-shaped particles, providing experimental evidence for its WD40 fold. We demonstrate that LRRK2 WD40 binds and sequesters synaptic vesicles via interaction with vesicle-associated proteins. In fact, a domain-based pulldown approach combined with mass spectrometric analysis identified LRRK2 as being part of a highly specific protein network involved in synaptic vesicle trafficking. In addition, we found that a C-terminal sequence variant associated with an increased risk of developing PD, G2385R, correlates with a reduced binding affinity of LRRK2 WD40 to synaptic vesicles. Our data demonstrate a critical role of the WD40 domain within LRRK2 function.
Abstract
Folding of individual domains in large proteins during translation helps to avoid otherwise prevalent inter-domain misfolding. How folding intermediates observed in vitro for the majority of ...proteins relate to co-translational folding remains unclear. Combining in vivo and single-molecule experiments, we followed the co-translational folding of the G-domain, encompassing the first 293 amino acids of elongation factor G. Surprisingly, the domain remains unfolded until it is fully synthesized, without collapsing into molten globule-like states or forming stable intermediates. Upon fully emerging from the ribosome, the G-domain transitions to its stable native structure via folding intermediates. Our results suggest a strictly sequential folding pathway initiating from the C-terminus. Folding and synthesis thus proceed in opposite directions. The folding mechanism is likely imposed by the final structure and might have evolved to ensure efficient, timely folding of a highly abundant and essential protein.
Photophysical studies of nonlinear lanthanide-doped photon upconverting nanoparticles (UCNPs) increasingly used in biophotonics and photovoltaics require absolute measurements of the excitation power ...density (P)-dependent upconversion luminescence (UCL) and luminescence quantum yields (ΦUC) for quantifying the material performance, UCL deactivation pathways, and possible enhancement factors. We present here the P-dependence of the UCL spectra, ΦUC, and slope factors of the different emission bands of representative 25 nm-sized oleate-capped β-NaYF4:17% Yb3+, 3% Er3+ UCNPs dispersed in toluene and as powder as well as ΦUC of 3 μm-sized upconversion particles (UCμP), all measured with a newly designed integrating sphere setup, enabling controlled variation of P over four orders of magnitude. This includes quantifying the influence of the beam shape on the measured ΦUC and comparison of experimental ΦUC with simulations utilizing the balancing power density model of the Andersson-Engels group and the simulated ΦUC of UCμP from the Berry group, underpinned by closely matching decay kinetics of our UC material. We obtained a maximum ΦUC of 10.5% for UCμP and a ΦUC of 0.6% and 2.1% for solid and dispersed UCNPs, respectively. Our results suggest an overestimation of the contribution of the purple and an underestimation of that of the red emission of β-NaYF4:Yb3+,Er3+: microparticles by the simulations of the Berry group. Moreover, our measurements can be used as a guideline to the absolute determination of UCL and ΦUC.
Toll-like receptor (TLR) activation induces inflammatory responses in macrophages by activating temporally defined transcriptional cascades. Whether concurrent changes in the cellular metabolism that ...occur upon TLR activation influence the quality of the transcriptional responses remains unknown. Here, we investigated how macrophages adopt their metabolism early after activation to regulate TLR-inducible gene induction. Shortly after TLR4 activation, macrophages increased glycolysis and tricarboxylic acid (TCA) cycle volume. Metabolic tracing studies revealed that TLR signaling redirected metabolic fluxes to generate acetyl-Coenzyme A (CoA) from glucose resulting in augmented histone acetylation. Signaling through the adaptor proteins MyD88 and TRIF resulted in activation of ATP-citrate lyase, which in turn facilitated the induction of distinct LPS-inducible gene sets. We postulate that metabolic licensing of histone acetylation provides another layer of control that serves to fine-tune transcriptional responses downstream of TLR activation. Our work highlights the potential of targeting the metabolic-epigenetic axis in inflammatory settings.
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•Macrophages adopt a transient metabolic state in response to TLR4 activation•MyD88 and TRIF synergistically facilitate signaling-driven changes in metabolism•Increases in glycolysis and ATP-citrate lyase activity foster histone acetylation•ATP-citrate lyase governs gene induction of a distinct LPS responsive gene set
TLR4 activation by LPS induces defined transcriptional cascades. Lauterbach et al. provide evidence that TLR activation induces a transient metabolic state that supports the transcriptional response. Mechanistically, they show that concerted increases in glycolytic flux and ATP-citrate lyase activity foster histone acetylation.
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