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International Journal of Molecular... Sep 2023Single-particle cryo-electron microscopy (cryo-EM SPA) has recently emerged as an exceptionally well-suited technique for determining the structure of membrane proteins... (Review)
Review
Single-particle cryo-electron microscopy (cryo-EM SPA) has recently emerged as an exceptionally well-suited technique for determining the structure of membrane proteins (MPs). Indeed, in recent years, huge increase in the number of MPs solved via cryo-EM SPA at a resolution better than 3.0 Å in the Protein Data Bank (PDB) has been observed. However, sample preparation remains a significant challenge in the field. Here, we evaluated the MPs solved using cryo-EM SPA deposited in the PDB in the last two years at a resolution below 3.0 Å. The most critical parameters for sample preparation are as follows: (i) the surfactant used for protein extraction from the membrane, (ii) the surfactant, amphiphiles, nanodiscs or other molecules present in the vitrification step, (iii) the vitrification method employed, and (iv) the type of grids used. The aim is not to provide a definitive answer on the optimal sample conditions for cryo-EM SPA of MPs but rather assess the current trends in the MP structural biology community towards obtaining high-resolution cryo-EM structures.
Topics: Membrane Proteins; Cryoelectron Microscopy; Specimen Handling; Single Molecule Imaging; Surface-Active Agents
PubMed: 37834233
DOI: 10.3390/ijms241914785 -
PloS One 2023Humanitarian crises such as disease outbreaks, conflict and displacement and natural disasters affect millions of people primarily in low- and middle-income countries.... (Review)
Review
Mapping the association between mental health and people's perceived and actual ability to practice hygiene-related behaviours in humanitarian and pandemic crises: A scoping review.
Humanitarian crises such as disease outbreaks, conflict and displacement and natural disasters affect millions of people primarily in low- and middle-income countries. Here, they often reside in areas with poor environmental health conditions leading to an increased burden of infectious diseases such as gastrointestinal and respiratory infections. Water, sanitation, and hygiene behaviours are critical to prevent such infections and deaths. A scoping review was conducted to map out what is known about the association between three mental health disorders and people's perceived and actual ability to practice hygiene-related behaviours, particularly handwashing, in humanitarian and pandemic crises. Published and grey literature was identified through database searches, humanitarian-relevant portals, and consultations with key stakeholders in the humanitarian sector. 25 publications were included, 21 were peer-reviewed published articles and four were grey literature publications. Most of the studies were conducted in mainland China (n = 12) and most were conducted in an outbreak setting (n = 20). Six studies found a positive correlation between handwashing and anxiety where participants with higher rates of anxiety were more likely to practice handwashing with soap. Four studies found an inverse relationship where those with higher rates of anxiety were less likely to wash their hands with soap. The review found mixed results for the association between handwashing and depression, with four of the seven studies reporting those with higher rates of depression were less likely to wash their hands, while the remaining studies found that higher depression scores resulted in more handwashing. Mixed results were also found between post-traumatic stress disorder (PTSD) and handwashing. Two studies found that lower scores of PTSD were associated with better hygiene practices, including handwashing with soap. The contradictory patterns suggest that researchers and practitioners need to explore this association further, in a wider range of crises, and need to standardize tools to do so.
Topics: Humans; Mental Health; Soaps; Pandemics; Hygiene; Anxiety Disorders; Sanitation; Hand Disinfection
PubMed: 38096240
DOI: 10.1371/journal.pone.0286494 -
International Journal of Molecular... Jul 2023Oxidases and peroxidases have found application in the field of chlorine-free organic dye degradation in the paper, toothpaste, and detergent industries. Nevertheless,...
Oxidases and peroxidases have found application in the field of chlorine-free organic dye degradation in the paper, toothpaste, and detergent industries. Nevertheless, their widespread use is somehow hindered because of their cost, availability, and batch-to-batch reproducibility. Here, we report the catalytic proficiency of a miniaturized synthetic peroxidase, Fe-Mimochrome VI*a, in the decolorization of four organic dyes, as representatives of either the heterocyclic or triarylmethane class of dyes. Fe-Mimochrome VI*a performed over 130 turnovers in less than five minutes in an aqueous buffer at a neutral pH under mild conditions.
Topics: Peroxidase; Coloring Agents; Reproducibility of Results; Peroxidases; Catalysis
PubMed: 37446248
DOI: 10.3390/ijms241311070 -
Nature Communications Oct 2023Plants are challenged by drastically different osmotic environments during growth and development. Adaptation to these environments often involves mechanosensitive ion...
Plants are challenged by drastically different osmotic environments during growth and development. Adaptation to these environments often involves mechanosensitive ion channels that can detect and respond to mechanical force. In the model plant Arabidopsis thaliana, the mechanosensitive channel MSL10 plays a crucial role in hypo-osmotic shock adaptation and programmed cell death induction, but the molecular basis of channel function remains poorly understood. Here, we report a structural and electrophysiological analysis of MSL10. The cryo-electron microscopy structures reveal a distinct heptameric channel assembly. Structures of the wild-type channel in detergent and lipid environments, and in the absence of membrane tension, capture an open conformation. Furthermore, structural analysis of a non-conductive mutant channel demonstrates that reorientation of phenylalanine side chains alone, without main chain rearrangements, may generate the hydrophobic gate. Together, these results reveal a distinct gating mechanism and advance our understanding of mechanotransduction.
Topics: Arabidopsis; Arabidopsis Proteins; Mechanotransduction, Cellular; Cryoelectron Microscopy; Ion Channels; Membrane Proteins
PubMed: 37805510
DOI: 10.1038/s41467-023-42117-5 -
Techniques in Coloproctology Jan 2024This systematic review and meta-analysis aimed to evaluate the safety and efficacy of sclerotherapy methods for hemorrhoidal disease (HD) over the past 40 years. (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
This systematic review and meta-analysis aimed to evaluate the safety and efficacy of sclerotherapy methods for hemorrhoidal disease (HD) over the past 40 years.
METHODS
The review followed the 2020 Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines. A comprehensive literature search was conducted, including studies reporting the use of sclerotherapy in patients with HD. Study eligibility criteria were defined, and data were extracted independently by the authors. Random-effects meta-analyses were performed to assess outcomes of interest.
RESULTS
Out of 1965 records identified, 44 studies met the inclusion criteria, involving 9729 patients. The majority of studies were conducted in Japan, followed by the UK, Italy, and Portugal. The median age of participants was 52 years, and the majority were male. The Goligher grade distribution indicated varying degrees of HD severity. Sclerotherapy was predominantly administered through anoscopy, with polidocanol being the most commonly used agent. The procedure was generally performed without pre-injection analgesia. The meta-analysis of 14 randomized controlled trials (RCTs) revealed that sclerotherapy was not inferior to control interventions in terms of success rate (risk ratio [RR] 1.00, 95% CI 0.71-1.41) and recurrence rate (RR 1.11, 95% CI 0.69-1.77), while resulting in fewer complications (RR 0.46, 95% CI 0.23-0.92).
CONCLUSIONS
This systematic review highlights the safety and efficacy of sclerotherapy for HD, which yields similar success rates and fewer complications compared to other conservative or surgical approaches. Further research is warranted to optimize sclerotherapy techniques and evaluate long-term outcomes.
REGISTRATION
PROSPERO 2023 CRD42023396910.
Topics: Male; Humans; Female; Middle Aged; Sclerotherapy; Hemorrhoids; Italy; Odds Ratio; Polidocanol
PubMed: 38261136
DOI: 10.1007/s10151-023-02908-w -
Proceedings of the National Academy of... Nov 2023During aging, the cellular response to unfolded proteins is believed to decline, resulting in diminished proteostasis. In model organisms, such as proteostatic decline... (Meta-Analysis)
Meta-Analysis
During aging, the cellular response to unfolded proteins is believed to decline, resulting in diminished proteostasis. In model organisms, such as proteostatic decline with age has been linked to proteome solubility shifts and the onset of protein aggregation. However, this correlation has not been extensively characterized in aging mammals. To uncover age-dependent changes in the insoluble portion of a mammalian proteome, we analyzed the detergent-insoluble fraction of mouse brain tissue by mass spectrometry. We identified a group of 171 proteins, including the small heat shock protein α-crystallin, that become enriched in the detergent-insoluble fraction obtained from old mice. To enhance our ability to detect features associated with proteins in that fraction, we complemented our data with a meta-analysis of studies reporting the detergent-insoluble proteins in various mouse models of aging and neurodegeneration. Strikingly, insoluble proteins from young and old mice are distinct in several features in our study and across the collected literature data. In younger mice, proteins are more likely to be disordered, part of membraneless organelles, and involved in RNA binding. These traits become less prominent with age, as an increased number of structured proteins enter the pellet fraction. This analysis suggests that age-related changes to proteome organization lead a group of proteins with specific features to become detergent-insoluble. Importantly, these features are not consistent with those associated with proteins driving membraneless organelle formation. We see no evidence in our system of a general increase of condensate proteins in the detergent-insoluble fraction with age.
Topics: Mice; Animals; Proteome; Detergents; Aging; Caenorhabditis elegans; Brain; Mammals
PubMed: 37906643
DOI: 10.1073/pnas.2310057120 -
IMeta Aug 2023The impact of antibacterial detergent on microbial exchanges and its subsequent effect on malodor in used towels were examined. Homogenization of microbiome among...
The impact of antibacterial detergent on microbial exchanges and its subsequent effect on malodor in used towels were examined. Homogenization of microbiome among postwashed and indoor dried towels that was dominated by known malodor-producing bacteria. The microbial exchange was attenuated, and the abundance of malodor-producing bacteria was reduced in towels laundered with antibacterial detergent. Reduction of malodorous volatile organic compounds produced from towels laundered with antibacterial detergent.
PubMed: 38867935
DOI: 10.1002/imt2.110 -
BioRxiv : the Preprint Server For... Jun 2024The T-cell receptor (TCR) is central to the ligand-dependent activation of T lymphocytes and as such orchestrates both adaptive and pathologic immune processes. However,...
The T-cell receptor (TCR) is central to the ligand-dependent activation of T lymphocytes and as such orchestrates both adaptive and pathologic immune processes. However, major questions remain regarding the structure and function of the human TCR. Here, we present cryogenic electron microscopy structures for the unliganded and HLA-bound human TCR-CD3 complex in nanodiscs that provide a native-like lipid environment. The unliganded structures reveal two related conformations that are distinct from its structure in detergent. These new "closed and compacted" conformations afford insights into the interactions between the TCR-CD3 and the membrane, including conserved surface patches that make extensive outer leaflet contact, and suggest novel conformational regulation by glycans. We show that the closed/compacted conformations, not the extended one previously reported in detergent, represent the unliganded resting state for the TCR-CD3 in vivo, underscoring the importance of structural interrogation of membrane proteins in native-like environments. By contrast, the structure of the HLA-bound complex in nanodiscs is in an open and extended conformation, showing that physiologic ligand binding is sufficient to induce substantial conformational change in the TCR-CD3 complex. We use conformation-locking disulfide mutants to show that ectodomain opening is necessary for maximal ligand-dependent TCR-CD3 activation, demonstrating that TCR-intrinsic conformational change is necessary for full TCR-CD3 activation and opening numerous avenues for immunoreceptor engineering.
PubMed: 37662363
DOI: 10.1101/2023.08.22.554360 -
Communications Biology Nov 2023Amyloid beta (Aβ) aggregation is a slow process without seeding or assisted nucleation. Sodium dodecyl sulfate (SDS) micelles stabilize Aβ42 small oligomers (in the...
Amyloid beta (Aβ) aggregation is a slow process without seeding or assisted nucleation. Sodium dodecyl sulfate (SDS) micelles stabilize Aβ42 small oligomers (in the dimer to tetramer range); subsequent SDS removal leads to a 150-kD Aβ42 oligomer. Dodecylphosphorylcholine (DPC) micelles also stabilize an Aβ42 tetramer. Here we investigate the detergent-assisted oligomerization pathway by solid-state NMR spectroscopy and molecular dynamics simulations. SDS- and DPC-induced oligomers have the same structure, implying a common oligomerization pathway. An antiparallel β-sheet formed by the C-terminal region, the only stable structure in SDS and DPC micelles, is directly incorporated into the 150-kD oligomer. Three Gly residues (at positions 33, 37, and 38) create holes that are filled by the SDS and DPC hydrocarbon tails, thereby turning a potentially destabilizing feature into a stabilizing factor. These observations have implications for endogenous Aβ aggregation at cellular interfaces.
Topics: Amyloid beta-Peptides; Detergents; Micelles; Protein Structure, Secondary
PubMed: 37989804
DOI: 10.1038/s42003-023-05556-w -
Membranes Jul 2023Membrane solubilization induced by Triton X-100 (TX-100) was investigated. Different membrane compositions and phase states were studied along the detergent titration....
Membrane solubilization induced by Triton X-100 (TX-100) was investigated. Different membrane compositions and phase states were studied along the detergent titration. Expected solubilization profiles were obtained but new information is provided. The fluorescence of nitrobenzoxadiazole (NBD)-labeled lipids indicates that the liquid-ordered (Lo)/liquid-disordered (Ld) phase coexistence is barely unaffected at sub-solubilizing detergent concentrations and highlights the vesicle-to-micelle transition. Moreover, the location of the NBD group in the bilayer emphasizes a detergent-membrane interaction in the case of the insoluble Lo phase membrane. It has also been shown that the molecular packing of the membrane loosens in the presence of TX-100, regardless of the solubilization profile. Motivated by studies on GPMVs, the solubilization of less ordered Lo phase membranes was considered in order to improve the effect of molecular packing on the extent of solubilization. Membranes composed of SM and Chol in an equimolar ratio doped with different amounts of PC were studied. The more ordered the Lo phase membrane is in the absence of detergent, the less likely it is to be solubilized. Furthermore, and in contrast to what is observed for membranes exhibiting an Lo/Ld phase coexistence, a very small decrease in the molecular packing of the Lo phase membrane radically modifies the extent of solubilization. These results have implications for the reliability of TX-100 insolubility as a method to detect ordered domains.
PubMed: 37505018
DOI: 10.3390/membranes13070652