Diffusion and Oligomerization States of the Muscarinic M Receptor in Live Cells─The Impact of Ligands and Membrane Disruptors.

G protein-coupled receptors (GPCRs) are a major gateway to cellular signaling, which respond to ligands binding at extracellular sites through allosteric conformational changes that modulate their interactions with G proteins and arrestins at intracellular sites. High-resolution structures in different ligand states, together with spectroscopic studies and molecular dynamics simulations, have revealed a rich conformational landscape of GPCRs. However, their supramolecular structure and spatiotemporal distribution is also thought to play a significant role in receptor activation and signaling bias within the native cell membrane environment.

Local Disordered Region Sampling (LDRS) for ensemble modeling of proteins with experimentally undetermined or low confidence prediction segments.

Summary: The Local Disordered Region Sampling (LDRS, pronounced loaders) tool is a new module developed for IDPConformerGenerator, a previously validated approach to model intrinsically disordered proteins (IDPs). The IDPConformerGenerator LDRS module provides a method for generating all-atom conformations of intrinsically disordered protein regions at N- and C-termini of and in loops or linkers between folded regions of an existing protein structure. These disordered elements often lead to missing coordinates in experimental structures or low confidence in predicted structures.

Delineating Structural Propensities of the 4E-BP2 Protein via Integrative Modeling and Clustering.

The intrinsically disordered 4E-BP2 protein regulates mRNA cap-dependent translation through interaction with the predominantly folded eukaryotic initiation factor 4E (eIF4E). Phosphorylation of 4E-BP2 dramatically reduces the level of eIF4E binding, in part by stabilizing a binding-incompatible folded domain. Here, we used a Rosetta-based sampling algorithm optimized for IDRs to generate initial ensembles for two phospho forms of 4E-BP2, non- and 5-fold phosphorylated (NP and 5P, respectively), with the 5P folded domain flanked by N- and C-terminal IDRs (N-IDR and C-IDR, respectively).

Local Disordered Region Sampling (LDRS) for Ensemble Modeling of Proteins with Experimentally Undetermined or Low Confidence Prediction Segments.

The Local Disordered Region Sampling (LDRS, pronounced ) tool, developed for the IDPConformerGenerator platform (Teixeira 2022), provides a method for generating all-atom conformations of intrinsically disordered regions (IDRs) at N- and C-termini of and in loops or linkers between folded regions of an existing protein structure. These disordered elements often lead to missing coordinates in experimental structures or low confidence in predicted structures. Requiring only a pre-existing PDB structure of the protein with missing coordinates or with predicted confidence scores and its full-length primary sequence, LDRS will automatically generate physically meaningful conformational ensembles of the missing flexible regions to complete the full-length protein.

The Present State of the Use of Waste Wood Ash as an Eco-Efficient Construction Material: A Review.

A main global challenge is finding an alternative material for cement, which is a major source of pollution to the environment because it emits greenhouse gases. Investigators play a significant role in global waste disposal by developing appropriate methods for its effective utilization. Geopolymers are one of the best options for reusing all industrial wastes containing aluminosilicate and the best alternative materials for concrete applications.

Single-molecule counting applied to the study of GPCR oligomerization.

Single-molecule counting techniques enable a precise determination of the intracellular abundance and stoichiometry of proteins and macromolecular complexes. These details are often challenging to quantitatively assess yet are essential for our understanding of cellular function. Consider G-protein-coupled receptors-an expansive class of transmembrane signaling proteins that participate in many vital physiological functions making them a popular target for drug development.

Integrative Conformational Ensembles of Sic1 Using Different Initial Pools and Optimization Methods.

Intrinsically disordered proteins play key roles in regulatory protein interactions, but their detailed structural characterization remains challenging. Here we calculate and compare conformational ensembles for the disordered protein Sic1 from yeast, starting from initial ensembles that were generated either by statistical sampling of the conformational landscape, or by molecular dynamics simulations. Two popular, yet contrasting optimization methods were used, ENSEMBLE and Bayesian Maximum Entropy, to achieve agreement with experimental data from nuclear magnetic resonance, small-angle X-ray scattering and single-molecule Förster resonance energy transfer.

Multisite phosphorylation and binding alter conformational dynamics of the 4E-BP2 protein.

Intrinsically disordered proteins (IDPs) play critical roles in regulatory protein interactions, but detailed structural/dynamic characterization of their ensembles remain challenging, both in isolation and when they form dynamic "fuzzy" complexes. Such is the case for mRNA cap-dependent translation initiation, which is regulated by the interaction of the predominantly folded eukaryotic initiation factor 4E (eIF4E) with the intrinsically disordered eIF4E binding proteins (4E-BPs) in a phosphorylation-dependent manner. Single-molecule Förster resonance energy transfer showed that the conformational changes of 4E-BP2 induced by binding to eIF4E are non-uniform along the sequence; while a central region containing both motifs that bind to eIF4E expands and becomes stiffer, the C-terminal region is less affected.

LF-EMF Compound Block Type Signal Activates Human Neutrophilic Granulocytes In Vivo.

This research aims to demonstrate in a randomized, placebo-controlled crossover design study that a nominal 5 μT low-frequency electromagnetic field (LF-EMF) signal for 30 min activates neutrophils in vivo in humans. Granularity of neutrophils was measured in blood samples of healthy human volunteers (n = 32) taken before and after exposure for both the exposure and control sessions. A significant decrease in the granularity, indicative of neutrophil activation, was observed both in the exposure measurements and the exposure minus control measurements.

Protein Dynamics to Define and Refine Disordered Protein Ensembles.

Intrinsically disordered proteins and unfolded proteins have fluctuating conformational ensembles that are fundamental to their biological function and impact protein folding, stability, and misfolding. Despite the importance of protein dynamics and conformational sampling, time-dependent data types are not fully exploited when defining and refining disordered protein ensembles. Here we introduce a computational framework using an elastic network model and normal-mode displacements to generate a dynamic disordered ensemble consistent with NMR-derived dynamics parameters, including transverse relaxation rates and Lipari-Szabo order parameters ( values).

Corn Cob Ash versus Sunflower Stalk Ash, Two Sustainable Raw Materials in an Analysis of Their Effects on the Concrete Properties.

The increased CO emissions determined by the cement industry led to continuous and intensive research on the discovery of sustainable raw materials with cementitious properties. One such raw material category is agricultural waste. This study involved research on the effects of corn cob ash and sunflower stalk ash, respectively, on compressive strength measured after 28 days and 3 months, the flexural and splitting tensile strengths, the resistance to repeated freeze-thaw cycles, and on the resistance to chemical attack of hydrochloric acid of the concrete.

The Synergy between Bio-Aggregates and Industrial Waste in a Sustainable Cement Based Composite.

The effects of the fly ash and of the sunflower stalks and corn cobs within a cement-matrix composite were studied under the aspects of density, compressive strength, splitting tensile strength, elasticity modulus, and resistance to repeated freeze-thaw cycles. In the research were developed 20 recipes of cement-based composite, including the reference composite. Fly ash was used as partial cement replacement (10, 20 and 30% by volume), and the vegetal aggregates made by corn cobs and sunflower stalks as partial replacement of the mineral aggregates (25 and 50% by volume).

Sunflower Stalks versus Corn Cobs as Raw Materials for Sustainable Concrete.

Concrete, the most common material in the building industry, involves the use of mineral aggregates that represent an exhaustible resource, despite their large availability. For a series of applications, these mineral aggregates can be replaced by vegetal ones, which represent an easy renewable natural resource. In this study, two types of vegetal raw materials, namely sunflower stalks and corn cobs, were used in developing 10 compositions of ecological microconcrete, with different percentages involved: 20%, 35%, 50%, 65% and 80%; they were analyzed from the perspectives of density, compressive strength, splitting tensile strength, resistance to repeated freeze-thaw cycles, modulus of elasticity and thermal conductivity.

Multifunctional nanoparticles as theranostic agents for therapy and imaging of breast cancer.

Over the last decade, there has been significant developments in nanotechnology, in particular for combined imaging and therapeutic applications (theranostics). The core or shell of nanoemulsions (NEs) can be loaded with various therapeutic agents, including drugs with low solubility for effective treatment, or various imaging agents for specific imaging modalities (e.g.

Ligand modulation of the conformational dynamics of the A adenosine receptor revealed by single-molecule fluorescence.

G protein-coupled receptors (GPCRs) are the largest class of transmembrane proteins, making them an important target for therapeutics. Activation of these receptors is modulated by orthosteric ligands, which stabilize one or several states within a complex conformational ensemble. The intra- and inter-state dynamics, however, is not well documented.

PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins.

The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.

Conformational Ensembles of an Intrinsically Disordered Protein Consistent with NMR, SAXS, and Single-Molecule FRET.

Intrinsically disordered proteins (IDPs) have fluctuating heterogeneous conformations, which makes their structural characterization challenging. Although challenging, characterization of the conformational ensembles of IDPs is of great interest, since their conformational ensembles are the link between their sequences and functions. An accurate description of IDP conformational ensembles depends crucially on the amount and quality of the experimental data, how it is integrated, and if it supports a consistent structural picture.

Extended Experimental Inferential Structure Determination Method in Determining the Structural Ensembles of Disordered Protein States.

Proteins with intrinsic or unfolded state disorder comprise a new frontier in structural biology, requiring the characterization of diverse and dynamic structural ensembles. We introduce a comprehensive Bayesian framework, the Extended Experimental Inferential Structure Determination (X-EISD) method, that calculates the maximum log-likelihood of a disordered protein ensemble. X-EISD accounts for the uncertainties of a range of experimental data and back-calculation models from structures, including NMR chemical shifts, J-couplings, Nuclear Overhauser Effects (NOEs), paramagnetic relaxation enhancements (PREs), residual dipolar couplings (RDCs), hydrodynamic radii ( ), single molecule fluorescence Förster resonance energy transfer (smFRET) and small angle X-ray scattering (SAXS).

Non-cooperative 4E-BP2 folding with exchange between eIF4E-binding and binding-incompatible states tunes cap-dependent translation inhibition.

Phosphorylation of intrinsically disordered eIF4E binding proteins (4E-BPs) regulates cap-dependent translation by weakening their ability to compete with eIF4G for eIF4E binding within the translation initiation complex. We previously showed that phosphorylation of T37 and T46 in 4E-BP2 induces folding of a four-stranded beta-fold domain, partially sequestering the canonical eIF4E-binding helix. The C-terminal intrinsically disordered region (C-IDR), remaining disordered after phosphorylation, contains the secondary eIF4E-binding site and three other phospho-sites, whose mechanisms in inhibiting binding are not understood.

Bayesian counting of photobleaching steps with physical priors.

Counting fluorescence photobleaching steps is commonly used to infer the number n of monomeric units of individual oligomeric protein complexes or misfolded protein aggregates. We present a principled Bayesian approach for counting that incorporates the statistics of photobleaching. Our physics-based prior leads to a simple and efficient numerical scheme for maximum a posteriori probability (MAP) estimates of the initial fluorophore number n^.

Malignant Transformation of a Filum Terminale Dermoid Tumor into Adenocarcinoma.

Background: Intraspinal dermoid tumors are usually rare benign growths that occur as a result of defects during neural tube formation. They make up less than 1% of tumors in the spine and are associated with spinal dysraphisms or sinus tracts. Although rare, malignant transformation into squamous cell carcinoma has been previously reported.

Publisher Correction: Exocyst dynamics during vesicle tethering and fusion.

The original version of this Article contained errors in the author affiliations. Affiliation 2 incorrectly read 'Department of Biochemistry and Molecular Genetics and Breast Surgery, Ehime University Graduate School of Medicine, 7910295, Japan' and affiliation 3 incorrectly read 'Department of Hepato-Biliary-Pancreatic and Breast Surgery, Ehime University Graduate School of Medicine, Matsuyama 7910295, Japan.' These errors have now been corrected in both the PDF and HTML versions of the Article.

Exocyst dynamics during vesicle tethering and fusion.

The exocyst is a conserved octameric complex that tethers exocytic vesicles to the plasma membrane prior to fusion. Exocyst assembly and delivery mechanisms remain unclear, especially in mammalian cells. Here we tagged multiple endogenous exocyst subunits with sfGFP or Halo using Cas9 gene-editing, to create single and double knock-in lines of mammary epithelial cells, and interrogated exocyst dynamics by high-speed imaging and correlation spectroscopy.