Single-cell unroofing: probing topology and nanomechanics of native membranes

Structural heterogeneity of the ion and lipid channel TMEM16F

Transmembrane protein 16 F (TMEM16F) is a Ca2+-activated homodimer which functions as an ion channel and a phospholipid scramblase. Despite the availability of several TMEM16F cryogenic electron microscopy (cryo-EM) structures, the mechanism of activation and substrate translocation remains controversial, possibly due to restrictions in the accessible protein conformational space. In this study, we use atomic force microscopy under physiological conditions to reveal a range of structurally and mechanically diverse TMEM16F assemblies, characterized by variable inter-subunit dimerization interfaces and protomer orientations, which have escaped prior cryo-EM studies. Furthermore, we find that Ca2+-induced activation is associated to stepwise changes in the pore region that affect the mechanical properties of transmembrane helices TM3, TM4 and TM6. Our direct observation of membrane remodelling in response to Ca2+ binding along with additional electrophysiological analysis, relate this structural multiplicity of TMEM16F to lipid and ion permeation processes. These results thus demonstrate how conformational heterogeneity of TMEM16F directly contributes to its diverse physiological functions.

Unfolding and identification of membrane proteins in situ

Single-molecule force spectroscopy (SMFS) uses the cantilever tip of an AFM to apply a force able to unfold a single protein. The obtained force-distance curve encodes the unfolding pathway, and from its analysis it is possible to characterize the folded domains. SMFS has been mostly used to study the unfolding of purified proteins, in solution or reconstituted in a lipid bilayer. Here, we describe a pipeline for analyzing membrane proteins based on SMFS, that involves the isolation of the plasma membrane of single cells and the harvesting of force-distance curves directly from it. We characterized and identified the embedded membrane proteins combining, within a Bayesian framework, the information of the shape of the obtained curves, with the information from Mass Spectrometry and proteomic databases. The pipeline was tested with purified/reconstituted proteins and applied to five cell types where we classified the unfolding of their most abundant membrane proteins. We validated our pipeline by overexpressing 4 constructs, and this allowed us to gather structural insights of the identified proteins, revealing variable elements in the loop regions. Our results set the basis for the investigation of the unfolding of membrane proteins in situ, and for performing proteomics from a membrane fragment.

Optimization of urolithiasis treatment and diagnosis in the Turkestan region

The article aims to identify the main problems in treating urological pathologies by analyzing scientific literature from this field and developing recommendations. The quantitative excretion of uric acid, urine volume, and pH are essential in the formation of uric acid stones. The most important risk factor for uric acid nephrolithiasis is the acidic reaction of urine, which is a prerequisite for the formation of urinary stones. When urine is alkalized, the pH should be 6-6.5. Drugs alkalize urine, and one should titrate using urine pH indicator paper until the level is stable. This study found that the spread of genitourinary diseases is increasing. This situation can be improved by monitoring and assessing epidemiological processes, preventing urological pathology, and optimizing medical care organization in the context of health care reform.

Effect of lipid peroxidation on dental healthcare workers

Aim and Objective:

The relevance of the study was explained by the fact that free radicals, known to be a product of lipid peroxidation, damage the integrity of cell membranes and corresponding intracellular structures, disrupting their functioning. The purpose of this cross-sectional study was to investigate the effect of free-radical lipid peroxidation in the blood on the body of dentists without diseases of the bronchi and lungs.

Materials and Methods:

The chemiluminescent properties of the blood hemolysate of 65 dentists were measured. Blood was collected in a test tube with an anticoagulant, and the plasma was aspirated with a Pasteur pipette. The hemolysate was aspirated two times. Distilled water was added to the sediment of erythrocytes, the mixture was shaken, and centrifuged. Statistical processing of morphometric indicators was carried out using the software package “Statistica 6.0.”

Results:

The direct dependence of the spontaneous chemiluminescence (SCL) growth parameters in the blood hemolysate of dentists on their length of service was determined.

Conclusion:

The conclusions indicate a direct correlation between the growth parameters of the SCL index in the blood hemolysate of dentists and their length of service. The applied value of this study lies in the possibility of practical application of the results obtained to qualitatively investigate the effect of lipid peroxidation processes on the body of dentists.

Structural insights into fusion mechanisms of small extracellular vesicles with model plasma membranes

Extracellular vesicles (EVs) are a potent intercellular communication system. Such small vesicles transport biomolecules between cells and throughout the body, strongly influencing the fate of recipient cells. Due to their specific biological functions they have been proposed as biomarkers for various diseases and as optimal candidates for therapeutic applications. Despite their extreme biological relevance, their mechanisms of interaction with the membranes of recipient cells are still hotly debated. Here, we propose a multiscale investigation based on atomic force microscopy, small angle X-ray scattering, small angle neutron scattering and neutron reflectometry to reveal structure-function correlations of purified EVs in interaction with model membrane systems of variable complex compositions and to spot the role of different membrane phases on the vesicle internalization routes. Our analysis reveals strong interactions of EVs with the model membranes and preferentially with the borders of protruding phase domains. Moreover, we found that upon vesicle breaking on the model membrane surface, the biomolecules carried by/on EVs diffuse with different kinetics rates, in a process distinct from simple fusion. The biophysical platform proposed here has clear implications on the modulation of EV internalization routes by targeting specific domains at the plasma cell membrane and, as a consequence, on EV-based therapies.

Automatic classification of single-molecule force spectroscopy traces from heterogeneous samples

MOTIVATION

Single-molecule force spectroscopy (SMFS) experiments pose the challenge of analysing protein unfolding data (traces) coming from preparations with heterogeneous composition (e.g. where different proteins are present in the sample). An automatic procedure able to distinguish the unfolding patterns of the proteins is needed. Here, we introduce a data analysis pipeline able to recognize in such datasets traces with recurrent patterns (clusters).

RESULTS

We illustrate the performance of our method on two prototypical datasets: ∼50 000 traces from a sample containing tandem GB1 and ∼400 000 traces from a native rod membrane. Despite a daunting signal-to-noise ratio in the data, we are able to identify several unfolding clusters. This work demonstrates how an automatic pattern classification can extract relevant information from SMFS traces from heterogeneous samples without prior knowledge of the sample composition.

AVAILABILITY AND IMPLEMENTATION

https://github.com/ninailieva/SMFS_clustering.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Recent advances in AFM-based biological characterization and applications at multiple levels

Atomic force microscopy (AFM) has found a wide range of bio-applications in the past few decades due to its ability to measure biological samples in natural environments at a high spatial resolution. AFM has become a key platform in biomedical, bioengineering and drug research fields, enabling mechanical and morphological characterization of live biological systems. Hence, we provide a comprehensive review on recent advances in the use of AFM for characterizing the biomechanical properties of multi-scale biological samples, ranging from molecule, cell to tissue levels. First, we present the fundamental principles of AFM and two AFM-based models for the characterization of biomechanical properties of biological samples, covering key AFM devices and AFM bioimaging as well as theoretical models for characterizing the elasticity and viscosity of biomaterials. Then, we elaborate on a series of new experimental findings through analysis of biomechanics. Finally, we discuss the future directions and challenges. It is envisioned that the AFM technique will enable many remarkable discoveries, and will have far-reaching impacts on bio-related studies and applications in the future.

Regulation Mechanism of Bubbling Deformation and Fracture Toughness of the Membrane by Asymmetric Phospholipids: A Model System Study

Dynamic regulation of the deformation modulus and fracture toughness of a membrane is critical to organelles and cells for matching their conflicting needs of resilient and fractured behaviors. These properties implement the protection of the function in the normal condition and the fission function in the endocytosis condition of a membrane. Naturally, a membrane contains phospholipids that have different hydrophilic and hydrophobic group length. The diffusion and aggregation of the phospholipids with asymmetry of the hydrophilic-hydrophobic ratio on the membrane play a key role in regulating the mechanical behaviors passively to the external force. In present work, the effects of the asymmetry of phospholipids on the bubbling deformation and fracture toughness of the membrane to external stretching are investigated in a model system. A disk-shaped micelle formed from the blend of symmetric and asymmetric diblock copolymers in a selective solvent is considered as the membrane sheet. Its mechanically responsive behaviors are investigated by self-consistent field theory. By analyzing the evolution of different components during the stretching process, the mechanism of formation of the bubbling structure is revealed. Moreover, the fracture toughness depending on the asymmetry of the phospholipids is determined quantitatively.