Biology subjects

Efremov, A. K.

Publications and source records attributed to Efremov, A. K..

6 recordsLinked to original sources

bioRxiv2026

Effect of nuclear electrostatic potential on the nucleoplasmic distribution of histones and nucleosome stability

Differences in the density of heterochromatic and euchromatic regions are often assumed to play an important role in determining the transcriptional state of chromatin by influencing its accessibility to transcription factors. Yet, experiments show that even the most densely packed chromatin domains are readily accessible to transcription factors. Thus, the molecular mechanisms underlying differences in the transcriptional states of hetero- and euchromatin remain poorly understood. In this study, using electrically charged mEGFP probes, we demonstrated that heterochromatin and euchromatin differ not only in density but also in the magnitude of the local electrostatic potential. Furthermore, the nucleoplasmic distribution of electrically charged proteins, such as histone-chaperone complexes, was found to correlate with the local electrostatic potential. Estimates based on experimental data have also shown that the difference in electrostatic potentials between heterochromatic and euchromatic regions could lead to unequal nucleosome stability in them, which was successfully confirmed experimentally. Subsequent theoretical calculations showed that this could shift the balance in the DNA-binding competition between transcription factors and nucleosomes, thereby explaining experimental observations that heterochromatin is less transcriptionally active than euchromatin. Overall, our study suggests the existence of a nuclear electrostatic potential-mediated pathway that may be involved in the regulation of gene transcription.

biophysics↗

bioRxiv2025

Optogenetic construction of de novo integrin-adhesion complexes reveals role for biocondensation in adhesion nucleation

Integrin-adhesion complexes (IACs) form spontaneously in cells on extracellular matrix substrates, allowing them to sense matrix composition and transduce force. However, IACs often do not form uniformly across a cell, which begs the question: What is required to nucleate an adhesion, and what factors enable the stabilization of an IAC once it has formed? Many factors have been suggested to promote formation and the subsequent stabilization of IACs. It is difficult to explicitly test these factors in vivo as IACs undergo constant remodeling. Here, we employ optogenetics to explicitly test the ability of talin in different activity and phase states to nucleate and stabilize IACs in regions where none are present. We find that fusion of intrinsically disordered regions directly to talin enhances its adhesion nucleation potential and allows new adhesions to be produced in response to optogenetic talin clustering. Similarly, expression of factors previously shown to enhance biocondensation in vitro, such as paxillin, the paxillin N-terminus, or unfolding of talin, allows for adhesion nucleation and biocondensation of talin. We show that these biocondensates of talin can cluster and activate integrins even in the absence of extracellular matrix. By applying optogenetic activation to regions of the cell with or without ventral actomyosin, we demonstrate actomyosin engagement promotes the formation and stability of adhesions. These results are corroborated by theoretical modelling which shows that phase separation of talin is enhanced by differential clutch formation in the presence of actomyosin thus enabling peripheral adhesion formation and stability. This work establishes a model in which increased cooperativity of talin enables IAC nucleation through talin biocondensation, which clusters and activates integrins. In addition to these findings, we generate multiple optogenetic tools that enable local nucleation or enhancement of IACs. HighlightsO_LIOptogenetic tools mediating talin biocondensation can locally induce focal adhesion formation C_LIO_LIPaxillin LD domains enable biocondensation of talin C_LIO_LIBiocondensation of talin enables IAC formation C_LIO_LIPhase separation of talin can activate integrins independently of ECM C_LIO_LIComputational model reconciles spatial variance in LLPS and IAC formation. C_LI

cell biology↗

bioRxiv2023

Elasticity of adhesion bonds determines multistable mechanosensitive behaviour of living cells.

The ability of cells to sense the mechanical properties of their microenvironment is essential to many physiological processes. The molecular clutch theory has played an important role in explaining many mechanosensitive cell behaviors. However, its current implementations have limited ability to understand how molecular heterogeneity, such as adhesion molecules with different elasticities, regulates the mechanical response of cell adhesion. In this study, we developed a model incorporating the experimentally measured elastic properties of such proteins to investigate their influence on cell adhesion. It was found that the model not only could accurately fit previous experimental measurements of cell traction force and retrograde actin flow, but also predicted multistablility of cell adhesion as well as a feedback loop between the densities of the extracellular matrix proteins and contractile myosin II motors in living cells. The existence of such a feedback loop was successfully confirmed in experiments. Taken together, our study provides a theoretical framework for understanding how the mechanical properties of adaptor proteins, local substrate deformations and myosin II contractility affect cell adhesion across different cell types and physiological conditions.

biophysics↗

bioRxiv2021

Size of the cell nucleus and its effect on the chromatin structure in living cells.

DNA-architectural proteins play a major role in organization of chromosomal DNA in living cells by packaging it into chromatin, whose spatial conformation is determined by an intricate interplay between the DNA-binding properties of architectural proteins and physical constraints applied to the DNA by a tight nuclear space. Yet, the exact effects of the cell nucleus size on DNA-protein interactions and chromatin structure currently remain obscure. Furthermore, there is even no clear understanding of molecular mechanisms responsible for the nucleus size regulation in living cells. To find answers to these questions, we developed a general theoretical framework based on a combination of polymer field theory and transfer-matrix calculations, which showed that the nucleus size is mainly determined by the difference between the surface tensions of the nuclear envelope and the endoplasmic reticulum membrane as well as the osmotic pressure exerted by cytosolic macromolecules on the nucleus. In addition, the model demonstrated that the cell nucleus functions as a piezoelectric element, changing its electrostatic potential in a size-dependent manner. This effect has been found to have a profound impact on stability of nucleosomes, revealing a previously unknown link between the nucleus size and chromatin structure. Overall, our study provides new insights into the molecular mechanisms responsible for regulation of the cell nucleus size, as well as the potential role of nuclear organization in shaping the cell response to environmental cues. SIGNIFICANCE STATEMENTThe cell nucleus plays a central role in the life of eukaryotic cells, providing the highest level of control of intracellular processes. Depending on the stage of the cell cycle and / or surrounding environment, the size of the cell nucleus may undergo changes that are believed to cause chromatin reorganization, affecting gene transcription. At present, however, there is no clear understanding of the molecular mechanisms that may be responsible for such regulation, whose exact effect on chromatin structure remains unclear. In this study, by developing an advanced computational approach, we explore these issues from a physical perspective, revealing previously unknown mechanisms contributing to organization of the cell nucleus and chromatin.

biophysics↗

bioRxiv2020

Mechanosensitive calcium signaling in filopodia

Filopodia are ubiquitous membrane projections that play crucial role in guiding cell migration on rigid substrates and through extracellular matrix by utilizing yet unknown mechanosensing molecular pathways. As recent studies show that Ca2+ channels localized to filopodia play an important role in regulation of their formation and since some Ca2+ channels are known to possess mechanosensing properties, activity of filopodial Ca2+ channels might be tightly interlinked with the filopodia mechanosensing function. We tested this hypothesis by monitoring changes in the intra-filopodial Ca2+ level in response to application of stretching force to individual filopodia of several cell types. It has been found that stretching forces of tens of pN strongly promote Ca2+ influx into filopodia, causing persistent Ca2+ oscillations that last for minutes even after the force is released. Most of the known mechanosensitive Ca2+ channels, such as Piezo 1, Piezo 2 and TRPV4, were found to be dispensable for the observed force-dependent Ca2+ influx. In contrast, L-type Ca2+ channels appear to be a key component in the discovered phenomenon. Since previous studies have shown that intra-filopodial transient Ca2+ signals play an important role in guidance of cell migration, our results suggest that the force-dependent activation of L-type Ca2+ channels may contribute to this process. Overall, our study reveals an intricate interplay between mechanical forces and Ca2+ signaling in filopodia, providing novel mechanistic insights for the force-dependent filopodia functions in guidance of cell migration. Significance statementWe found that tensile forces of tens of pN applied to individual filopodia trigger Ca2+ influx through L-type Ca2+ channels, producing persistent Ca2+ oscillations inside mechanically stretched filopodia. Resulting elevation of the intra-filopodial Ca2+ level in turn leads to downstream activation of calpain protease, which is known to play a crucial role in regulation of the cell adhesion dynamics. Thus, our work suggests that L-type channel-dependent Ca2+ signaling and the mechanosensing function of filopodia are coupled to each other, synergistically governing cell adhesion and motion in a force-dependent manner. Since L-type Ca2+ channels have been previously found in many different cell types, such as neural or cancer cells, the above mechanism is likely to be widespread among various cell lines.

cell biology↗

bioRxiv2017

Force dependence of filopodia adhesion: involvement of myosin II and formins

Filopodia are dynamic membrane protrusions driven by polymerization of an actin filament core, mediated by formin molecules at the filopodia tips. Filopodia can adhere to the extracellular matrix and experience both external and cell generated pulling forces. The role of such forces in filopodia adhesion is however insufficiently understood. Here, we induced sustained growth of filopodia by applying pulling force to their tips via attached fibronectin-coated beads trapped by optical tweezers. Strikingly, pharmacological inhibition or knockdown of myosin IIA, which localized to the base of filopodia, resulted in weakening of filopodia adherence strength. Inhibition of formins, which caused detachment of actin filaments from formin molecules, produced similar effect. Thus, myosin IIA-generated centripetal force transmitted to the filopodia tips through interactions between formins and actin filaments are required for filopodia adhesion. Force-dependent adhesion led to preferential attachment of filopodia to rigid versus fluid substrates, which may underlie cell orientation and polarization.

cell biology↗