Biophysical reviews最新文献

Membrane-active peptides (MAPs) are versatile molecules that interact with lipid bilayers, facilitating processes such as antimicrobial defense, anticancer activity, and membrane translocation. Given that most MAPs are cationic, their selectivity for specific cell membranes has traditionally been attributed to variations in membrane surface charge. However, growing evidence suggests that electrostatics alone cannot fully explain MAPs selectivity. Instead, MAPs activity is also strongly influenced by other membrane biophysical properties, such as lipid packing, phase state, curvature, and the spatial distribution of hydrophobic and charged residues within the peptide sequence. In this review, we summarize the current knowledge on the biophysical determinants of MAPs selectivity. We begin by examining membrane and cell surface electrostatics and their influence on MAPs-membrane interactions, including electrostatically driven peptide conformational changes and lipid recruitment. We then broaden the discussion to include non-electrostatic factors, such as membrane curvature and rheology, which are primarily influenced by sterol or hopanoid content, as well as acyl chain unsaturation and branching. Together, these processes highlight that MAPs selectivity is not governed by any single membrane property but instead emerges from a synergistic interplay of electrostatic, hydrophobic, and topological factors.

Supplementary information: The online version contains supplementary material available at 10.1007/s12551-025-01309-7.

According to the World Health Organization (WHO), cardiovascular diseases are the leading cause of death worldwide. Several diseases have been linked to changes in cellular mechanical properties, including those affecting the heart. Atomic force microscopy (AFM) has proven to be one of the most effective techniques for precisely determining the topography and mechanical properties of adherent living cells. In this review, we provide a short chronological overview of key studies conducted using AFM on cardiac cells or cardiomyocytes with clinical and medical significance. These studies have contributed and continue to enhance our understanding of the pathological processes affecting the heart and clarify the role of cell mechanics in cardiac and cardiovascular diseases.

About one-third of the proteins synthesized in eukaryotic cells are directed to the secretory pathway, where close to 70% are being N-glycosylated. N-glycosylation is a crucial modification for various cellular processes, including endoplasmic reticulum (ER) glycoprotein folding quality control, lysosome delivery, and cell signaling. The defects in N-glycosylation can lead to severe developmental diseases. For the proteins to be glycosylated, they must be translocated to the ER through the Sec61 translocon channel, either via co-translationally or post-translationally. N-glycosylation not only could accelerate post-translational translocation but may also enhance protein stability, while protein folding can assist in their movement into the ER. However, the precise mechanisms by which N-glycosylation and folding influence translocation remain poorly understood. The chaperone BiP is essential for post-translational translocation, using a "ratchet" mechanism to facilitate protein entry into the ER. Although research has explored how BiP interacts with protein substrates, there has been less focus on its binding to glycosylated substrates. Here, we review the effect of N-glycosylation on protein translocation, employing single-molecule studies and ensembles approaches to clarify the roles of BiP and N-glycosylation in these processes. Our review explores the possibility of a direct relationship between translocation and a ratchet effect of glycosylation and the importance of BiP in binding glycosylated proteins for the ER quality control system.

Supplementary information: The online version contains supplementary material available at 10.1007/s12551-025-01313-x.

Atomic force microscopy (AFM) is a scanning imaging technique able to work at the nanoscale. It uses a cantilever with a tip to move across samples' surface and a laser to measure the cantilever bending, enabling the assessment of interaction forces between tip and sample and creating a three-dimensional visual representation of its surface. AFM has been gaining notoriety in the biomedical field due to its high-resolution images, as well as due to its ability to measure the inter- and intramolecular interaction forces involved in the pathophysiology of many diseases. Here, we highlight some of the current applications of AFM in the biomedical field. First, a brief overview of the AFM technique is presented. This theoretical framework is then used to link AFM to its novel translational applications, handling broad clinical questions in different areas, such as infectious diseases, cardiovascular diseases, cancer, and neurodegenerative diseases. Morphological and nanomechanical characteristics such as cell height, volume, stiffness, and adhesion forces may serve as novel parameters used to tailor patient care through nanodiagnostics, individualized risk stratification, and therapeutic monitoring. Despite an increasing development of AFM biomedical research with patient cells, showing its unique capabilities in terms of resolution, speed, and accuracy, there is a notable need for applied AFM research in clinical settings. More translational research with AFM may provide new grounds for the valuable collaboration between biomedical researchers and healthcare professionals.

Frataxin is a small protein involved in the rare disease Friedreich's ataxia. During the last few years, significant knowledge has been gained concerning frataxin folding, structure, dynamics, and function. In eukaryotic organisms, it is located in the mitochondrial matrix, and recently, its macromolecular context was revealed. This protein is part of a decameric supercomplex consisting of six subunits required for iron-sulfur cluster assembly, where two of them alternate in a mutually exclusive manner. Regarding Frataxin, pathogenic variants were studied, and while some exhibited reduced conformational stability, others presented an altered function. In this review, we focused on different aspects concerning the biophysics and the biochemistry of frataxin and its partners, as well as on the current knowledge regarding proteostasis and post-translational modifications. The involvement of frataxin and its partners in diseases will also be addressed, including the current therapeutic approaches. Finally, a section is dedicated to understanding the phylogenetic distribution of frataxin.

Traditional methodologies to study in vitro biological processes include simplified laboratory models where different parameters can be measured in a very controlled environment. The most used of these practices is cell plate-culturing in aqueous media. In this minimalistic model, essential components of the biological system might be ignored. One of them, disregarded for a long time, is the extracellular matrix (ECM). Extracellular matrix in eukaryotic cells is not only a frame for cells and biological components, but also an active partner of cellular metabolism and participates in several normal and pathological biological processes in a dynamic manner. ECM of eukaryotic cells has a very complex structure. Also, its mechanical properties (stiffness, viscoelasticity) depend on the organ it is associated with, and may vary from a very fluid (plasma) to a very solid (bones) structure. ECM structure and composition are very dynamic and experience temporal structural and topological changes, affecting all the existing interactions. When mimicking the ECM, three aspects are considered: the chemical environment and the physical and structural properties. In this review, we present two lines of research studying the role of the ECM in two biological implications: membrane fluidity heterogeneity and protein retention and aggregation. For these studies, we used biopolymeric matrices with very controlled features to evaluate the two events. We use traditional biochemical techniques and fluorescence microscopy to study the biological systems and traditional polymer techniques (rheology, SEM) to characterize the polymeric matrices.

Ca²⁺ plays a crucial role in signaling pathways in all eukaryotic cells, including trypanosomatids. These represent a large family of parasites including the causative agents of several human infectious diseases, such as Chagas' disease and leishmaniasis. Accordingly, the intracellular free Ca²⁺ concentration ([Ca²⁺]_i) is subject to rigorous regulation. In these parasites, the cytosolic concentration is maintained at approximately 100 nM by various intracellular organelles, including the single mitochondrion, the endoplasmic reticulum, and acidocalcisomes, which as compartments, are limited to capacity confines. It is therefore the responsibility of plasma membrane mechanisms to ensure the long-term regulation of [Ca²⁺]_i, whereas a plasma membrane Ca²⁺ channel is responsible for Ca²⁺ entry and a Ca²⁺-ATPase regulates extrusion. However, the identification of this channel has remained a challenge until the ligand that induces its opening was identified: the sphingolipid sphingosine. Miltefosine, the only oral medication currently approved for the treatment of leishmaniasis, has been shown to mimic sphingosine. This review outlines the history of the trypanosomatid Ca²⁺ channel, beginning with its initial discovery and concluding with its incorporation into giant liposomes. This enabled the channel to be characterized by electrophysiological studies using "patch clamp" techniques. These studies revealed similarities and significant differences when compared with the human orthologue, which could be exploited for therapeutic purposes. Given that previous research has indicated the potential existence of an L-type VGCC in various trypanosomatids, we conducted a comparative analysis of putative genomic sequences, which demonstrated that, despite the low level of primary identity, this Ca²⁺ channel exhibits functional and structural homology with the mammalian counterpart.

Current developments in specialized software and computer power make the simulation of large molecular assemblies a technical possibility despite their computational cost. Coarse-grained (CG) approaches simplify molecular complexity and reduce computational costs while preserving intermolecular physical/chemical interactions. These methods enable virus simulations, making them more accessible to research groups with limited supercomputing resources. However, setting up and running molecular dynamics simulations of multimillion systems requires specialized molecular modeling, editing, and visualization skills. Moreover, many issues related to the computational setup, the choice of simulation engines, and the force fields that rule the intermolecular interactions require particular attention and are key to attaining a realistic description of viral systems at the fully atomistic or CG levels. Here, we provide an overview of the current challenges in simulating entire virus particles and the potential of the SIRAH force field to address these challenges through its implementations for CG and multiscale simulations.

The application of cyclic stretch could represent a novel therapeutic method for fighting cancer. Research indicates that this mechanical stimulus selectively induces cell death in cancer mesenchymal-like cells while enhancing the migration and proliferation of healthy epithelial cells. Although the mechanisms have been examined through the lenses of cell signalling, gene expression, and biochemical processes, a significant gap persists in our understanding of the physical factors that drive cellular responses. This study aims to clarify the importance of physical factors, particularly the viscoelastic characteristics of the cell membrane, including actin cytoskeleton and lipid bilayer, and how their coupling affects bilayer bending and activation of the mechanosensitive Piezo1 channels in response to cyclic stretch in both epithelial and cancer cells. The bending of the bilayer surrounding Piezo1 molecules affects their conformations, which in turn influences calcium influx. This bending is contingent upon the coupling between the cell membrane and extracellular matrix. The primary factors contributing to the mechanically induced apoptosis of cancer cells are the perturbation of intracellular calcium homeostasis and disruption of focal adhesions.

Despite its long history and widespread use, conventional bright-field optical microscopy has received recent attention as an excellent option to perform accurate, label-free, imaging of biological objects. As with any imaging system, bright-field produces an ill-defined representation of the specimen, in this case characterized by intertwined phase and amplitude in image formation, invisibility of phase objects at exact focus, and both positive and negative contrast present in images. These drawbacks have prevented the application of bright-field to the accurate imaging of unlabeled specimens. To address these challenges, a variety of methods using hardware, software or both have been developed, with the goal of providing solutions to the inverse imaging problem set in bright-field. We revise the main operating principles and characteristics of bright-field microscopy, followed by a discussion of the solutions (and potential limitations) to reconstruction in two dimensions (2D). We focus on methods based on conventional optics, including defocusing microscopy, transport of intensity, ptychography and deconvolution. Advances to achieving three-dimensional (3D) bright-field imaging are presented, including methods that exploit multi-view reconstruction, physical modeling, deep learning and conventional digital image processing. Among these techniques, optical sectioning in bright-field microscopy (OSBM) constitutes a direct approach that captures z-image stacks using a standard microscope and applies digital filters in the spatial domain, yielding inverse-imaging solutions in 3D. Finally, additional techniques that expand the capabilities of bright-field are discussed. Label-free, inverse imaging in conventional optical microscopy thus emerges as a powerful biophysical tool for accurate 2D and 3D imaging of biological samples.