Biophysical reviews最新文献

{"title":"Studying biological events using biopolymeric matrices.","authors":"Joao Aguilar, Silvana A Rosú, José Ulloa, German Gunther, Bruno F Urbano, M Alejandra Tricerri, Susana A Sánchez","doi":"10.1007/s12551-025-01303-z","DOIUrl":"https://doi.org/10.1007/s12551-025-01303-z","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"385-394"},"PeriodicalIF":4.9,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The discovery of the Sph-gated plasma membrane Ca²⁺ channel in trypanosomatids. A difficult path for a surprising kind of L-Type VGCC.","authors":"Gustavo Benaim, Christian Gabriel Calderón Artavia, Cecilia Castillo, María Carolina Pérez-Gordones, María Luisa Serrano","doi":"10.1007/s12551-025-01300-2","DOIUrl":"https://doi.org/10.1007/s12551-025-01300-2","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"709-722"},"PeriodicalIF":4.9,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075035/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Challenges in simulating whole virus particles and how to fix them with the SIRAH force field.","authors":"Lucianna Helene Silva Santos, Sergio Pantano","doi":"10.1007/s12551-025-01305-x","DOIUrl":"https://doi.org/10.1007/s12551-025-01305-x","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"285-292"},"PeriodicalIF":4.9,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075059/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Making sense of blobs, whorls, and shades: methods for label-free, inverse imaging in bright-field optical microscopy.","authors":"Braulio Gutiérrez-Medina","doi":"10.1007/s12551-025-01301-1","DOIUrl":"https://doi.org/10.1007/s12551-025-01301-1","url":null,"abstract":"<p><p>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 <i>z</i>-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.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"335-345"},"PeriodicalIF":4.9,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075049/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Surfactant protein SP-B: one ring to rule the molecular and biophysical mechanisms of the pulmonary surfactant system.","authors":"Alejandro Alonso, Bárbara Olmeda, Jesús Pérez-Gil","doi":"10.1007/s12551-025-01285-y","DOIUrl":"https://doi.org/10.1007/s12551-025-01285-y","url":null,"abstract":"<p><p>Pulmonary surfactant is a lipid/protein complex crucial to maintain mammalian lungs open, as it facilitates breathing mechanics through a dramatic reduction of surface tension at the air-liquid interface. Intensive research during a few decades has identified many of the molecular actors defining the molecular and biophysical mechanisms of surfactant at the airspaces. Pulmonary surfactant protein SP-B has been undoubtedly identified as the most important and essential molecule to allow for air breathing in the mammalian lungs, as its absence is incompatible with life. We now know that SP-B directs the assembly of surfactant complexes into the lamellar bodies of type II pneumocytes, their secretion, adsorption, and reorganization at the interface as well as the homeostasis of the surfactant layer during different pathophysiological contexts. This review summarizes current models on SP-B structure and biophysical function, supporting how the activity of SP-B may be crucial for the design and production of a new generation of therapeutic products in respiratory medicine.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"653-666"},"PeriodicalIF":4.9,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075752/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of ionizing radiations of different qualities and delivery types on blood cells.","authors":"Analía Inés Alet, Sabrina Porini, Bibiana Doris Riquelme, Alessandra Bisio, Emanuele Scifoni, Mariel Elisa Galassi","doi":"10.1007/s12551-025-01302-0","DOIUrl":"https://doi.org/10.1007/s12551-025-01302-0","url":null,"abstract":"<p><p>This review explores the effects of ionizing radiation on blood and its components, focusing on its applications, biological impacts, and implications for medical and occupational settings. Ionizing radiation is a cornerstone of modern medicine, playing a critical role in diagnostic imaging, cancer treatment, and preventive measures, such as the irradiation of blood units to prevent transfusion-associated graft-versus-host disease. However, it also induces significant alterations in blood cells, including genetic damage, immune suppression, and changes in hematological, biochemical, and hemorheological parameters, depending on the dose, dose rate, and type of radiation. Conventional radiotherapy, hadron therapy, and the emerging FLASH modality exhibit distinct effects on blood. Hadron therapy and FLASH radiotherapy could reduce oxidative stress preserving red blood cell deformability more effectively than conventional methods, thereby minimizing systemic toxicity. However, the underlying mechanisms remain a topic of ongoing investigation. Additionally, studies reveal how different types of radiation, including gamma rays, X-rays, electron beams, and hadrons, uniquely influence blood cells, underscoring the complexity of radiobiological interactions. Challenges and controversies, such as the long-term hematological impact of radiation exposure, individual variability in response, and the potential of radioprotective strategies and immune system stimulation are also addressed. Insights into hemorheological changes and the development of personalized approaches are critical for optimizing therapeutic outcomes and safety protocols. By synthesizing current knowledge, this review emphasizes the need for further research on the effects of ionizing radiation on blood to bridge gaps in understanding and enhance clinical and practical applications.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"579-590"},"PeriodicalIF":4.9,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075073/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Generation of cellular reactive oxygen and nitrogen species by exposure to ultraviolet radiation.","authors":"Macarena Menoni, Pablo Alcoba, María J Zuluaga, R Daniel Peluffo","doi":"10.1007/s12551-025-01298-7","DOIUrl":"https://doi.org/10.1007/s12551-025-01298-7","url":null,"abstract":"<p><p>Reactive oxygen and nitrogen species, such as superoxide and peroxynitrite anions, are produced in our body as a result of normal metabolic functions or under pathologic conditions (oxidative and nitro-oxidative stress). A well-documented battery of antioxidant enzymes and cofactors are in place to fight this stress and restore the redox balance of the cell. However, comprehensive information on the generation of these reactive species by exposing cell components to ultraviolet (UV) light, specifically UVA and UVB sunlight, is scarce or missing. In this short review, we attempt to cover several enzymes and cofactors that are targets of UV radiation as it relates to the production (or consumption) of these oxidants, and, when known, discuss the underlying mechanisms. Because of their key importance, UV light effects on DNA are briefly discussed.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"547-560"},"PeriodicalIF":4.9,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Liquid‒liquid phase separation and poly(ADP‒ribosyl)ation in the context of ultraviolet radiation-induced stress in mammalian cells.","authors":"Daniela Mejías, Valentina Seballos, Laura Lafon-Hughes","doi":"10.1007/s12551-025-01294-x","DOIUrl":"https://doi.org/10.1007/s12551-025-01294-x","url":null,"abstract":"<p><p>Poly(ADP‒ribose) polymerases (PARPs) consume NAD⁺ to synthesize poly(ADP‒ribose) (PAR) primarily via post-translational modification. PAR is degraded mainly by poly (ADP-ribose) glycohydrolase (PARG). PAR can be linear or branched and can have up to 200 monomers. With two phosphates per monomer, PAR is highly negatively charged. PAR can be recognized by specific protein domains and has been described as a \"glue\" or scaffold for the assembly of multiprotein complexes. PAR is involved in several diverse cellular structures and functions, including DNA replication, transcription, DNA repair, chromatin structure and imprinting regulation, mitotic spindle assembly, cell‒cell junctions, cytoplasmic granule formation, biomineralization and the formation of pathological aggregates. Here, we review the effects of ultraviolet radiation (UVR) on mammalian cells, emphasizing the participation of PAR metabolism in the novel paradigm of liquid‒liquid phase separation (LLPS). Further studies demand interdisciplinary approaches, undoubtedly requiring contributions from biophysicists.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s12551-025-01294-x.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"499-510"},"PeriodicalIF":4.9,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075067/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biophysics of SARS-CoV-2 spike protein's receptor-binding domain interaction with ACE2 and neutralizing antibodies: from computation to functional insights.","authors":"Fernando Luís Barroso da Silva, Karen Paco, Aatto Laaksonen, Animesh Ray","doi":"10.1007/s12551-025-01276-z","DOIUrl":"https://doi.org/10.1007/s12551-025-01276-z","url":null,"abstract":"<p><p>The spike protein encoded by the SARS-CoV-2 has become one of the most studied macromolecules in recent years due to its central role in COVID-19 pathogenesis. The spike protein's receptor-binding domain (RBD) directly interacts with the host-encoded receptor protein, ACE2. This review critically examines computational insights into RBD's interaction with ACE2 and with therapeutic antibodies designed to interfere with this interaction. We begin by summarizing insights from early computational studies on pre-pandemic SARS-CoV-1 RBD interactions and how these early studies shaped the understanding of SARS-CoV-2. Next, we highlight key theoretical contributions that revealed the molecular mechanisms behind the binding affinity of SARS-CoV-2 RBD against ACE2, and the structural changes that have enhanced the infectivity of emerging variants. Special attention is given to the \"RBD charge rule\", a predictive framework for determining variant infectivity based on the electrostatic properties of the RBD. Towards applying the computational insights to therapy, we discuss a multiscale computational protocol for optimizing monoclonal antibodies to improve binding affinity across multiple spike protein variants, including representatives from the Omicron family. Finally, we explore how these insights can inform the development of future vaccines and therapeutic interventions for combating future coronavirus diseases.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"309-333"},"PeriodicalIF":4.9,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075047/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New therapeutic strategies for malaria.","authors":"Alessandro Sá Pinheiro, Patricia Rieken Macedo Rocco, Celso Caruso-Neves, Ana Acacia Sá Pinheiro","doi":"10.1007/s12551-025-01296-9","DOIUrl":"https://doi.org/10.1007/s12551-025-01296-9","url":null,"abstract":"<p><p>Malaria is a life-threatening parasitic disease and remains a significant global health problem, associated with high morbidity and mortality. Malaria cases are widely spread, but the highest incidence occurs in tropical and subtropical areas, especially in developing countries. Despite all efforts to control the disease, the number of cases increased by 5 million from 2021 to 2022. The mechanisms of malaria pathogenesis are still not fully understood. This, combined with the parasite's recurrent ability to develop resistance to standard treatments, hinders effective disease management and control. Therefore, a deep understanding of parasite biology, along with the various aspects of host-parasite interactions, is essential for malaria elimination. Extracellular vesicles (EVs) are membrane-enclosed vesicles which are secreted by a variety of cells. These tiny structures have emerged as a key component in the mechanisms of pathogenesis of different parasitic diseases, promoting cell-to-cell communication, even in distance. In this review, we explore the latest advancements in EV research in the malaria field, focusing on their role in pathophysiology, as well as their potential as diagnostic tools, alternative therapeutic strategies, and vaccine development. We conclude by highlighting key elements in EV research that could provide insights into the translational application of EVs.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"701-707"},"PeriodicalIF":4.9,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075036/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}