Biophysical reviews最新文献

Biophysical reviews (ISSUE 2 2025): LAFeBS, alive, kicking, and growing: the story continues... 生物物理评论（2025年第2期）：LAFeBS，活着，踢，成长：故事还在继续……

IF 4.9

Biophysical reviews Pub Date : 2025-04-23 eCollection Date: 2025-04-01 DOI: 10.1007/s12551-025-01315-9

R Daniel Peluffo, Rosangela Itri, Leandro Rs Barbosa, Silvia Del Valle Alonso, Francisco L González Flecha

引用次数: 0

On the free energy of protein folding in optical tweezers experiments. 光镊实验中蛋白质折叠自由能的研究。

IF 4.9

Biophysical reviews Pub Date : 2025-04-22 eCollection Date: 2025-04-01 DOI: 10.1007/s12551-025-01310-0

Christian A M Wilson, Camila G Corrêa

{"title":"On the free energy of protein folding in optical tweezers experiments.","authors":"Christian A M Wilson, Camila G Corrêa","doi":"10.1007/s12551-025-01310-0","DOIUrl":"https://doi.org/10.1007/s12551-025-01310-0","url":null,"abstract":"Free energy is a critical parameter in understanding the equilibrium in chemical reactions. It enables us to determine the equilibrium proportion between the different species in the reaction and to predict in which direction the reaction will proceed if a change is performed in the system. Historically, to calculate this value, bulk experiments were performed where a parameter was altered at a gradual rate to change the population until a new equilibrium was established. In protein folding studies, it is common to vary the temperature or chaotropic agents in order to change the population and then to extrapolate to physiological conditions. Such experiments were time-consuming due to the necessity of ensuring equilibrium and reversibility. Techniques of single-molecule manipulation, such as optical/magnetic tweezers and atomic force microscopy, permit the direct measurement of the work performed by a protein undergoing unfolding/refolding at particular forces. Also, with the development of non-equilibrium free energy theorems (Jarzynski equality, Crooks fluctuation theorem, Bennett acceptance ratio, and overlapping method), it is possible to obtain free energy values in experiments far from equilibrium. This review compares different methodologies and their application in optical tweezers. Interestingly, in many proteins, discrepancies in free energy values obtained through different methods suggest additional complexities in the folding pathway, possibly involving intermediate states such as the molten globule. Further studies are needed to confirm their presence and significance.Supplementary information: The online version contains supplementary material available at 10.1007/s12551-025-01310-0.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"231-245"},"PeriodicalIF":4.9,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075763/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075798","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}

引用次数: 0

Unlocking the power of membrane biophysics: enhancing the study of antimicrobial peptides activity and selectivity. 释放膜生物物理学的力量：加强抗菌肽活性和选择性的研究。

IF 4.9

Biophysical reviews Pub Date : 2025-04-12 eCollection Date: 2025-04-01 DOI: 10.1007/s12551-025-01312-y

Brandt Bertrand, Carlos Munoz-Garay

{"title":"Unlocking the power of membrane biophysics: enhancing the study of antimicrobial peptides activity and selectivity.","authors":"Brandt Bertrand, Carlos Munoz-Garay","doi":"10.1007/s12551-025-01312-y","DOIUrl":"https://doi.org/10.1007/s12551-025-01312-y","url":null,"abstract":"The application of membrane-active antimicrobial peptides (AMPs) is considered to be a viable alternative to conventional antibiotics for treating infections caused by multidrug-resistant pathogenic microorganisms. In vitro and in silico biophysical approaches are indispensable for understanding the underlying molecular mechanisms of membrane-active AMPs. Lipid bilayer models are widely used to mimic and study the implication of various factors affecting these bio-active molecules, and their relationship with the physical parameters of the different membranes themselves. The quality and resemblance of these models to their target is crucial for elucidating how these AMPs work. Unfortunately, over the last few decades, no notable efforts have been made to improve or refine membrane mimetics, as it pertains to the elucidation of AMPs molecular mechanisms. In this review, we discuss the importance of improving the quality and resemblance of target membrane models, in terms of lipid composition and distribution, which ultimately directly influence physical parameters such as charge, fluidity, and thickness. In conjunction, membrane and peptide properties determine the global effect of selectivity, activity, and potency. It is therefore essential to define these interactions, and to do so, more refined lipid models are necessary. In this review, we focus on the significant advancements in promoting biomimetic membranes that closely resemble native ones, for which thorough biophysical characterization is key. This includes utilizing more complex lipid compositions that mimic various cell types. Additionally, we discuss important considerations to be taken into account when working with more complex systems.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"605-625"},"PeriodicalIF":4.9,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075066/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075905","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}

引用次数: 0

How enzyme functions evolve: genetic, structural, and kinetic perspectives. 酶的功能是如何进化的：基因、结构和动力学的观点。

IF 4.9

Biophysical reviews Pub Date : 2025-04-11 eCollection Date: 2025-04-01 DOI: 10.1007/s12551-025-01314-w

Nicolás Fuentes-Ugarte, Martin Pereira-Silva, Isaac Cortes-Rubilar, Gabriel Vallejos-Baccelliere, Victoria Guixé, Victor Castro-Fernandez

{"title":"How enzyme functions evolve: genetic, structural, and kinetic perspectives.","authors":"Nicolás Fuentes-Ugarte, Martin Pereira-Silva, Isaac Cortes-Rubilar, Gabriel Vallejos-Baccelliere, Victoria Guixé, Victor Castro-Fernandez","doi":"10.1007/s12551-025-01314-w","DOIUrl":"https://doi.org/10.1007/s12551-025-01314-w","url":null,"abstract":"Understanding the emergence or loss of enzyme functions comprises several approaches, such as genetic, structural, and kinetic studies. Promiscuous enzyme activities have been proposed as starting points for the emergence of novel enzyme functions, for example, through genetic models such as neofunctionalization and subfunctionalization. In both cases, neutral evolution would fix gene redundancy, critical in relaxing functional constraints and allowing specific mutations to drive innovation. The evolution of enzyme activities has a structural basis, with genetic mutations modifying the active site architecture, conformational dynamics, or interaction networks, which leads to the creation, enhancement, or restriction of enzyme functions where epistatic interactions are crucial. These structural changes impact the described kinetic mechanisms like ground-state stabilization (affinity), transition-state stabilization (catalysis), or a combination of both. Case studies across diverse enzyme families illustrate these principles, emphasizing the interplay between genetic, structural, and kinetic approaches. Finally, we discuss the importance of understanding evolutionary mechanisms and their impact on protein engineering and drug design for biomedical and industrial applications. However, these studies highlight that further experimental evolutionary data collection is necessary to enable the training of advanced machine learning models for use in biotechnological applications.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"467-478"},"PeriodicalIF":4.9,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075042/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075934","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}

引用次数: 0

Biological physics to uncover cell signaling. 揭示细胞信号的生物物理学。

IF 4.9

Biophysical reviews Pub Date : 2025-04-10 eCollection Date: 2025-04-01 DOI: 10.1007/s12551-025-01308-8

Silvina Ponce Dawson

引用次数: 0

Selectivity of membrane-active peptides: the role of electrostatics and other membrane biophysical properties. 膜活性肽的选择性：静电和其他膜生物物理性质的作用。

IF 4.9

Biophysical reviews Pub Date : 2025-04-10 eCollection Date: 2025-04-01 DOI: 10.1007/s12551-025-01309-7

Iván Felsztyna, Vanesa V Galassi, Natalia Wilke

{"title":"Selectivity of membrane-active peptides: the role of electrostatics and other membrane biophysical properties.","authors":"Iván Felsztyna, Vanesa V Galassi, Natalia Wilke","doi":"10.1007/s12551-025-01309-7","DOIUrl":"https://doi.org/10.1007/s12551-025-01309-7","url":null,"abstract":"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.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"591-604"},"PeriodicalIF":4.9,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075820","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}

引用次数: 0

Mechanics and disease of heart cells/cardiomyocytes explored through atomic force microscopy: present and future. 通过原子力显微镜探索心脏细胞/心肌细胞的力学和疾病：现在和未来。

IF 4.9

Biophysical reviews Pub Date : 2025-04-09 eCollection Date: 2025-04-01 DOI: 10.1007/s12551-025-01307-9

Lihuén Villarreal, Mateo Fontes-Silva, Laura Mendaro, Gerardo Romanelli, Juan C Benech

引用次数: 0

Mechanical effect of protein glycosylation on BiP-mediated post-translational translocation and folding in the endoplasmic reticulum. 蛋白质糖基化对bip介导的内质网翻译后易位和折叠的机械作用。

IF 4.9

Biophysical reviews Pub Date : 2025-04-07 eCollection Date: 2025-04-01 DOI: 10.1007/s12551-025-01313-x

Christian A M Wilson, Hilda M Alfaro-Valdés, Merve Kaplan, Cecilia D'Alessio

{"title":"Mechanical effect of protein glycosylation on BiP-mediated post-translational translocation and folding in the endoplasmic reticulum.","authors":"Christian A M Wilson, Hilda M Alfaro-Valdés, Merve Kaplan, Cecilia D'Alessio","doi":"10.1007/s12551-025-01313-x","DOIUrl":"https://doi.org/10.1007/s12551-025-01313-x","url":null,"abstract":"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.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"435-447"},"PeriodicalIF":4.9,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074954","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}

引用次数: 0

Nanotechnology meets medicine: applications of atomic force microscopy in disease. 纳米技术与医学：原子力显微镜在疾病中的应用。

IF 4.9

Biophysical reviews Pub Date : 2025-04-03 eCollection Date: 2025-04-01 DOI: 10.1007/s12551-025-01306-w

Zita Matias, Catarina S Lopes, Nuno C Santos, Filomena A Carvalho

{"title":"Nanotechnology meets medicine: applications of atomic force microscopy in disease.","authors":"Zita Matias, Catarina S Lopes, Nuno C Santos, Filomena A Carvalho","doi":"10.1007/s12551-025-01306-w","DOIUrl":"https://doi.org/10.1007/s12551-025-01306-w","url":null,"abstract":"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.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"359-384"},"PeriodicalIF":4.9,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075069/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075728","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}

引用次数: 0

Frataxin: from the sequence to the biological role. 卵黄蛋白：从序列到生物学作用。

IF 4.9

Biophysical reviews Pub Date : 2025-04-03 eCollection Date: 2025-04-01 DOI: 10.1007/s12551-025-01311-z

María Florencia Pignataro, Martín Ezequiel Noguera, María Georgina Herrera, Ernesto Andrés Roman, Javier Santos

{"title":"Frataxin: from the sequence to the biological role.","authors":"María Florencia Pignataro, Martín Ezequiel Noguera, María Georgina Herrera, Ernesto Andrés Roman, Javier Santos","doi":"10.1007/s12551-025-01311-z","DOIUrl":"https://doi.org/10.1007/s12551-025-01311-z","url":null,"abstract":"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.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"449-465"},"PeriodicalIF":4.9,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075029/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075899","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}

引用次数: 0