Biophysical journal最新文献

{"title":"Synergistic effect of PIP2 and PIP3 on membrane-induced phase separation of integrin complexes.","authors":"Chiao-Peng Hsu,Arsenii Hordeichyk,Jonas Aretz,Reinhard Fässler,Andreas R Bausch","doi":"10.1016/j.bpj.2025.04.011","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.04.011","url":null,"abstract":"The assembly of integrin adhesion complexes at the inner leaflet of the plasma membrane regulates cell adhesion to the extracellular matrix. The multivalent protein interactions within the complexes and with the cell membrane display characteristics of membrane-associated biomolecular condensates driven by liquid-liquid phase separation. The composition of lipids and the distribution of the cell membrane are crucial for forming integrin adhesion complexes. Here, we report that PIP2 and PIP3in the model membrane synergistically regulate the formation of membrane-induced integrin adhesion condensates, which consist of β1 tails, kindlin, talin, paxillin, and FAK. We show that the preferential bindings of kindlin to PIP3 and talin to PIP2 enhance their recruitment to the membrane, which in turn increases the probability of membrane-associated phase separation. Our results indicate that modulating the intricate balance of membrane composition is a strategy to localize integrin adhesion complexes and optimize their density on lipid membranes.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"6 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143841061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decoding SP-D and glycan binding mechanisms using a novel computational workflow.","authors":"Deng Li,Mona S Minkara","doi":"10.1016/j.bpj.2025.04.007","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.04.007","url":null,"abstract":"Surfactant protein D (SP-D) plays an important role in the innate immune system by recognizing and binding to glycans on the surface of pathogens, facilitating their clearance. Despite its importance, the detailed binding mechanisms between SP-D and various pathogenic surface glycans remain elusive due to the limited experimentally solved protein-glycan crystal structures. To address this, we developed and validated a computational workflow that integrates Induced Fit Docking, MMGBSA binding free energy calculations, and Binding Pose MetaDynamics simulations to accurately predict stable SP-D-glycan complex structure and binding mechanisms. By utilizing this workflow, we identified primary and secondary binding sites in SP-D critical for glycan recognition and uncovered a calcium chelation mode correlating with high binding affinity. To demonstrate the workflow's utility, we investigated the binding of pilin glycan from Pseudomonas aeruginosa (P. aeruginosa) to surfactant protein A (SP-A), SP-D, and mannose-binding lectin (MBL). We found that SP-D exhibited the most stable binding with pilin glycan versus SP-A and MBL, highlighting its potential role in the innate immune response against P. aeruginosa infection. These findings deepen our understanding of SP-D's role in the innate immune response and provide a basis for engineering SP-D variants for therapeutic applications. Moreover, our computational workflow can serve as a powerful tool for exploring protein-ligand interactions in diverse biologically significant systems. It provides a robust framework to guide experimental studies and accelerates the development of novel therapeutics, effectively bridging the gap between computational insights and practical applications.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"5 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143822783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modeling Platelet P2Y_1/12 Pathway to Integrin Activation.","authors":"Keshav B Patel, Wolfgang Bergmeier, Aaron L Fogelson","doi":"10.1016/j.bpj.2025.04.004","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.04.004","url":null,"abstract":"<p><p>Through experimental studies, many details of the pathway of integrin αIIbβ3 activation by ADP during the platelet aggregation process have been mapped out. ADP binds to two separate G protein coupled receptors on platelet surfaces, leading to alterations in the regulation of the small GTPase RAP1. We seek to (1) gain insights into the relative contributions of both pathways to RAP1-mediated integrin activation and to (2) predict wildtype and mutated cell behavior in response to a continuous range of external agonist concentrations. To this end, we develop a dynamical systems model detailing the action of each protein in the two pathways up to the regulation of RAP1. We perform a parameter estimation using flow cytometry data to determine a number of unknown rate constants. We then validate with already published data; in particular, the model confirmed the effect of impaired P2Y₁ receptor desensitization or reduced RASA3 expression on RAP1 activation. We then predict the effect of protein expression levels on integrin activation and show that components of the P2Y₁₂ pathway are critical to the regulation of integrin. This model aids in our understanding of interindividual variability in platelet response to ADP and therapeutic P2Y₁₂ inhibition. It also provides a more detailed view of platelet activation in the ongoing mathematical study of platelet aggregation.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of curvature on growing films of microorganisms.","authors":"Yuta Kuroda, Takeshi Kawasaki, Andreas M Menzel","doi":"10.1016/j.bpj.2025.04.003","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.04.003","url":null,"abstract":"<p><p>To provide insight into the basic properties of emerging structures when bacteria or other microorganisms conquer surfaces, it is crucial to analyze their growth behavior during the formation of thin films. In this regard, many theoretical studies focus on the behavior of elongating straight objects. They repel each other through volume exclusion and divide into two halves when reaching a certain threshold length. However, in reality, hardly any object of a certain elongation is perfectly straight. Therefore, we here study the consequences of the curvature of individuals on the growth of colonies and thin active films. This individual curvature, so far hardly considered, turns out to qualitatively affect the overall growth behavior of the colony. Particularly, strings of stacked curved cells emerge that show branched structures, while the size of orientationally ordered domains in the colony is significantly decreased. Furthermore, we identify emergent spatio-orientational coupling that is not observed in colonies of straight cells. Our results are important for a fundamental understanding of the interaction and spreading of microorganisms on surfaces, with implications for medical applications and bioengineering.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heterogenous condensates of transcription factors in embryonic stem cells: Molecular simulations.","authors":"Azuki Mizutani, Cheng Tan, Yuji Sugita, Shoji Takada","doi":"10.1016/j.bpj.2025.04.001","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.04.001","url":null,"abstract":"<p><p>Biomolecular condensates formed via liquid-liquid phase separation are ubiquitous in cells, especially in the nucleus. While condensates containing one or two kinds of biomolecules have been relatively well characterized, those with more heterogenous biomolecular components and interactions between biomolecules inside are largely unknown. This study used residue-resolution molecular dynamics (MD) simulations to investigate heterogeneous protein assemblies that include four master transcription factors in mammalian embryonic stem cells: Oct4, Sox2, Klf4, and Nanog. MD simulations of the mixture systems showed highly heterogeneous and dynamic behaviors; protein condensates mainly contain Sox2, Klf4, and Nanog, while most Oct4 are dissolved into the dilute phase. The condensate forms loosely interacting clusters where Klf4 is the most abundant, suggesting that Klf4 serves as a scaffold of the condensate, and Sox2 and Nanog are bound to Klf4 for stabilizing the condensate. Oct4 is moderately recruited to the condensate, serving as a client mainly via its interaction with Sox2. This study highlights the importance of inter-molecular interaction between different transcription factors on the condensate formations with heterogeneous biomolecular components.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biophysical characterization of anion channels in Mitochondrion-Endoplasmic-Reticulum Contact sites (MERCs).","authors":"Shridhar Kiran Sanghvi, Denis Gabrilovich, Satish K Raut, Ajay Gopalan, Aryan Singh, Harmeet Rireika Bhachu, Mayukha Dyta, Veronica Loyo-Celis, Jenna Thuma, Devasena Ponnalagu, Jonathan Davis, Shubha Gururaja Rao, Harpreet Singh","doi":"10.1016/j.bpj.2025.04.002","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.04.002","url":null,"abstract":"<p><p>The mitochondrion-endoplasmic reticulum (ER) contact sites (MERCs, also known as mitochondrial-associated membranes (MAMs)) are specialized regions of the endoplasmic reticulum that are in close proximity to the mitochondrion. These organelle structures play essential roles in a variety of processes, such as calcium signaling, lipid metabolism, renin-angiotensin-aldosterone system control, the unfolded protein response, and autophagy. MERCs are known to actively participate in ion transport between the ER and mitochondria. Although active calcium channels in MERCs have been detected, limited studies have been carried out to identify or characterize functional anion channels. Here, we tested whether functional anion channels are present in MERCs. We isolated MERCs from mouse organs (heart and brain) and reconstituted them in planar bilayers. The single-channel properties were recorded in the presence of various anion channel blockers or antagonists (IAA-94, DIDS, A9C, and NPPB). We corroborated the presence of anion channels targeted by these drugs using immunoblotting and immunocytochemistry. Biochemical analysis and immunocytochemistry corroborate that CLIC4, CLIC3, and VDACs are present in MERCs. Our results indicate that anion channels are active in MERCs, which could play a pertinent role in intracellular organelle communication.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Several common methods of making vesicles (except an emulsion method) capture intended lipid ratios.","authors":"Heidi M J Weakly, Kent J Wilson, Gunnar J Goetz, Emily L Pruitt, Amy Li, Libin Xu, Sarah L Keller","doi":"10.1016/j.bpj.2025.03.029","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.029","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143787689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromatin unfolding via loops can drive clustered transposon insertion.","authors":"Roshan Prizak, Aaron Gadzekpo, Lennart Hilbert","doi":"10.1016/j.bpj.2025.03.038","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.038","url":null,"abstract":"<p><p>Transposons, DNA sequences capable of relocating within the genome, make up a significant portion of eukaryotic genomes and are often found in clusters. Within the cell nucleus, the genome is organized into chromatin, a structure with varying degrees of compaction due to three-dimensional folding. Transposon insertion or activation can lead to chromatin decompaction, increasing accessibility and potentially facilitating further nearby insertions. This positive feedback between chromatin unfolding and transposon insertion may result in transposon clustering. Here, we combine bioinformatics with polymer modeling to explore possible mechanisms and conditions that promote clustered transposon insertions. Our analysis of human cell line genomic repeat data reveals extensive clustering of heterochromatic LINE-1 elements and euchromatic Alu elements. For Alu elements, this clustering correlates with increased chromatin accessibility. Both Alu and LINE-1 deviate in their sequence-inherent flexibility from the overall genome, with above-average flexibility for Alu and below-average flexibility for most LINE-1 sequences. Flexibility was highest in young transposons, so that young Alu and LINE-1 exceed overall genome flexibility. We developed an according polymer model of transposon insertion, consisting of a self-attracting chromatin domain. Transposon insertions locally disrupt self-attraction, leading to unfolding of the domain as more transposons are inserted. In simulations where transposons are inserted adjacent to existing ones, we observed gradual unfolding through loop extensions from a folded core. Including transposases as explicit particles, our model shows that adjacent transposon insertion occurs when densely packed chromatin excludes transposases or when insertion rates exceed the thermal equilibration rate of polymer configurations. We conclude that (i) dense chromatin packing that hinders transposase access as well as (ii) a local loss of compaction upon transposon insertion favor clustered transposon insertion via loop formation. This biophysical mechanism of clustered insertion site preference would act in combination with selective pressures shaping transposon distribution over evolutionary time scales.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacteriorhodopsin proton-pumping mechanism: successes and challenges in computational approaches.","authors":"Ana-Nicoleta Bondar, Jeremy C Smith","doi":"10.1016/j.bpj.2025.03.035","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.035","url":null,"abstract":"<p><p>Bacteriorhodopsin (bR) is perhaps the best-studied proton pump. Over about four decades, research on this fascinating photocyclic light-driven protein inspired the development of key experimental and computational methodologies that are now widely used in membrane protein studies. We review here failures and successes in computational approaches that have been applied to study the bR proton-transfer steps. Conflict between experimental results pertaining to the proton transfer mechanisms in the early photocycle intermediates was resolved by detailed quantum mechanical/molecular mechanical (QM/MM) computation, the results of which were confirmed more than a decade later. Key to this approach was the realization that, to understand how the pump works and achieves directional transfer of protons, the individual reaction steps-proton transfer and reorganization of the internal hydrogen-bond network- needed to be considered within the context of the energy landscape of the complete reaction cycle.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143787684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In Silico Design of Foldable Lasso Peptides.","authors":"John D M Nguyen, Gabriel C A da Hora, Marcus C Mifflin, Andrew G Roberts, Jessica M J Swanson","doi":"10.1016/j.bpj.2025.03.036","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.036","url":null,"abstract":"<p><p>Lasso peptides are a unique class of natural products with distinctively threaded structures, conferring exceptional stability against thermal and proteolytic degradation. Despite their promising biotechnological and pharmaceutical applications, reported attempts to prepare them by chemical synthesis result in forming the nonthreaded branched-cyclic isomer, rather than the desired lassoed structure. This is likely due to the entropic challenge of folding a short, threaded motif prior to chemically mediated cyclization. Accordingly, this study aims to better understand and enhance the relative stability of pre-lasso conformations-the essential precursor to lasso peptide formation-through sequence optimization, chemical modification, and disulfide incorporation. Using Rosetta fixed backbone design, optimal sequences for several class II lasso peptides are identified. Enhanced sampling with well-tempered metadynamics confirmed that designed sequences derived from the lasso structures of rubrivinodin and microcin J25 exhibit a notable improvement in pre-lasso stability relative to the competing nonthreaded conformations. Chemical modifications to the isopeptide bond-forming residues of microcin J25 further increase the probability of pre-lasso formation, highlighting the beneficial role of non-canonical amino acid residues. Counterintuitively, the introduction of a disulfide cross-link decreased pre-lasso stability. Although cross-linking inherently constrains the peptide structure, decreasing the entropic dominance of unfolded phase space, it hinders the requisite wrapping of the N-terminal end around the tail to adopt the pre-lasso conformation. However, combining chemical modifications with the disulfide cross-link results in further pre-lasso stabilization, indicating that the ring modifications counteract the constraints and provide a cooperative benefit with cross-linking. These findings lay the groundwork for further design efforts to enable synthetic access to the lasso peptide scaffold.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}