Biophysical journal最新文献_第3页

Molecular origins of high viscosity in concentrated solutions of monoclonal antibodies 单克隆抗体浓溶液中高粘度的分子起源

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-06-25 DOI: 10.1016/j.bpj.2025.06.024

Arjun Valiya Parambathu, David J. Rosenman, Sandeep Yadav, Abraham M. Lenhoff

{"title":"Molecular origins of high viscosity in concentrated solutions of monoclonal antibodies","authors":"Arjun Valiya Parambathu, David J. Rosenman, Sandeep Yadav, Abraham M. Lenhoff","doi":"10.1016/j.bpj.2025.06.024","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.06.024","url":null,"abstract":"Concentrated monoclonal antibody (mAb) solutions can allow subcutaneous administration of effective doses of the therapeutic, but for some mAbs this leads to anomalously high viscosities; mAb-mAb association, leading to formation of clusters or gels, is often the driver of such behavior. Statistical mechanical considerations suggest that such association is likely to be dominated by a single binding configuration. In this work we probe the possible molecular origins of this behavior using atomistic molecular simulations of a mAb known to display high viscosity at low salt concentrations. Orientational exploration identified a small number of high-affinity mAb-mAb configurations based on non-electrostatic contributions to the protein interactions, which reflect the geometric complementarity characteristic of biomolecular recognition. Consideration of electrostatic interactions, which account for most salt effects, adds several tens of <ce:italic>kT</ce:italic> of attraction to select configurations, although there are uncertainties in the electrostatic calculations using the Poisson-Boltzmann approach. The resulting overall attractive energies, greater than 40 <ce:italic>kT</ce:italic>, support the existence of a single attractive configuration strong enough to form a mAb network at high concentrations. Simulations with increased ionic strength or for small numbers of point mutations predict some but not all observed experimental trends. Independent molecular dynamics (MD) simulations for two select configurations showed partial agreement with the previous results. Overall, while the molecular origin of high viscosity is plausibly due to a single strongly bound configuration, unambiguous identification of this configuration is limited by the numerical accuracy of the underlying calculations.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"94 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144503832","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}

引用次数: 0

Multiplexed stamp-transfer AFM deposition improves resolution of protein-DNA conformational states. 多路印迹转移AFM沉积提高了蛋白质- dna构象状态的分辨率。

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-06-25 DOI: 10.1016/j.bpj.2025.06.027

Emily Lentz,Zimeng Li,Corey Davis,Dorothy Erie

{"title":"Multiplexed stamp-transfer AFM deposition improves resolution of protein-DNA conformational states.","authors":"Emily Lentz,Zimeng Li,Corey Davis,Dorothy Erie","doi":"10.1016/j.bpj.2025.06.027","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.06.027","url":null,"abstract":"Single-molecule analysis of atomic force microscopy (AFM) images is a powerful tool for characterizing the structural and conformational properties of proteins, DNA, and protein-DNA complexes, as well as nonbiological molecules, such as polymers. Since the invention of AFM in 1986, significant technical advances have been made, including faster scan speeds and automated image collection and analysis. Deposition methods, however, remain essentially unchanged. Typically, several microliters of the sample are dropped onto a mica surface (unmodified or modified), allowed to spread, rinsed with water, and dried. Although this method is generally effective, it remains a chokepoint to efficiently collecting AFM data. To alleviate this bottleneck, we invented a stamp-transfer method to deposit multiple samples simultaneously onto a mica surface for imaging. We fabricate arrays of microwells in a silicon chip, fill them with samples, and bring the silicon chip into soft contact with mica to transfer the sample. This method not only allows the simultaneous deposition of multiple different protein and DNA samples, but it also expands the buffer conditions for deposition of DNA and protein-DNA complexes onto an unmodified the mica surface into the physiological-salt range. Furthermore, our data indicate that the stamp-transfer deposition significantly improves the ability to resolve different conformational states of protein-DNA complexes from one another. Finally, this method can be readily automated and has the potential revolutionize AFM imaging both by improving resolution and making it \"high throughput\".","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"26 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144488179","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}

引用次数: 0

Molecular origins of high viscosity in concentrated solutions of monoclonal antibodies. 单克隆抗体浓溶液中高粘度的分子起源。

IF 3.2 3区生物学

Biophysical journal Pub Date : 2025-06-25 DOI: 10.1016/j.bpj.2025.06.024

Arjun Valiya Parambathu, David J Rosenman, Sandeep Yadav, Abraham M Lenhoff

{"title":"Molecular origins of high viscosity in concentrated solutions of monoclonal antibodies.","authors":"Arjun Valiya Parambathu, David J Rosenman, Sandeep Yadav, Abraham M Lenhoff","doi":"10.1016/j.bpj.2025.06.024","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.06.024","url":null,"abstract":"Concentrated monoclonal antibody (mAb) solutions can allow subcutaneous administration of effective doses of the therapeutic, but for some mAbs this leads to anomalously high viscosities; mAb-mAb association, leading to formation of clusters or gels, is often the driver of such behavior. Statistical mechanical considerations suggest that such association is likely to be dominated by a single binding configuration. In this work we probe the possible molecular origins of this behavior using atomistic molecular simulations of a mAb known to display high viscosity at low salt concentrations. Orientational exploration identified a small number of high-affinity mAb-mAb configurations based on non-electrostatic contributions to the protein interactions, which reflect the geometric complementarity characteristic of biomolecular recognition. Consideration of electrostatic interactions, which account for most salt effects, adds several tens of kT of attraction to select configurations, although there are uncertainties in the electrostatic calculations using the Poisson-Boltzmann approach. The resulting overall attractive energies, greater than 40 kT, support the existence of a single attractive configuration strong enough to form a mAb network at high concentrations. Simulations with increased ionic strength or for small numbers of point mutations predict some but not all observed experimental trends. Independent molecular dynamics (MD) simulations for two select configurations showed partial agreement with the previous results. Overall, while the molecular origin of high viscosity is plausibly due to a single strongly bound configuration, unambiguous identification of this configuration is limited by the numerical accuracy of the underlying calculations.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504810","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}

引用次数: 0

Local enrichment of cardiolipin to transient membrane undulations 心磷脂局部富集引起瞬态膜波动

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-06-25 DOI: 10.1016/j.bpj.2025.06.025

Christopher T. Lee, Kailash Venkatraman, Itay Budin, Padmini Rangamani

{"title":"Local enrichment of cardiolipin to transient membrane undulations","authors":"Christopher T. Lee, Kailash Venkatraman, Itay Budin, Padmini Rangamani","doi":"10.1016/j.bpj.2025.06.025","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.06.025","url":null,"abstract":"Organelles such as mitochondria have characteristic shapes that are critical to their function. Recent efforts have revealed that the curvature contributions of individual lipid species can be a factor in the generation of membrane shape in these organelles. Inspired by lipidomics data from yeast mitochondrial membranes, we used Martini coarse-grained molecular dynamics simulations to investigate how lipid composition facilitates membrane shaping. We found that increasing lipid saturation increases bending rigidity while reducing the monolayer spontaneous curvature. We also found that systems containing cardiolipin exhibited decreased bending rigidity and increased spontaneous curvature when compared to bilayers containing its precursor, phosphatidylglycerol. This finding contradicts some prior experimental results that suggest that bilayers containing tetraoleoyl cardiolipin have greater rigidity than dioleoyl phosphatidylcholine bilayers. To investigate this discrepancy, we analyzed our simulations for correlations between lipid localization and local curvature. We found that there are transient correlations between curved lipids such as cardiolipin (CDL) and phosphatidylethanolamine (PE) and curvature; these interactions enrich specific bilayer undulatory modes and cause bilayer softening. Furthermore, we show that curvature-localization of some lipids such as cardiolipin can influence lipids in the opposing leaflet. These observations add to the emerging evidence that lipid geometric features give rise to local interactions, which can cause membrane compositional heterogeneities. The cross-talk between composition-driven tuning of membrane properties and membrane shape has implications for membrane organization and its related functions.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"242 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144503831","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}

引用次数: 0

Voltage Gating and 4-aminopyridine Inhibition in Shaker Kv Channel Revealed by Closed-State Model. 电压门控和4-氨基吡啶在激振器Kv通道中的抑制作用

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-06-24 DOI: 10.1016/j.bpj.2025.06.029

Bernardo I Pinto-Anwandter

{"title":"Voltage Gating and 4-aminopyridine Inhibition in Shaker Kv Channel Revealed by Closed-State Model.","authors":"Bernardo I Pinto-Anwandter","doi":"10.1016/j.bpj.2025.06.029","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.06.029","url":null,"abstract":"The generation and propagation of action potentials in neurons relies on the coordinated activation of voltage-dependent sodium and potassium channels. The Kv1 (Shaker) family of potassium channels drives the repolarization phase of the action potential by opening and closing their pore, a process controlled by a voltage sensor domain. However, a molecular description of how the voltage sensor domain drives pore gating has been constrained by a lack of closed-state structures. Here, we present a structural model of the closed Shaker channel that reveals the structural basis of voltage gating. Using AlphaFold2-based conformational sampling, we identified a partially activated state of the voltage sensor which, when modeled with the full channel, produced a closed state. Based on this model we demonstrate that breaking a backbone hydrogen bond between the S4-S5 linker and S5 helices is a critical part of the activation pathway. Docking studies revealed a hydrophobic cavity in the closed pore that binds 4-aminopyridine, a potassium channel inhibitor used to enhance nerve conduction in multiple sclerosis. Our results demonstrate how the voltage sensor movement drives pore opening and provide a structural framework for developing new therapeutic agents targeting the closed state. We anticipate that the novel methods used in this work will allow the characterization of conformational dynamics in voltage-gated ion channels, enabling drug design efforts focused on state-dependent modulation of ion channels for neurological disorders treatment.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"26 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144488188","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}

引用次数: 0

A multiscale theory for mesenchymal cell migration in straight or curved channel confinement. 间充质细胞在直线或弯曲通道约束下迁移的多尺度理论。

IF 3.2 3区生物学

Biophysical journal Pub Date : 2025-06-24 DOI: 10.1016/j.bpj.2025.06.020

Wenya Shu, C Nadir Kaplan

{"title":"A multiscale theory for mesenchymal cell migration in straight or curved channel confinement.","authors":"Wenya Shu, C Nadir Kaplan","doi":"10.1016/j.bpj.2025.06.020","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.06.020","url":null,"abstract":"Mesenchymal cells navigate the extracellular matrix (ECM) in vivo by processing both its mechanical properties and confinement geometry. Here we develop a multiscale whole-cell theory to investigate cell spreading and migration in two-dimensional (2D) viscoelastic channel confinements of varying width and curvature. Our simulations show that, in straight channels, the cell migration speed depends monotonically on the substrate elastic stiffness, which is otherwise biphasic on an unconfined substrate. This is because confinement enforces directional spreading while reducing the spreading area, which results in lower intracellular viscous drag on the nucleus and a higher net traction force of polarized cells in our model. In contrast, we find that confinement curvature slows down cell migration since the friction forces between the bending cell and the confinement walls increase with curvature. We validate our model with experimental data for cell migration in straight channels spanning a wide range of the ECM stiffness as well as in curved channels. Our model illuminates the intertwined effects of substrate viscoelasticity and confinement geometry on cell spreading and migration in complex microenvironments, revealing that channel curvature can hierarchically override substrate mechanics to dominate migration regulation. The study paves the way for designing scaffolds that leverage curvature and confinement to steer controllable cell migration.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144494092","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}

引用次数: 0

Asymmetry and Heterogeneity in the Plasma Membrane. 质膜的不对称性和非均质性。

IF 3.2 3区生物学

Biophysical journal Pub Date : 2025-06-23 DOI: 10.1016/j.bpj.2025.06.026

Teppei Yamada, Wataru Shinoda

{"title":"Asymmetry and Heterogeneity in the Plasma Membrane.","authors":"Teppei Yamada, Wataru Shinoda","doi":"10.1016/j.bpj.2025.06.026","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.06.026","url":null,"abstract":"Plasma membranes (PMs) exhibit asymmetry between their two leaflets in terms of phospholipid headgroups, unsaturation, and resulting membrane properties such as packing and fluidity. Lateral heterogeneity, including the formation of lipid domains, is another crucial aspect of PMs with significant biological implications. However, the nature and even the existence of lipid domains in the two leaflets of PMs remain elusive, hindering a complete understanding of the significance of lipid asymmetry. Using coarse-grained molecular dynamics simulation of the asymmetric PM, we find that the outer leaflet lipids are highly ordered and largely uniformly distributed, whereas the inner leaflet separates into nanoscale (≈10 nm) highly ordered and more disordered domains, exhibiting highly dynamic domain fusion and fission events. This structural asymmetry is further reinforced by asymmetric lateral stress resulting from a cholesterol bias toward the outer leaflet. These findings suggest distinct functional roles for the two leaflets, modulated by asymmetric lateral stress. Additionally, comparing the phase behavior of asymmetric and fully scrambled PMs reveals a key determinant of domain size: intact PMs maintain nanoscale domains, while cell-derived giant PM vesicles, which have lost the strict lipid asymmetry, exhibit microscale domains.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144483095","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}

引用次数: 0

Microscopic Insight into HIV Fusion Peptide-Mediated Dehydration and Packing Regulation in Membranes. HIV融合肽介导的脱水和膜内包装调控的显微观察。

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-06-23 DOI: 10.1016/j.bpj.2025.06.023

Shovon Swarnakar,Anurag Chaudhury,Maximilian W A Skoda,Hirak Chakraborty,Jaydeep K Basu

{"title":"Microscopic Insight into HIV Fusion Peptide-Mediated Dehydration and Packing Regulation in Membranes.","authors":"Shovon Swarnakar,Anurag Chaudhury,Maximilian W A Skoda,Hirak Chakraborty,Jaydeep K Basu","doi":"10.1016/j.bpj.2025.06.023","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.06.023","url":null,"abstract":"Human immunodeficiency virus (HIV) infection is believed to occur through the entry of virion into mammalian cells engineered by the interaction of its fusion peptide in particular gp41 with the plasma membranes. Despite having a significant understanding of the biochemical pathways of HIV infection a viable remedy is yet to be achieved. This necessitates the evaluation of peptide-induced microscopic biophysical changes of the host membrane that support viral entry. In this report, we present the first detailed microscopic insights into the mechanisms of gp41-mediated host membrane dehydration and packing regulation, obtained through the combined use of neutron reflectivity and fluorescence microscopy, which together provide high-resolution structural information. We observe that the highest gp41 activity occurs in phase-separated membranes with the lowest compression modulus and headgroup ordering. The introduction of charged lipids coupled with phase homogenization leads to a significant reduction of gp41 mediated dehydration and packing modulation despite reduced headgroup ordering in such membranes. Interestingly maximum fusion peptide penetration occurs in the charged membranes suggesting a very subtle interplay of membrane composition and peptide penetration and localization requirements which determine the activity of HIV fusion peptide which is likely to be of great significance for their fusogenicity. We suggest that our study and its outcomes could also be relevant for other fusogenic enveloped viruses and hence could have far-reaching implications for developing remedial action not just against HIV but other similar enveloped viruses.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"36 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478788","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}

引用次数: 0

Structural mapping of patient-associated KCNMA1 gene variants 患者相关KCNMA1基因变异的结构定位

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-06-21 DOI: 10.1016/j.bpj.2025.06.012

Hans J. Moldenhauer, Kelly Tammen, Andrea L. Meredith

引用次数: 0

Recent Advances in Machine Learning and Coarse-Grained Potentials for Biomolecular Simulations and Their Applications 生物分子模拟中机器学习和粗粒度电位的最新进展及其应用

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-06-20 DOI: 10.1016/j.bpj.2025.06.019

Adolfo B. Poma, Alejandra Hinostroza Caldas, Luis F. Cofas-Vargas, Michael S. Jones, Andrew L. Ferguson, Leonardo Medrano Sandonas

{"title":"Recent Advances in Machine Learning and Coarse-Grained Potentials for Biomolecular Simulations and Their Applications","authors":"Adolfo B. Poma, Alejandra Hinostroza Caldas, Luis F. Cofas-Vargas, Michael S. Jones, Andrew L. Ferguson, Leonardo Medrano Sandonas","doi":"10.1016/j.bpj.2025.06.019","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.06.019","url":null,"abstract":"Biomolecular simulations played a crucial role in advancing our understanding of the complex dynamics in biological systems with applications ranging from drug discovery to the molecular characterization of virus-host interactions. Despite their success, biomolecular simulations face inherent challenges due to the multiscale nature of biological processes, which involve intricate interactions across a wide range of length- and timescales. All-atom (AA) molecular dynamics provides detailed insights at atomistic resolution, yet it remains limited by computational constraints, capturing only short timescales and small conformational changes. In contrast, coarse-grained (CG) models extend simulations to biologically relevant time and length scales by reducing molecular complexity. However, CG models sacrifice atomic-level accuracy, making the parameterization of reliable and transferable potentials a persistent challenge. This review discusses recent advancements in machine learning (ML)-driven biomolecular simulations, including the development of ML potentials with quantum-mechanical accuracy, ML-assisted backmapping strategies from CG to AA resolutions, and widely used CG potentials. By integrating ML and CG approaches, researchers can enhance simulation accuracy while extending time and length scales, overcoming key limitations in the study of biomolecular systems.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"14 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144335449","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}

引用次数: 0