Biophysical journal最新文献

{"title":"Spatial Charge-Hydrophobicity Configuration Modulates Cationic Peptide Transport in Cartilage.","authors":"Bill Hakim,Timothy L Boyer,Srirupa Chakraborty,Ambika G Bajpayee","doi":"10.1016/j.bpj.2025.09.023","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.09.023","url":null,"abstract":"Charge-based delivery systems offer a promising approach for targeting dense, negatively charged tissues such as cartilage, which presents a significant transport barrier due to its high fixed charge density (FCD) from aggrecan glycosaminoglycans (GAGs). Cationic nano-carriers, including peptide-based systems, can overcome these barriers by leveraging electrostatic interactions to enhance intra-tissue penetration. However, the effectiveness of these carriers depends not only on their net positive charge, which drives Donnan partitioning, but also on the precise spatial arrangement of cationic and hydrophobic residues, which influences transport, binding, and retention. In this study, we investigated the impact of spatial charge distribution and hydrophobicity on the intra-cartilage transport and retention of arginine-rich cationic peptide carriers (CPCs) with a net charge of +14, optimized for effective cartilage targeting. Using both experimental methods and molecular modeling, we examined the transport properties of CPCs with varied charge and hydrophobic cluster arrangements in healthy and degenerated cartilage with different FCDs. Our findings reveal that peptides with a higher degree of clustered cationic or hydrophobic residues exhibit greater intra-cartilage diffusivity due to weaker binding interactions with aggrecan GAGs and a more flexible structural conformation that incurs an entropic penalty. However, while hydrophobic residues can enhance intra-tissue retention, particularly in degenerated tissues, they also promote competitive binding within synovial fluid (SF), emphasizing the need for hydrophilic designs. Overall, our results indicate that evenly distributed cationic residues and minimal hydrophobicity yield the most effective carriers for deep, long-term tissue penetration, providing a framework for the rational design of tissue-targeting cationic peptide carriers. The design principles established in this work can be broadly applied to the rational development of cationic carriers for targeted drug delivery in a wide range of negatively charged tissues.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"105 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145083402","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":"Markovian state models uncover casein kinase 1 dynamics that govern circadian period.","authors":"Clarisse Gravina Ricci, Jonathan M Philpott, Megan R Torgrimson, Alfred M Freeberg, Rajesh Narasimamurthy, Emilia Pécora de Barros, Rommie Amaro, David M Virshup, J Andrew McCammon, Carrie L Partch","doi":"10.1016/j.bpj.2025.09.022","DOIUrl":"10.1016/j.bpj.2025.09.022","url":null,"abstract":"<p><p>Circadian rhythms in mammals are tightly regulated through phosphorylation of period (PER) proteins by casein kinase 1 (CK1, subtypes δ and ε). CK1 acts on at least two different regions of PER with opposing effects: phosphorylation of phosphodegron regions leads to PER degradation, whereas phosphorylation of the familial advanced sleep phase (FASP) region leads to PER stabilization. To investigate how substrate selectivity is encoded by the conformational dynamics of CK1, we performed a large set of independent molecular dynamics simulations of wild-type CK1 and the tau mutant (R178C) that biases kinase activity toward a phosphodegron. We used Markovian state models to integrate the simulations into a single model of the conformational landscape of CK1 and used Gaussian accelerated molecular dynamics to build the first molecular model of CK1 and the unphosphorylated FASP motif. These findings were biochemically validated using in vitro kinase assays and provide a mechanistic view of CK1, establishing how the activation loop acts as a key molecular switch to control substrate selectivity. We show that the wild-type CK1 prefers a \"loop down\" conformation that binds FASP, whereas the tau mutant favors an alternative conformation of the activation loop and significantly accelerates the dynamics of CK1. This reshapes the binding cleft in a way that impairs FASP binding and would ultimately lead to PER destabilization. Finally, we identified a potential binding pocket that could be targeted to influence the conformational state of this molecular switch and lead to predictable changes in circadian period. Our integrated approach offers a detailed model of CK1's conformational landscape and its relevance to normal, mutant, and druggable circadian timekeeping.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145085076","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":"Membrane protein hydration bridges polymer physics and biology.","authors":"C Swathi K Menon,Thomas Huber,Lauren E Thaller,Andrey V Struts,Evelyn W Cheng,Zachary T Bachler,Suchithranga M D C Perera,Thomas P Sakmar,Michael F Brown","doi":"10.1016/j.bpj.2025.09.020","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.09.020","url":null,"abstract":"Understanding the role of water in membrane protein structure and function is crucial for elucidating the mechanisms that govern cellular processes. Recent experiments with the G-protein-coupled receptor (GPCR) archetype rhodopsin have shed light on polymer osmotic effects as an important metric for studying hydration in membrane protein activation. Still, to gain mechanistic insights into the multifaceted problem of membrane protein hydration involving lipids, membranes, and polymers, one needs information at atomistic resolution. Recent advances in molecular dynamics simulations have made capturing such information possible. Here we review membrane protein hydration as a multidisciplinary research topic at the intersection of polymer physics and biology through a computational lens using rhodopsin as an example. Recent advances and challenges in spectroscopic and structural approaches to study hydration in proteins are discussed generally, and for membrane proteins specifically. We explore the synergy between polymer physical chemistry and membrane protein hydration by reviewing the contributions of lattice models, polymer osmolytes, and crowding to motivate the need for computational methods in studying membrane protein hydration. Finally, we discuss recent advances in understanding hydration in membrane proteins, using rhodopsin as an example, through hybrid Monte Carlo/molecular dynamics simulations.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"40 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145083403","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":"PIP2 regulation of TRPV4 channels: Binding sites and dynamic coupling.","authors":"Jian Huang, Jianhan Chen","doi":"10.1016/j.bpj.2025.08.006","DOIUrl":"10.1016/j.bpj.2025.08.006","url":null,"abstract":"<p><p>Transient Receptor Potential subfamily V4 (TRPV4) is a nonselective cation channel that plays important roles in thermo-sensing, osmoregulation, nociception, and bone homeostasis. The activities of TRV4 channels are known to be regulated by phosphatidylinositol 4,5-bisphosphate (PIP2), even though its molecular basis remains poorly understood at present. Existing studies reveal great uncertainty or even controversy on the binding sites as well as functional effects of PIP2 on TRPV4. Analysis of available cryo-EM structures suggests that the previously proposed sites on the N-terminal domain and the ankyrin repeat domain are too distal from the membrane interface and thus unlikely to be the primary sites for PIP2 regulation. Instead, we have identified two possible PIP2 binding sites near the cytosolic membrane interface using structural analysis and molecular docking. Atomistic simulations and free energy analysis reveal that these two sites belong to a single broad binding groove, where PIP2 binding is dynamic and can sample multiple configurations of interactions with positively charged side chains within the groove. These local free energy minima are separated by small free energy barriers and offer ∼4 kcal/mol stability with respect to the membrane bulk. Furthermore, dynamic network analysis suggests that PIP2 binding in the predicted groove can modulate the dynamic coupling between various domains of TRPV4, potentially priming the channel for responding to various stimuli. Together, these results provide important new insights on the possible molecular basis of PIP2 binding and regulation of TRPV4 activities.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"3037-3048"},"PeriodicalIF":3.1,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12413238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144798075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inferring diffusion, reaction, and exchange parameters from imperfect FRAP.","authors":"Enrico Lorenzetti, Celia Municio-Diaz, Nicolas Minc, Arezki Boudaoud, Antoine Fruleux","doi":"10.1016/j.bpj.2025.07.036","DOIUrl":"10.1016/j.bpj.2025.07.036","url":null,"abstract":"<p><p>Fluorescence recovery after photobleaching (FRAP) is broadly used to investigate the dynamics of molecules in cells and tissues, notably to quantify diffusion coefficients. FRAP is based on the spatiotemporal imaging of fluorescent molecules after an initial bleaching of fluorescence in a region of the sample. Although a large number of methods have been developed to infer kinetic parameters from experiments, it is still a challenge to fully characterize molecular dynamics from noisy experiments in which diffusion is coupled to other molecular processes or in which the initial bleaching profile is not perfectly controlled. To address this challenge, we have developed HiFRAP to quantify the reaction- (or exchange-) diffusion kinetic parameters from FRAP under imperfect experimental conditions. HiFRAP is based on a low-rank approximation of a kernel related to the model Green's function and is implemented as an ImageJ/Python macro for (potentially curved) one-dimensional systems and for two-dimensional systems. To the best of our knowledge, HiFRAP offers features that have not been combined together: making no assumption on the initial bleaching profile, which does not need to be known; accounting for the limitation of the optical setup by diffraction; inferring several kinetic parameters from a single experiment; providing errors on parameter estimation; and testing model goodness. In the future, our approach could be applied to other dynamical processes described by linear partial differential equations, which could be useful beyond FRAP, in experiments where the concentration fields are monitored over space and time.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"2941-2960"},"PeriodicalIF":3.1,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144788176","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":"Ciliary wavelength has its limits.","authors":"Louis G Woodhams","doi":"10.1016/j.bpj.2025.08.015","DOIUrl":"10.1016/j.bpj.2025.08.015","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"2929-2930"},"PeriodicalIF":3.1,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144881985","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":"Combinatorial sample- and back-focal-plane imaging. Pt. I: Instrument and acquisition parameters affecting BFP images and their analysis.","authors":"Omer Shavit, Hervé Suaudeau, Carine Julien, Hodaya Klimovsky, Natalia Mañas-Chavernas, Adi Salomon, Martin Oheim","doi":"10.1016/j.bpj.2025.08.009","DOIUrl":"10.1016/j.bpj.2025.08.009","url":null,"abstract":"<p><p>The back-focal plane (BFP) of a high-numerical aperture objective contains the fluorophore radiation pattern, which encodes information about the axial fluorophore position, molecular orientation and the local refractive index of the embedding medium. BFP image acquisition and analysis are common to conoscopy, k-space imaging, supercritical-angle fluorescence, and single-molecule detection, but they are rarely being used in biological fluorescence. This work addresses a critical gap in quantitative microscopy by enabling reliable, real-time BFP imaging under low-light conditions and/or short exposure times, typical of biological experiments. By systematically analyzing how key parameters-such as Bertrand lens position, defocus, pixel size, and binning-affect BFP image quality and supercritical-angle fluorescence/undercritical-angle fluorescence ratios, we provide a robust framework for accurate axial fluorophore localization and near-membrane refractive index measurements. The described hardware and software integration allows for multidimensional image series and online quality control, reducing experimental error and enhancing reproducibility. Our contributions lay the foundation for standardized BFP imaging across laboratories, expanding its application to dynamic biological systems, and opening the door to machine-learning-based analysis pipelines. Ultimately, this work transforms BFP imaging from an expert-dependent technique into a reproducible and scalable tool for surface-sensitive fluorescence microscopy.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"3075-3091"},"PeriodicalIF":3.1,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833838","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":"Geometry effects on protein mobility in a synapse.","authors":"Simon Dannenberg, Sofiia Reshetniak, Sarah Mohammadinejad, Silvio O Rizzoli, Stefan Klumpp","doi":"10.1016/j.bpj.2025.08.007","DOIUrl":"10.1016/j.bpj.2025.08.007","url":null,"abstract":"<p><p>It is generally assumed that synaptic function requires a tight regulation of the mobility and localization of synaptic proteins. Evidence for this hypothesis has been difficult to gather. Protein mobility can be measured via fluorescence recovery after photobleaching (FRAP), but the interpretation of the results remains challenging. In this study, we perform in silico FRAP experiments to study the effects of the synaptic geometry and/or protein binding to synaptic vesicles on protein mobility. We matched simulations with published FRAP data for 40 different synaptic proteins, to obtain diffusion coefficients, vesicle-binding rates, and binding times. Importantly, we identify two mechanisms that govern the obtained recovery times: redistribution of material inside the synaptic bouton and inflow through the axon. We show that their dissection is crucial for the correct interpretation of FRAP experiments, especially for proteins binding to synaptic vesicles.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"3049-3059"},"PeriodicalIF":3.1,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144811675","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":"Single-cell memory matters in collective migration.","authors":"Ruihan Hou,Jinglei Hu","doi":"10.1016/j.bpj.2025.09.017","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.09.017","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"9 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145071784","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":"Annotating the x-ray diffraction pattern of vertebrate striated muscle.","authors":"Natalia A Koubassova, Debabrata Dutta, Weikang Ma, Andrey K Tsaturyan, Thomas Irving, Raúl Padrón, Roger Craig","doi":"10.1016/j.bpj.2025.09.019","DOIUrl":"10.1016/j.bpj.2025.09.019","url":null,"abstract":"<p><p>Low-angle x-ray diffraction is a powerful technique for analyzing the molecular structure of the myofilaments of striated muscle in situ. It has contributed greatly to our understanding of the relaxed, 430-Å repeating organization of myosin heads in thick filaments in skeletal and cardiac muscle. Using x-ray diffraction, changes in filament structure can be detected on the angstrom length scale and millisecond timescale, leading to models that are the foundation of our understanding of the structural basis of contraction. As with all x-ray fiber diffraction studies, interpretation requires modeling, which has previously been based on low-resolution knowledge of thick filament structure and is complicated by the contributions of multiple filament components to most x-ray reflections. Here, we use an atomic model of the human cardiac thick filament C-zone, derived from cryo-EM in the presence of the myosin inhibitor, mavacamten, to compute objectively the contributions of myosin heads, tails, titin, and cMyBP-C to the diffraction pattern, by including/excluding these components in the calculations. Our results support some previous interpretations but contradict others. We confirm that the myosin heads are responsible for most of the intensity on the myosin layer lines, including the M3 meridional. Contrary to expectation, we find that myosin tails contribute little to the pattern, including the M6 meridional; this reflection arises mainly from heads and other components. The M11 layer line (39-Å spacing) arises mostly from the curved and kinked structure of titin, which allows 11 ∼42-Å-long domains to fit into the 430-Å repeat. The M11 spacing can be used as a measure of strain in the myosin filament backbone as there is negligible head contribution. The computed layer lines account well for the experimentally determined pattern. These insights should aid future understanding of the x-ray pattern of intact muscle in different conditions such as contraction and drug treatment.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145069064","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}