Biophysical journal最新文献

{"title":"Core physical principles of allostery","authors":"Eric Rouviere,Olivier Rivoire,Rama Ranganathan","doi":"10.1016/j.bpj.2026.09.031","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.09.031","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"23 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149050297","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":"Recovering membrane interaction kinetics of single molecules from 3D tracking data.","authors":"Erik Lundin, Ivan L Volkov, Magnus Johansson","doi":"10.1016/j.bpj.2026.07.029","DOIUrl":"10.1016/j.bpj.2026.07.029","url":null,"abstract":"<p><p>Interactions between cytosolic biomolecules and the bacterial inner membrane are fundamental to many cellular processes, yet directly measuring their binding kinetics in living cells remains challenging. Conventional 2D single-molecule tracking analyses can be insufficient, particularly when membrane association does not markedly alter the diffusion rate. Here, we present a method to recover membrane interaction kinetics from 3D single-molecule trajectories in rod-shaped bacteria. Using simulated 3D tracking data, we identify membrane-associated motion by quantifying how well short trajectory segments follow the circular curvature of the cell membrane. The resulting measure is further analyzed using a hidden Markov modeling framework, enabling robust discrimination between cytosolic and membrane-bound states and capturing the dynamics of state transitions without requiring diffusion-rate changes or direct colocalization with membrane markers. This work establishes a general framework for extracting membrane interaction kinetics from 3D single-molecule tracking data in live bacteria and highlights the value of realistic microscopy simulations for quantitative interpretation and systematic bias assessment.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"4839-4850"},"PeriodicalIF":3.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148683316","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":"Spatiotemporal 4D Whole-cell Modeling of a Minimal Autotroph Reveals Central Carbon Metabolism Regulated Locally by Protein Megacomplexes via Post-translational Modifications under Light Disturbance","authors":"Connah G.M. Johnson,Aaron Chan,Jordan Rozum,August George,Amar D. Parvate,Pavlo Bohutskyi,Doo Nam Kim,Song Feng,Zachary Johnson,Natalie Sadler,Marci Garcia,Xiaolu Li,Jesse Trejo,Ruonan Wu,William Sineath,Lindsey N. Anderson,James E. Evans,Angad P. Mehta,Wei-Jun Qian,Zaida Luthey-Schulten,Margaret S. Cheung","doi":"10.1016/j.bpj.2026.08.020","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.08.020","url":null,"abstract":"Photosynthetic microorganisms rely on multiple central-carbon-metabolism pathways to adapt to fluctuating light and energy availability across diel cycles. Mechanistic insight into the regulatory dynamics of this adaptation requires integrating processes that operate across disparate timescales, from rapid redox-dependent post-translational modifications (PTMs) to slower changes in protein expression and metabolic pathway usage. Here, we develop a whole-cell four-dimensional (3D + time) model of the marine cyanobacterium Prochlorococcus marinus MED4 that explicitly represents the spatial, subcellular organization of key carbon fixation enzymes and genetic information processes coupled to a non-spatial genome-scale metabolic model (GSMM). We combine perturbative, time-resolved multi-omics measurements and cryo-ET derived 3D segmented volumes as constraints for this dynamic 4D framework. The integration of experiments and modeling across defined light regimes enables quantitative validation of system-level responses and forecasting under distinct light disturbances.\u0000We test the hypothesis that light-dependent redox PTMs regulate carbon fixation by controlling the structural assembly of a protein megacomplex, the “dark complex,” at a conserved regulatory node of the Calvin–Benson cycle (CBC) in cyanobacteria. Our model shows that subcellular spatial organization buffers rapid light-induced changes in thylakoid reaction rates, which are followed by redox-PTM-mediated sequestration or release of CBC enzymes in the dark complex, ultimately impacting carbon fixation dynamics within carboxysomes. Comparison with an equivalently parameterized well-mixed stochastic model demonstrates the importance of spatial heterogeneity in understanding phenotypic robustness. Spatiotemporal sequestration creates a timing hierarchy spanning seconds to hours and noise-buffering behavior that cannot be recovered from well-mixed phenomenological models or purely time-resolved descriptions. Constrained by spatial heterogeneity, local enzyme stoichiometry and diffusion-limited assembly/disassembly determine effective stochastically varying control kinetics.\u0000Diffusion-driven fluctuations amplify transcription of highly expressed genes, whereas PTM-dependent regulation on enzyme stoichiometry maintains perturbation-driven phenotypic outcomes. 4D whole cell modeling with perturbation-based multi-modal experiments unlocks the ability to probe adaptive, spatiotemporally resolved mechanisms in photosynthetic machinery and light-dependent central carbon metabolism. The outcome of this work addresses a critical gap in genotype-to-phenotype inference and expands modeling and design capabilities for understudied or genetically intractable autotrophs such as P. marinus MED4.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"13 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148821556","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":"Constant-pH molecular dynamics simulations of closed and open states of a proton-gated ion channel","authors":"Anton Jansen,Paul Bauer,Rebecca J. Howard,Berk Hess,Erik Lindahl","doi":"10.1016/j.bpj.2026.08.019","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.08.019","url":null,"abstract":"Although traditional molecular dynamics simulations successfully capture a variety of different molecular interactions, the protonation states of titratable residues are kept static. A recent constant-pH molecular dynamics implementation in the GROMACS package allows pH effects to be captured dynamically, and promises to provide both the accuracy and computational performance required for studying pH-mediated conformational dynamics in large, complex systems containing hundreds of titratable residues. Here, we demonstrate the applicability of this constant-pH implementation by simulating the proton-gated ion channel GLIC at resting and activating pH, starting from closed and open structures. Our simulations identify residues E26 and E35 as especially pH-sensitive and reveal state-dependent pKa shifts at multiple residues, as well as side chain and domain rearrangements in line with the early stages of gating. Our results are consistent with several previous experimental findings, demonstrating the applicability of constant-pH simulations to elucidate pH-mediated activation mechanisms in multidomain membrane proteins, likely extensible to other complex systems.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"36 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148806058","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":"The transmembrane domain regulates the kinetics of the SARS-CoV-2 spike conformational transition","authors":"Avijeet Kulshrestha,Arkadeep Banerjee,Sahil Lall,Shachi Gosavi","doi":"10.1016/j.bpj.2026.08.014","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.08.014","url":null,"abstract":"The homotrimeric SARS-CoV-2 spike glycoprotein comprises two subunits: S1, which recognizes host-receptors through its receptor-binding domains (RBDs), and S2, anchored to the viral membrane through its transmembrane domain (TMD), which facilitates the fusion of the viral envelope with the host cell membrane. Upon host-receptor engagement and proteolytic activation, S1 dissociates and triggers a large conformational transition in S2, involving structural rearrangements in the S2 ectomembrane-domains and the TMD. While studies have focused on the ectomembrane-domain dynamics, the TMD has typically been modeled as being in a trimeric state. Here, we use molecular dynamics simulations of a coarse-grained structure-based model (SBM) with an implicit membrane to investigate the role of TMD dynamics in modulating S2 conformational conversion. We first recapitulate previous results from an all-atom SBM with a trimeric TMD and re-emphasize that the extended pre-hairpin intermediate state of S2, which brings the two membranes into apposition, is a byproduct of the prefusion-to-postfusion transition. Next, by introducing dynamics into the TMD, we find a late fusion intermediate structurally similar to a recent cryo-EM structure. A dynamic TMD also makes the conformational transition faster. Simulations including the S1/S2 complex reveal coupled RBD-TMD dynamics: when all three RBDs are in the closed state, they can stabilize the TMD in a trimeric configuration, whereas the opening of a single RBD can trigger a transition to a dynamic TMD. So, the dynamics and the conformational preferences of the TMD can be tuned by the presence and conformation of S1. There is some evidence that the TMDs of class I viral fusion proteins, such as spike, contribute to viral fusion by modulating membrane properties. Our simulations indicate an expanded role for the function of the TMD, where it can directly regulate the kinetics of S2 conformational transitions.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"36 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148768888","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":"Lamin A-regulated chromatin organization regulates transcription factor binding","authors":"Yuxuan Huang,Alişya A. Anlaş","doi":"10.1016/j.bpj.2026.08.016","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.08.016","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"6 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148768894","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-Molecule Force Spectroscopy Reveals a High-Force Requirement for Dissociation of Integrin Transmembrane Domains","authors":"Mandana Christine Hadawi,Bin Li,Monja Fink,Daniel Bublitz,Andreas Walbrun,Ulrike Majdic,Reinhard Fässler,Matthias Rief","doi":"10.1016/j.bpj.2026.08.017","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.08.017","url":null,"abstract":"Integrins are bidirectional mechanochemical receptors that transmit signals upon ligand binding to the cytoskeleton (outside-in) and cytoskeletal forces back across the membrane (inside-out) to the integrin-ligand bond. Integrins are activated prior to ligand binding, which involves large conformational rearrangements across the extracellular, transmembrane, and cytoplasmic regions. While the conformational and energetic basis of outside-in activation is increasingly well defined, the mechanical forces required for separating the tightly packed αβ transmembrane (TM) helices during inside-out signaling remain largely unknown.\u0000Here, we directly quantify the forces required to dissociate integrin TM domains (TMDs) in a lipid environment. Engineered α5β1 polypeptides consisting of TMDs and cytoplasmic tails were reconstituted into lipid nanodiscs and probed using single-molecule optical tweezers. Mechanical marker domains on each cytoplasmic tail verified correct vectorial force application, and fluorescent lipids confirmed nanodisc integrity.\u0000We find that the heterodimeric TM complex is a mechanically robust unit. In wild-type constructs, no TMD separation was observed in repeated pulls up to ∼35 pN. Point mutations in the β1-TMD (G744L, L748R) that weaken TMD interactions revealed discrete splitting events.\u0000The high mechanical forces necessary for TMD separation support a “ratchet-like” role for mechanical forces in inside-out signaling: rather than actively opening closed TMDs they prevent re-closing of spontaneously split TMDs thus keeping them open and activated.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"160 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148768889","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":"Multiscale Synchronization in Beta Cell Networks: Connecting Cellular Oscillations to Hormone Secretion","authors":"Uroš Barać, Andraž Stožer, Marko Gosak","doi":"10.1016/j.bpj.2026.08.013","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.08.013","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"11 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148755366","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":"The isolated Stachel peptide of the adhesion G protein-coupled receptor ADGRG6 is predominantly disordered with local helical propensity","authors":"Tucker J. Shriver,Sandra Berndt,Scott A. Robson,Austin D. Dixon,Ines Liebscher,Joshua J. Ziarek","doi":"10.1016/j.bpj.2026.08.012","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.08.012","url":null,"abstract":"Several members of the adhesion subfamily of G protein-coupled receptors (aGPCRs) are capable of self-activation by an internal agonist sequence (aka the Stachel) that’s exposed upon removal or conformational changes of the N-terminal fragment of the receptor. Synthetic peptides derived from the Stachel sequence can be used as exogenous agonists. In the inactive form of the full-length receptor, the Stachel is sequestered as the β13-strand within the GPCR Autoproteolysis-INducing (GAIN) domain, but it engages the seven transmembrane region as a helix when it is either an intramolecular sequence or a synthetic peptide. Little is known about the molecular details underlying this transition, but we hypothesize that a disordered conformation is central to this intermediate state in receptor activation. Despite the primarily helical Stachel AlphaFold3 and PEP-FOLD4 models predicted with high confidence for the entire aGPCR subfamily, computational predictions and biophysical experiments reveal a predominantly disordered conformation in solution. Investigating the ADGRG6 (also known as GPR126) Stachel peptide, circular dichroism (CD) and nuclear magnetic resonance (NMR) experiments reveal a predominantly random coil conformation in aqueous buffer, polar detergent micelles, and zwitterionic lipids. Titration of trifluoroethanol uncovered a two-state equilibrium between an unfolded and helix-containing conformation with NMR localizing a single-turn helix to residues L846-L849. Taken together, these data indicate the ADGRG6 Stachel peptide is primarily disordered with a subset adopting partial helical structures, likely requiring the steric hindrance of the receptor binding pocket to fully induce helix formation in an induced fit mechanism.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"159 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148768887","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":"Phenotypic memory of hypoxic exposure duration drives tumor invasion dynamics","authors":"Gopinath Sadhu, Paras Jain, Ritesh Kumar Meena, Jason T. George, Mohit Kumar Jolly","doi":"10.1016/j.bpj.2026.08.010","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.08.010","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"377 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148755367","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}