Biophysical reports最新文献

{"title":"A dynamic duo: Copper metalloregulators and continuous-wave electron spin resonance spectroscopy.","authors":"Alysia Mandato, Sunil Saxena, Sharon Ruthstein","doi":"10.1016/j.bpr.2026.100259","DOIUrl":"10.1016/j.bpr.2026.100259","url":null,"abstract":"<p><p>This review highlights the use of continuous-wave electron spin resonance (ESR) spectroscopy to investigate protein site-specific dynamics and metal coordination in bacterial copper metalloregulators. ESR provides direct insight into how metal binding influences conformational flexibility, revealing how similar proteins can employ distinct mechanisms of transcriptional regulation. Studies of the activator CueR and the repressor CsoR show that these systems use fundamentally different strategies to control gene expression. CueR functions as a stable dimer that activates transcription through metal-induced conformational changes rather than oligomeric transitions. In E. coli, Cu(I) binding rapidly increases dynamics in the DNA-binding domain, while in Pseudomonas aeruginosa, CueR exhibits a more gradual, DNA-dependent response that reflects adaptation to alternative copper resistance pathways. In contrast, CsoR exists in a dynamic equilibrium between dimeric and tetrameric states, with oligomerization playing a central role in its repressor mechanism. Small shifts in subunit exchange may fine-tune DNA binding and facilitate dissociation upon Cu(I) coordination. This review demonstrates how ESR spectroscopy can capture the subtle structural and dynamical differences that define metalloregulator function and highlight the diversity of bacterial strategies for maintaining metal homeostasis.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100259"},"PeriodicalIF":2.6,"publicationDate":"2026-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101592/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147494870","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}

{"title":"Distinct disassembly modes shape cytoskeletal assembly and fluctuations.","authors":"Md Sorique Aziz Momin, Michaela Cohen, Lishibanya Mohapatra","doi":"10.1016/j.bpr.2026.100263","DOIUrl":"10.1016/j.bpr.2026.100263","url":null,"abstract":"<p><p>How distinct cytoskeletal structures assemble and maintain their characteristic sizes on different timescales while drawing from a shared pool of subunits remains an open question in cell biology. Experiments indicate that mechanisms promoting the disassembly of these structures and replenishing the pool may play a vital role. Here, we compare two disassembly models: one with a constant monomer loss rate and another that is size dependent, where structures lose filament fragments through severing. Using analytical calculations and simulations, we examine their effects on the assembly of two structure types, filaments and bundles composed of linear filaments, both in isolation and when co-assembling in a shared pool. We find that both models control assembly and regulate structure size in distinct ways. However, the assembly of both structures to their steady-state size is accelerated with severing, accompanied by a faster decay of autocorrelations in their length fluctuations. Moreover, we find that severing can regulate multiple structures assembling from a shared pool, constraining them to defined sizes. Our study identifies key parameters governing assembly kinetics and fluctuation dynamics associated with each disassembly mode, highlights measurable quantities such as coefficient of variation and bundle tapering that can help distinguish between different disassembly mechanisms, and reveals specific signatures of structures assembling in a limited monomer pool. Together, these results provide a framework for experiments to identify assembly-control mechanisms in cytoskeletal structures and elucidate the role specific disassembly modes can have in modulating structure formation and maintenance.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100263"},"PeriodicalIF":2.6,"publicationDate":"2026-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13195333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790205","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}

{"title":"Objective clustering protocol for single-molecule data: A lifetime vs. intensity study.","authors":"Michael A C Lovemore, Bertus van Heerden, Joshua L Botha, Tjaart P J Krüger","doi":"10.1016/j.bpr.2026.100262","DOIUrl":"10.1016/j.bpr.2026.100262","url":null,"abstract":"<p><p>Single-molecule spectroscopy (SMS) is an exceptionally sensitive technique, but its inherently limited photon budget produces noisy data that can readily lead to subjective analyses, fitting errors, and reduced statistical power, obscuring true subpopulations and their dynamics. Here, we present an unbiased, objective method to cluster two-dimensional single-molecule data and demonstrate it on fluorescence lifetime-intensity correlations. The clustering method is based on Gaussian mixture modeling, with the optimal number of clusters determined through information criteria (the Akaike and Bayesian information criteria and integrated completed likelihood) and supplemented by cluster-quality metrics such as average cluster tightness and the fraction of points outside confidence ellipses, which guide the selection of statistically robust and physically meaningful clusters. The protocol was benchmarked on simulated datasets spanning clean, smeared, and noisy overlap-limited regimes and applied to experimental data from Alexa Fluor 647 and QD605. This approach reliably recovers relevant subpopulations even in the presence of noise and overlapping distributions, providing an objective framework for analyzing single-molecule heterogeneity, with limitations arising primarily under severe geometric overlap or extreme state-occupancy imbalance where distinct populations are no longer separable.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100262"},"PeriodicalIF":2.6,"publicationDate":"2026-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13156630/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790160","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}

{"title":"Bedaquiline inhibits the ATP synthase leak channel and prevents glutamate-induced neuronal death.","authors":"Amrendra Kumar, Olesia Lunko, Erin Smith, Ikram Mezghani, Subhash Eedarapalli, Yangyu Wu, Khondoker Adeba Ferdous, Emma Amjad, Han-A Park, Nelli Mnatsakanyan","doi":"10.1016/j.bpr.2026.100265","DOIUrl":"10.1016/j.bpr.2026.100265","url":null,"abstract":"<p><p>F_OF₁-ATP synthase is one of the most abundant proteins of the mitochondrial inner membrane and the primary enzyme responsible for ATP production in eukaryotic cells. Nevertheless, it was recently reported to play a prominent role in cell death by forming a large-conductance leak channel in the mitochondrial permeability transition pore (mPTP), making it a promising therapeutic target. Bedaquiline (BDQ), a member of the diarylquinoline class of drugs, was shown to selectively inhibit the catalytic activity of Mycobacterium tuberculosis ATP synthase with no effect on the mammalian enzyme. Here, we report a new role for BDQ as a potent inhibitor of the ATP synthase c-subunit leak channel in mammals. BDQ inhibited the single-channel activity of porcine heart ATP synthase in planar lipid bilayer recordings and inner membrane channel activity of porcine mitochondria in patch-clamp recordings, and it prevented glutamate-induced cell death in primary hippocampal neurons. These findings reveal the potential new application of BDQ for treating mPTP-related diseases by targeting the ATP synthase c-subunit leak channel.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100265"},"PeriodicalIF":2.6,"publicationDate":"2026-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13234225/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147870631","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}

{"title":"Effect of the gut microbiota metabolite phenylacetylglycine on cardiac Ca²⁺ signaling.","authors":"Elisa Bovo, Aleksey V Zima","doi":"10.1016/j.bpr.2026.100260","DOIUrl":"10.1016/j.bpr.2026.100260","url":null,"abstract":"<p><p>Phenylacetylglutamine (PAGln) and phenylacetylglycine (PAGly) are small molecules derived from the metabolism of phenylalanine by gut microbiota. Elevated levels of PAGln and PAGly in serum have been associated with increased risks for cardiovascular diseases. It has been suggested that PAGln and PAGly reduce cardiac contraction by blunting the adrenergic response during sympathetic stimulation. However, little is known about whether the effect of PAGln and PAGly on the heart function is associated with an alteration of intracellular Ca²⁺ homeostasis. Here, we studied the effect of PAGly on Ca²⁺ regulation in mouse ventricular myocytes, as PAGly is the predominant phenylalanine metabolite in rodent's serum. Analysis of cytosolic Ca²⁺ dynamics revealed that PAGly (100 μM) increases action potential-induced Ca²⁺ transients and sarcoplasmic reticulum Ca²⁺ load. These effects of PAGly were significantly smaller than those produced by the adrenergic receptor agonist isoproterenol (ISO; 0.1 μM). The adrenergic receptor blocker propranolol (10 μM) and the protein kinase A inhibitor H89 (10 μM) prevented the PAGly effects on intracellular Ca²⁺ dynamics. Further analysis of Ca²⁺ regulation revealed that pretreatment of cardiomyocytes with PAGly reduced the stimulatory effect of ISO on intracellular Ca²⁺ dynamics. Concurrently, PAGly did not produce any stimulatory effects on intracellular Ca²⁺ in the presence of ISO. In conclusion, PAGly regulates intracellular Ca²⁺ dynamics in ventricular myocytes by activating the adrenergic receptor-mediated signaling, but less efficiently than selective adrenergic agonists. By interacting with adrenergic receptors, PAGly might blunt the stimulatory effect of sympathetic stimulation.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100260"},"PeriodicalIF":2.6,"publicationDate":"2026-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13098594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147625165","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}

{"title":"Dynamic velocity response of E. coli powered by proteorhodopsin.","authors":"Silvio Bianchi, Giacomo Donini, Maria Cristina Cannarsa, Giacomo Frangipane, Roberto Di Leonardo","doi":"10.1016/j.bpr.2026.100254","DOIUrl":"10.1016/j.bpr.2026.100254","url":null,"abstract":"<p><p>Escherichia coli swimming motility is powered by the flagellar motor, a rotary nanomachine driven by inward proton flux through its torque-generating stators. How these proton currents arise from proton motive force is often described using a simple circuit model, in which the membrane acts as a capacitor discharging through the flagellar motors and other resistive proton channels. By monitoring the swimming activity of E. coli expressing a light-driven outward proton pump, we probe the dynamical response of the system under tunable optical driving and test the limits of simplified circuit-based description. Our results show that the flagellar motors are not the main sink for proton motive force discharge. Instead, other membrane channels carry a larger proton current and exhibit a nonlinear resistive behavior. Using the same experimental approach, we directly quantify proteorhodopsin pumping activity as a function of illumination wavelength and compare it with previously reported absorption spectra.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100254"},"PeriodicalIF":2.6,"publicationDate":"2026-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12994061/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147313079","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}

{"title":"Biophysical Reports: Announcing new \"method review\" articles.","authors":"Melanie Cocco","doi":"10.1016/j.bpr.2026.100264","DOIUrl":"https://doi.org/10.1016/j.bpr.2026.100264","url":null,"abstract":"","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"6 2","pages":"100264"},"PeriodicalIF":2.7,"publicationDate":"2026-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147935776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mimicking oxidative damage in γS-crystallin with site-specific incorporation of 5-hydroxytryptophan.","authors":"Yeonseong Seo, Zane G Long, Tsoler K Demerdjian, Acts A Avenido, Carter T Butts, Rachel W Martin","doi":"10.1016/j.bpr.2026.100251","DOIUrl":"10.1016/j.bpr.2026.100251","url":null,"abstract":"<p><p>The human eye lens plays an essential role in vision by focusing light onto the retina. This transparent tissue consists of densely packed crystallin proteins that exhibit remarkable solubility despite minimal protein turnover. Post-translational modifications that accumulate over a lifetime can reduce crystallin solubility, resulting in the precipitation or phase separation of protein aggregates. Oxidation is a common type of modification that can cause such opacification of the lens, particularly in age-related cataract. Here, we study the oxidation of W163 in γS-crystallin, a structural lens protein that is particularly vulnerable to oxidative stress. We were motivated by previous findings reporting the oxidation of this residue in diseased and UV- and γ-irradiated samples. Using genetic code expansion (GCE), we incorporated an oxidation mimic, 5-hydroxytryptophan (5HTP), at position 163 of γS-crystallin (γS-W163(5HTP)). This subtle change in the structural and electronic properties of its side chain is hypothesized to destabilize the hydrophobic core of the C-terminal domain. γS-W163(5HTP) was characterized and compared to the wild-type (γS-WT). Although the overall fold and stability of the two proteins were comparable, the aggregation of γS-W163(5HTP) was triggered at notably lower temperatures compared to γS-WT. Subsequent investigation of this observation using both simulations and experiments suggests a potential mechanism for polymerization as well as oxidation-induced conformational changes that may cause susceptibility to thermal aggregation. Our findings highlight the utility of GCE platforms for systematically evaluating the impact of post-translational modifications on disease-related proteins.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100251"},"PeriodicalIF":2.6,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12915173/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145999899","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}

{"title":"Photoelectrical control of apoptosis and autophagy.","authors":"Mohammad Mohammadiaria","doi":"10.1016/j.bpr.2025.100241","DOIUrl":"10.1016/j.bpr.2025.100241","url":null,"abstract":"<p><p>Controlling cancer cell fate through membrane depolarization, reactive oxygen species (ROS) dynamics, and voltage-gated ion channel (VGIC) activation represents a rapidly advancing paradigm in bioelectronic oncology. Electrically excitable cancer cells-including glioblastoma, retinoblastoma, SH-SY5Y neuroblastoma, MCF-7, and MDA-MB-231-exhibit distinct electrophysiological and redox sensitivities that govern their responsiveness to photoelectrical stimulation. Here, we develop an integrated theoretical and transcriptomic framework describing how photocapacitive and photofaradaic stimulation modulates intracellular calcium signaling, mitochondrial membrane potential (ΔΨm), and ROS homeostasis to determine apoptotic, autophagic, or proliferative outcomes. Experimental data sets from GSE59612, GSE103224 (glioblastoma), GSE97508 (retinoblastoma), and GSE45827 (breast cancer) parameterize VGIC families, antioxidant pathways, and cell death modules. New simulations using a measured 20-Hz photovoltaic waveform show that photocapacitive depolarization elevates glioblastoma ROS levels to ∼150-160 μM over 30 min, placing cells within a proliferative-to-autophagic transition region, with a small apoptotic component. Mapping these ROS trajectories to a bifurcation-based cell fate model reveals glioblastoma-specific redox thresholds that align with transcriptomic VGIC and antioxidant signatures. By unifying stimulation physics, bioelectrical modeling, and omics-based parameterization, this work provides a predictive foundation for designing photovoltaic cancer therapies tuned to cell-type-specific electrophysiological and redox landscapes. Moreover, in MDA-MB-231 cells the same stimulation induces a controlled, early-stage autophagy response, providing an intrinsic antiinflammatory benefit that can suppress early tumorigenic signaling.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100241"},"PeriodicalIF":2.7,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12757480/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145650188","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}

{"title":"Single-cell vibration analysis for potential diagnostic applications.","authors":"Jared J Topham, Ali Al-Khaz'Aly, Salim Ghandorah, Tvara Parikh, Farshad Farshidfar, Matthias Amrein","doi":"10.1016/j.bpr.2026.100252","DOIUrl":"10.1016/j.bpr.2026.100252","url":null,"abstract":"<p><p>Vibrational frequency profiling (VFP) using optical tweezers has emerged as a promising technique to characterize single-cell behavior for diagnostic applications. These applications include cancer screening, identifying bacterial resistance to antibiotics, and assessing cellular response to metabolic treatments. Previously, we demonstrated that vibrational profiling can successfully differentiate samples in real time using single-cell vibrational signatures. However, the sensitivity of this approach and its ability to be applied across variable experimental conditions and cell lines have not been well identified. This study builds on previous work, demonstrating the feasibility of our established vibrational analysis to quantitively assess whether changes in experimental design can improve model separation of different cell types. U251 human glioblastoma cells and A549 human lung carcinoma cells were used as our model system. We illustrate this capability through three examples: 1) comparing an open Petri dish to closed microfluidic chambers, 2) synchronizing cells in the cell cycle, and 3) altering medium viscosity. These factors were selected for their potential to influence signal quality and model accuracy. Vibrations were collected using optical tweezers, were Fourier transformed to produce power spectra, and were then parameterized using peak detection, extracting area under the curve values. Peaks were aggregated across samples and classified using partial least squares discriminant analysis. Partial least squares discriminant analysis classification was performed with 70/30 train-test splits of data and 10-fold cross-validation. Petri-dishes yielded a more well-classified sample than microfluidics chambers (F1 score 0.89 vs. 0.79). Synchronized cells reduced vibrational variability and improved classification (F1 score 0.83 vs. 0.79). Increased viscosity produced slight classifier improvements (F1 score 0.81 vs. 0.79). These findings demonstrate that VFPs are sensitive to the mechanical and environmental context of cell measurement, highlighting that careful standardization of experimental conditions is crucial for developing reproducible and clinically translatable VFP-based diagnostic platforms.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100252"},"PeriodicalIF":2.6,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12915227/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145999931","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}