Biophysical journal最新文献

{"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}

{"title":"Glycolysis model shows that allostery maintains high ATP and limits accumulation of intermediates.","authors":"Mangyu Choe, Tal Einav, Rob Phillips, Denis V Titov","doi":"10.1016/j.bpj.2025.03.037","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.037","url":null,"abstract":"<p><p>Glycolysis is a conserved metabolic pathway that produces ATP and biosynthetic precursors. It is not well understood how the control of mammalian glycolytic enzymes through allosteric feedback and mass action accomplishes various tasks of ATP homeostasis, such as controlling the rate of ATP production, maintaining high and stable ATP levels, ensuring that ATP hydrolysis generates a net excess of energy, and maintaining glycolytic intermediate concentrations within physiological levels. To investigate these questions, we developed a biophysical model of glycolysis based on enzyme rate equations derived from in vitro kinetic data. This is the first biophysical model of human glycolysis that successfully recapitulates the above tasks of ATP homeostasis and predicts absolute concentrations of glycolytic intermediates and isotope tracing kinetics that align with experimental measurements in human cells. We use the model to show that mass action alone is sufficient to control the ATP production rate and maintain the high energy of ATP hydrolysis. Meanwhile, allosteric regulation of hexokinase (HK) and phosphofructokinase (PFK) by ATP, ADP, inorganic phosphate, and glucose-6-phosphate is required to maintain high ATP levels and to prevent uncontrolled accumulation of phosphorylated intermediates of glycolysis. Allosteric feedback achieves the latter by maintaining HK and PFK enzyme activity at one-half of ATP demand and, thus, inhibiting the reaction of Harden and Young, which otherwise converts glucose to supraphysiological levels of phosphorylated glycolytic intermediates at the expense of ATP. Our methodology provides a roadmap for a quantitative understanding of how metabolic homeostasis emerges from the activities of individual enzymes.</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":"143787687","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":"Comparison of BH3-dependent and BH3-independent membrane interactions of pro-apoptotic factor BAX.","authors":"Mykola V Rodnin, Victor Vasquez-Montes, Pierce T O'Neil, Alexander Kyrychenko, Alexey S Ladokhin","doi":"10.1016/j.bpj.2025.03.034","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.034","url":null,"abstract":"<p><p>The pro-apoptotic factor BAX is a key member of the Bcl-2 family of apoptotic regulators. BAX functions by permeating the outer mitochondrial membrane, a process that begins with the targeting of soluble BAX to the membrane. Once associated, BAX refolds, inserts into the bilayer, and ultimately assembles into a multimeric pore of unknown structure. BAX targeting is initiated by an activation signal that can arise from two pathways: (a) a BH3-dependent one in which BAX is activated by one of the BH3-only effectors such as tBid, or (b) a recently discovered BH3-independent pathway, where BAX activity is modulated by changes in lipid composition. In this study, we gain further insight into how these two pathways function, and how their function is impacted by anti-apoptotic factor Bcl-xL. We use fluorescence spectroscopy to compare the BH3-dependent and BH3-independent interactions of BAX with model membranes of varying lipid compositions. We investigate membrane association using FRET between Donor-labeled BAX and Acceptor-labeled vesicles. We monitor membrane insertion by observing changes in the spectral properties of the environment-sensitive probe NBD, which we selectively attached to a series of single-cysteine BAX mutants. Finally, we study membrane permeation through BAX-induced leakage of soluble markers loaded into vesicles. Our results show that BAX-induced permeabilization of zwitterionic vesicles is more efficient for the BH3-dependent pathway compared to the BH3-independent pathway; however, permeabilization of cardiolipin-containing vesicles is equally efficient for both the BH3-dependent and BH3-independent pathways. Interestingly, while anionic lipids are not necessary for the initial BH3-independent membrane association of BAX, they are critical for subsequent stages of membrane insertion and pore assembly. The spectroscopic response of NBD-labeled BAX is comparable for both interaction modes, indicating a similar structure for the final inserted state. We found that the Bcl-xL factor inhibits vesicle permeabilization by preventing BAX from interacting with the bilayer.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778883","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":"Barrier effects on the kinetics of cohesin-mediated loop extrusion.","authors":"Leiyan Chen, Zhenquan Zhang, Zihao Wang, Liu Hong, Haohua Wang, Jiajun Zhang","doi":"10.1016/j.bpj.2025.03.026","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.026","url":null,"abstract":"<p><p>Chromosome organization mediated by structural maintenance of chromosome complexes is crucial in many organisms. Cohesin extrudes chromatin into loops that are thought to lengthen until it is obstructed by CTCF proteins. In complex cellular environments, the loop extrusion machinery may encounter other chromatin-binding proteins. How these proteins interfere with the cohesin-meditated extrusion process is largely unexplored, but recent experiments have shown that some proteins serve as physical barriers that block cohesin translocation. Other proteins containing a cohesin-interaction motif serve as chemical barriers to induce cohesin pausing through interactions with it. Here, we develop an analytically solvable approach for the loop extrusion model incorporating barriers to investigate the effect of the barrier on the passive extrusion process. To further quantify the impact of barriers, we calculate the mean looping time it takes for cohesin to translocate to form a stable loop before dissociation. Our finding reveals that the physical barrier can accelerate the loop formation, and the degree of acceleration is closely related to the impedance strength of the physical barrier. In particular, the synergy of the cohesin loading site and the physical barrier site accelerates loop formation more significantly. The proximity of the cohesin loading site to the barrier site facilitates the rapid formation of stable loops in long genomes, which implies loop extrusion and chromatin-binding proteins might shape functional genomic organization. Conversely, chemical barriers consistently impede loop formation, with increasing impedance strength of the chemical barrier leading to longer loop formation time. Our study contributes to a more comprehensive understanding of the complexity of the loop extrusion process, providing a new perspective on the potential mechanisms of gene regulation.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778879","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":"Super-resolution algorithms for Imaging FCS enhancement: A comparative study.","authors":"Shambhavi Pandey, Nithin Pathoor, Thorsten Wohland","doi":"10.1016/j.bpj.2025.03.031","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.031","url":null,"abstract":"<p><p>Understanding the structure and dynamics of biological systems is often limited by the trade-off between spatial and temporal resolution. Imaging fluorescence correlation spectroscopy (ImFCS) is a powerful technique for capturing molecular dynamics with high temporal precision but remains diffraction-limited. This constraint poses challenges for quantifying dynamics of subcellular structures like membrane-proximal cortical actin fibers. Computational super-resolution microscopy (CSRM) presents an accessible strategy for enhancing spatial resolution without specialized instrumentation, enabling compatibility with ImFCS. In this study, we evaluated various CSRM techniques, including super-resolution radial fluctuations (SRRF), mean-shift super-resolution (MSSR), and multiple signal classification imaging (MUSICAL), among others, using TIRF datasets of actin fibers labeled with F-tractin-mApple. By combining structural masks from TIRF and CSRM, we distinguished off-fiber, mixed, and on-fiber regions for region-specific diffusion analyses. Although all CSRM algorithms improve ImFCS data analysis, SRRF demonstrated superior performance in identifying cortical actin fibers, showing minimal variance in on-fiber diffusion coefficients. These findings establish a framework for integrating CSRM with ImFCS to achieve high-resolution spatial and dynamic characterization of subcellular structures from single measurements.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778886","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":"Dynamical instability is a major cause of cardiac action potential variability.","authors":"Daisuke Sato, Bence Hegyi, Crystal M Ripplinger, Donald M Bers","doi":"10.1016/j.bpj.2025.02.007","DOIUrl":"10.1016/j.bpj.2025.02.007","url":null,"abstract":"<p><p>Increased beat-to-beat QT interval variability (QTV) in the electrocardiogram is strongly associated with ventricular arrhythmias and sudden cardiac death, yet its origins remain poorly understood. While heart rate variability decreases with deteriorating cardiac health, QTV increases, suggesting distinct underlying mechanisms. The stochastic nature of ion channel gating is a potential source of cardiac variability. However, the law of large numbers suggests that, with billions of channels in the heart, this stochasticity should be minimized. In this study, we tested the hypothesis that dynamical instability amplifies stochastic ion channel fluctuations, leading to increased action potential (AP) variability. Using a mathematical model of ventricular myocytes, we investigated the relationship between AP variability and voltage instability. Our results demonstrate that stochastic gating alone cannot cause large AP variability, but dynamical instability significantly amplifies this variability. We found a positive correlation between voltage instability, indicated by the slope of the AP duration restitution curve, and AP duration variability. Notably, the largest variability occurred at the onset of alternans when considering every other beat. These findings provide a mechanistic explanation for increased QTV in pathological conditions and suggest that measuring QTV using every other beat may predict the onset of alternans and severity of alternans. Our study highlights the critical role of dynamical instability in cardiac electrical variability and offers new insights into the mechanisms underlying arrhythmogenesis.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"1042-1048"},"PeriodicalIF":3.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143405271","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":"Sphingomyelin slows interfacial hydrogen-bonding dynamics in lipid membranes.","authors":"Cong Xu, James E Fitzgerald, Edward Lyman, Carlos R Baiz","doi":"10.1016/j.bpj.2025.02.020","DOIUrl":"10.1016/j.bpj.2025.02.020","url":null,"abstract":"<p><p>Interfacial hydrogen bonding (H-bonding) partly determines membrane structure, heterogeneity, and dynamics. Given the chemical diversity of lipids, it is important to understand how composition determines lipid-lipid interactions and how those are translated to H-bond populations and dynamics. Here, we investigate the role of palmitoyl sphingosylphosphorylcholine (PSM) in modulating lipid H-bond networks in combination with dipalmitoyl phosphatidylcholine (DPPC) using ultrafast two-dimensional infrared (2D IR) spectroscopy and molecular dynamics simulations. We report composition-dependent H-bond ensembles for ester and amide carbonyls, with increased H-bond populations and slower dynamics with higher PSM concentrations. Specifically, amide carbonyl 2D IR spectra indicate that PSM, acting as an H-bond donor, partially replaces water-mediated interactions, with the number of direct lipid-lipid H-bonds constituting up to 20% of the total. These interactions create comparatively stable H-bond networks that significantly slow interfacial dynamics. 2D IR spectra show an H-bond lifetime slowdown of 45% in an equimolar mixture of the two lipids compared to DPPC alone. This study highlights PSM's dual role in H-bonding, which increases membrane viscosity and stabilizes lipid interfaces, providing molecular insights into the role of sphingolipids in cell membranes. The findings further emphasize the synergy of experimental and computational approaches for extracting molecular-level insights into interfacial lipid-lipid and lipid-water interactions in heterogeneous membranes.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"1158-1165"},"PeriodicalIF":3.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522530","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":"Quality control maps: Real-time quantitative control of single-molecule localization microscopy data.","authors":"Sébastien Mailfert, Meriem Djendli, Roxane Fabre, Didier Marguet, Nicolas Bertaux","doi":"10.1016/j.bpj.2025.02.018","DOIUrl":"10.1016/j.bpj.2025.02.018","url":null,"abstract":"<p><p>Single-molecule localization microscopy (SMLM) has revolutionized the understanding of cellular organization by reconstructing informative images with quantifiable spatial distributions of molecules far beyond the optical diffraction limit. Much effort has been devoted to optimizing localization accuracy. One such approach is the assessment of SMLM data quality in real time rather than after lengthy postacquisition analysis, which nevertheless represents a computational challenge We overcame this difficulty by implementing an innovative mathematical approach we designed to drastically reduce the computational analysis of particle localization. Our quality control maps (QCM) workflow enables a much higher rate of data processing compared to that limited by the frequency required by current cameras. Accordingly, using an innovative computational approach for the detection step and an estimator based on a Gaussian model of the point spread function, subpixel particle locations and their accuracy can be determined through a straightforward analytical calculation without the need for iterations. As a true parameter-free algorithm, QCM is robust and adaptable to all types of SMLM data, with high speed enabling the real-time calculation of quantitative quality control indicators. Such features are compatible with smart microscopy, the concept of which depends on the adjustment of acquisition parameters in real time according to analytical results. Finally, the offline QCM mode can be used as a tool to evaluate synthetic or previously acquired data, as well as to teach the basic concepts of SMLM.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"1132-1145"},"PeriodicalIF":3.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514659","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":"Synaptic cleft geometry modulates NMDAR opening probability by tuning neurotransmitter residence time.","authors":"María Hernández Mesa, Kimberly J McCabe, Padmini Rangamani","doi":"10.1016/j.bpj.2025.01.019","DOIUrl":"10.1016/j.bpj.2025.01.019","url":null,"abstract":"<p><p>Synaptic morphology plays a critical role in modulating the dynamics of neurotransmitter diffusion and receptor activation in interneuron communication. Central physical aspects of synaptic geometry, such as the curvature of the synaptic cleft, the distance between the presynaptic and postsynaptic membranes, and the surface-area-to-volume ratio of the cleft, crucially influence glutamate diffusion and N-methyl-D-aspartate receptor (NMDAR) opening probabilities. In this study, we developed a stochastic model for receptor activation using realistic synaptic geometries. Our simulations revealed substantial variability in NMDAR activation, showing a significant impact of synaptic structure on receptor activation. Next, we designed a theoretical study with idealized cleft geometries to understand the impact of different biophysical properties on receptor activation. Specifically, we found that increasing the curvature of the synaptic membranes could compensate for reduced NMDAR activation when the synaptic cleft width was large. Additionally, nonparallel membrane configurations, such as convex presynapses or concave postsynaptic densities, maximize NMDAR activation by increasing the surface-area-to-volume ratio, thereby increasing glutamate residence time and reducing glutamate escape. Furthermore, clustering NMDARs within the postsynaptic density significantly increased receptor activation across different geometric conditions and mitigated the effects of synaptic morphology on NMDAR opening probabilities. These findings highlight the complex interplay between synaptic geometry and receptor dynamics and provide important insights into how structural modifications can influence synaptic efficacy and plasticity. By considering the major physical factors that affect neurotransmitter diffusion and receptor activation, our work offers a comprehensive understanding of how variations in synaptic geometry may regulate neurotransmission.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"1058-1072"},"PeriodicalIF":3.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057950","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":"Morphological trapping of neurotransmitters in synaptic clefts: A new dimension in neural plasticity.","authors":"Bugra Kaytanli, Mattia Bacca","doi":"10.1016/j.bpj.2025.02.026","DOIUrl":"10.1016/j.bpj.2025.02.026","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"1035-1037"},"PeriodicalIF":3.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536384","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}