Biophysical journal最新文献

{"title":"Functionally distinct SNARE motifs of SNAP25 cooperate in SNARE assembly and membrane fusion","authors":"Katelyn N. Kraichely, Connor R. Sandall, Binyong Liang, Volker Kiessling, Lukas K. Tamm","doi":"10.1016/j.bpj.2024.12.034","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.12.034","url":null,"abstract":"Intracellular membrane traffic involves controlled membrane fission, and fusion and is essential for eukaryotic cell homeostasis. Most intracellular fusion is facilitated by Soluble <ce:italic>N</ce:italic>-ethylmaleimide sensitive factor attachment protein receptor (SNARE) proteins, which catalyze membrane merging by assembly of a coiled helical bundle of four 60- to 70-residue “SNARE motifs.” Perhaps no intracellular fusion reaction is as tightly regulated as that at the neuronal synapse, mediated by the synaptic vesicle SNARE Synaptobrevin-2 and the presynaptic plasma membrane SNAREs Syntaxin-1a and SNAP25. SNAP25 is different from its partner SNAREs: it contributes not one but two SNARE motifs to the final complex and instead of transmembrane domains is anchored in the membrane by post-translational palmitoylation of a long flexible linker between the SNARE motifs. Despite reports of structural and functional differences between the two SNARE motifs, many models of SNARE assembly and fusion consider SNAP25 to be a single functional unit and do not address how linking two distinct motifs in a single polypeptide contributes to synaptic SNARE assembly and fusion. To investigate whether SNAP25’s two SNARE motifs regulate each other’s folding and ability to assemble with other SNAREs, we determined their secondary structures in isolation and in the context of the whole protein by NMR spectroscopy and correlated the ability of the individual membrane-anchored SNARE motifs to interact with Syntaxin-1a and catalyze fusion in FRET-based binding and single-particle fusion assays, respectively. Our results demonstrate that the isolated N-terminal SNARE motif of SNAP25 promotes stronger Syntaxin-1a binding on membranes and more efficient fusion than wild-type SNAP25, while the C-terminal SNARE motif binds only transiently and facilitates kinetically delayed fusion. By comparing the functional properties of the single motifs to those of the full-length protein, we propose a new model of SNAP25 self-regulation in SNARE assembly and membrane fusion.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"67 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142939680","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":"Active Matter in the Nucleus: Chromatin Remodeling Drives Nuclear Force Dissipation.","authors":"Soham Ghosh","doi":"10.1016/j.bpj.2024.12.026","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.12.026","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"17 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142887512","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":"Vesicle docking and fusion pore modulation by the neuronal calcium sensor Synaptotagmin-1.","authors":"Maria Tsemperouli, Sudheer Kumar Cheppali, Félix Rivera-Molina, David Chetrit, Ane Landajuela, Derek Toomre, Erdem Karatekin","doi":"10.1016/j.bpj.2024.12.023","DOIUrl":"10.1016/j.bpj.2024.12.023","url":null,"abstract":"<p><p>Synaptotagmin-1 (Syt1) is a major calcium sensor for rapid neurotransmitter release in neurons and hormone release in many neuroendocrine cells. It possesses two tandem cytosolic C2 domains that bind calcium, negatively charged phospholipids, and the neuronal SNARE complex. Calcium binding to Syt1 triggers exocytosis, but how this occurs is not well understood. Syt1 has additional roles in docking dense-core vesicles (DCVs) and synaptic vesicles to the plasma membrane and in regulating fusion pore dynamics. Thus, Syt1 perturbations could affect release through vesicle docking, fusion triggering, fusion pore regulation, or a combination of these. Here, using a human neuroendocrine cell line, we show that neutralization of highly conserved polybasic patches in either C2 domain of Syt1 impairs both DCV docking and efficient release of serotonin from DCVs. Interestingly, the same mutations resulted in larger fusion pores and faster release of serotonin during individual fusion events. Thus, Syt1's roles in vesicle docking, fusion triggering, and fusion pore control may be functionally related.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142885160","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":"Amyloid beta Aβ1-40 activates Piezo1 channels in brain capillary endothelial cells.","authors":"Xin Rui Lim,Luc Willemse,Osama F Harraz","doi":"10.1016/j.bpj.2024.12.025","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.12.025","url":null,"abstract":"Amyloid-beta (Aβ) peptide accumulation on blood vessels in the brain is a hallmark of neurodegeneration. While Aβ peptides constrict cerebral arteries and arterioles, their impact on capillaries is less understood. Aβ was recently shown to constrict brain capillaries through pericyte contraction, but whether-and if so how-Aβ affects endothelial cells (ECs) remains unknown. ECs represent the predominant vascular cell type in the cerebral circulation, and we recently showed that the mechanosensitive ion channel Piezo1 is functionally expressed in the plasma membrane of ECs. Since Aβ disrupts membrane structures, we hypothesized that Aβ1-40, the predominantly deposited isoform in the cerebral circulation, alters endothelial Piezo1 function. Using patch clamp electrophysiology and freshly isolated capillary ECs, we assessed the impact of Aβ1-40 peptide on single-channel Piezo1 activity. We show that Aβ1-40 increased Piezo1 open probability and the channel open time. Aβ1-40 effects were absent when Piezo1 was genetically deleted or when a superoxide dismutase/catalase mimetic was used. Further, Aβ1-40 enhanced Piezo1 mechanosensitivity and lowered the pressure of half-maximal Piezo1 activation. Our data collectively suggest that Aβ1-40 facilitates higher Piezo1-mediated cation influx in brain ECs. These novel findings have the potential to unravel the possible involvement of Piezo1 modulation in the pathophysiology of neurodegenerative diseases characterized by Aβ accumulation.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"8 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142887511","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":"Driving forces of proton-pumping rhodopsins.","authors":"Akari Okuyama, Shoko Hososhima, Hideki Kandori, Satoshi P Tsunoda","doi":"10.1016/j.bpj.2024.09.007","DOIUrl":"10.1016/j.bpj.2024.09.007","url":null,"abstract":"<p><p>Proton-pumping rhodopsins are light-driven proton transporters that have been discovered from various microbiota. They are categorized into two groups: outward-directed and inward-directed proton pumps. Although the directions of transport are opposite, they are active proton transporters that create an H⁺ gradient across a membrane. Here, we aimed to study the driving force of the proton-pumping rhodopsins and the effect of ΔΨ and ΔpH on their pumping functions. We systematically characterized the H⁺ transport properties of nine different rhodopsins, six outward-directed H⁺ pumps and three inward-directed pumps, by patch-clamp measurements after expressing them in mammalian cells. The driving force of each pump was estimated from the slope of the current-voltage relations (I-V plot). Notably, among the tested rhodopsins, we found a large variation in driving forces, ranging from 83 to 399 mV. The driving force and decay rate of each pump current exhibited a good correlation. We determined driving forces under various pHs. pH dependency was less than predicted by the Nernst potential in most of the rhodopsins. Our study demonstrates that the H⁺-pumping rhodopsins from different organisms exhibit various pumping properties in terms of driving force, kinetics, and pH dependency, which could be evolutionarily derived from adaptations to their environments.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"4274-4284"},"PeriodicalIF":3.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145034","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":"Proton reactions: From basic science to biomedical applications.","authors":"Ana-Nicoleta Bondar, Thomas E DeCoursey","doi":"10.1016/j.bpj.2024.11.013","DOIUrl":"10.1016/j.bpj.2024.11.013","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"E1-E5"},"PeriodicalIF":3.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142791101","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":"Hidden water's influence on rhodopsin activation.","authors":"Zachary T Bachler, Michael F Brown","doi":"10.1016/j.bpj.2024.11.012","DOIUrl":"10.1016/j.bpj.2024.11.012","url":null,"abstract":"<p><p>Structural biology relies on several powerful techniques, but these tend to be limited in their ability to characterize protein fluctuations and mobility. Overreliance on structural approaches can lead to omission of critical information regarding biological function. Currently there is a need for complementary biophysical methods to visualize these mobile aspects of protein function. Here, we review hydrostatic and osmotic pressure-based techniques to address this shortcoming for the paradigm of rhodopsin. Hydrostatic and osmotic pressure data contribute important examples, which are interpreted in terms of an energy landscape for hydration-mediated protein dynamics. We find that perturbations of rhodopsin conformational equilibria by force-based methods are not unrelated phenomena; rather they probe various hydration states involving functional proton reactions. Hydrostatic pressure acts on small numbers of strongly interacting structural or solvent-shell water molecules with relatively high energies, while osmotic pressure acts on large numbers of weakly interacting bulk-like water molecules with low energies. Local solvent fluctuations due to the hydration shell and collective water interactions affect hydrogen-bonded networks and domain motions that are explained by a hierarchical energy landscape model for protein dynamics.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"4167-4179"},"PeriodicalIF":3.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11700366/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643366","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":"Kinetic network modeling with molecular simulation inputs: A proton-coupled phosphate symporter.","authors":"Yu Liu, Chenghan Li, Meghna Gupta, Robert M Stroud, Gregory A Voth","doi":"10.1016/j.bpj.2024.03.035","DOIUrl":"10.1016/j.bpj.2024.03.035","url":null,"abstract":"<p><p>Phosphate, an essential metabolite involved in numerous cellular functions, is taken up by proton-coupled phosphate transporters of plants and fungi within the major facilitator family. Similar phosphate transporters have been identified across a diverse range of biological entities, including various protozoan parasites linked to human diseases, breast cancer cells with increased phosphate requirements, and osteoclast-like cells engaged in bone resorption. Prior studies have proposed an overview of the functional cycle of a proton-driven phosphate transporter (PiPT), yet a comprehensive understanding of the proposed reaction pathways necessitates a closer examination of each elementary reaction step within an overall kinetic framework. In this work, we leverage kinetic network modeling in conjunction with a \"bottom-up\" molecular dynamics approach to show how such an approach can characterize the proton-phosphate co-transport behavior of PiPT under different pH and phosphate concentration conditions. In turn, this allows us to reveal the prevailing reaction pathway within a high-affinity phosphate transporter under different experimental conditions and to uncover the molecular origin of the optimal pH condition of this transporter.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"4191-4199"},"PeriodicalIF":3.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140317742","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 MD simulations of the protonation-triggered conformational switching in diphtheria toxin translocation domain.","authors":"Nuno F B Oliveira, Alexey S Ladokhin, Miguel Machuqueiro","doi":"10.1016/j.bpj.2024.08.023","DOIUrl":"10.1016/j.bpj.2024.08.023","url":null,"abstract":"<p><p>Protonation of key residues in the diphtheria toxin translocation (T)-domain triggered by endosomal acidification is critical for inducing a series of conformational transitions critical for the cellular entry of the toxin. Previous experiments revealed the importance of histidine residues in modulating pH-dependent transitions. They suggested the presence of a \"safety latch\" preventing premature refolding of the T-domain by a yet poorly understood mechanism. Here, we used constant-pH molecular dynamics simulations to systematically investigate the protonation sequence in the wild-type T-domain and the following mutants: H223Q, H257Q, E259Q, and H223Q/H257Q. Comparison of these computational results with previous experimental data on T-domain stability and activity with the H-to-Q replacements confirms the role of H223 (pK_a = 6.5) in delaying the protonation of the main trigger, H257 (pK_a = 2.2 in the WT and pK_a = 4.9 in H223Q). Our calculations also reveal a very low pK_a for a neighboring acidic residue E259, which does not get protonated even during simulations at pH 3. This residue also contributes to the formation of the safety latch, with the pK_a of H257 increasing from 2.2 to 5.1 upon E259Q replacement. In contrast, the latter replacement has virtually no effect on the protonation of the H223. Thus, we conclude that the interplay of the protonation in the H223/H257/E259 triad has evolved to prevent triggering the accidental refolding of the T-domain by a fluctuation in the protonation of the main trigger at neutral pH, before the incorporation of the toxin inside the endosome. Subsequent acidification of the endosome overcomes the safety latch and triggers conformational switching via repulsion of H223⁺ and H257⁺. This protonation/conformation relationship corroborates experimental findings and offers a detailed stepwise molecular description of the transition mechanism, which can be instrumental in optimizing the potential applications of the T-domain for targeted delivery of therapies to tumors and other diseased acidic tissues.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"4266-4273"},"PeriodicalIF":3.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142104005","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":"Interior pH-sensing residue of human voltage-gated proton channel H_v1 is histidine 168.","authors":"Mingzhe Shen, Yandong Huang, Zhitao Cai, Vladimir V Cherny, Thomas E DeCoursey, Jana Shen","doi":"10.1016/j.bpj.2024.07.027","DOIUrl":"10.1016/j.bpj.2024.07.027","url":null,"abstract":"<p><p>The molecular mechanisms governing the human voltage-gated proton channel hH_v1 remain elusive. Here, we used membrane-enabled hybrid-solvent continuous constant pH molecular dynamics (CpHMD) simulations with pH replica exchange to further evaluate the structural models of hH_v1 in the closed (hyperpolarized) and open (depolarized) states recently obtained with MD simulations and explore potential pH-sensing residues. The CpHMD titration at a set of symmetric pH conditions revealed three residues that can gain or lose protons upon channel depolarization. Among them, residue H168 at the intracellular end of the S3 helix switches from the deprotonated to the protonated state and its protonation is correlated with the increased tilting of the S3 helix during the transition from the closed to the open state. Thus, the simulation data suggest H168 as an interior pH sensor, in support of a recent finding based on electrophysiological experiments of H_v1 mutants. We propose that protonation of H168 acts as a key that unlocks the closed channel configuration by increasing the flexibility of the S2-S3 linker, which increases the tilt angle of S3 and enhances the mobility of the S4 helix, thus promoting channel opening. Our work represents an important step toward deciphering the pH-dependent gating mechanism of hH_v1.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"4211-4220"},"PeriodicalIF":3.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141756970","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}