Biophysical journal最新文献

{"title":"Isomerization of PhotoGb3 in Phase-separated Pore-spanning Membranes alters Shiga toxin Organization.","authors":"Larissa Socrier,Somayeh Ahadi,Mark Skamrahl,Daniel B Werz,Claudia Steinem","doi":"10.1016/j.bpj.2025.07.011","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.07.011","url":null,"abstract":"The lateral organization of Shiga toxin bound to a lipid membrane is significantly influenced by the fatty acid geometry of its receptor glycolipid Gb3, which is crucial for the protein's internalization into the host cell. To control the lipid geometry, we used a photoisomerizable azobenzene derivative of Gb3 (photo-Gb3) that can be switched between a trans- and cis-configuration under light. We reconstituted this photo-Gb3 into liquid-disordered (ld)/liquid-ordered (lo) phase-separated pore-spanning membranes (PSMs), creating freestanding bilayer parts (f-PSMs) composed of an lo-phase surrounded by ld-phase on the pore rims (s-PSMs). Upon UV irradiation, we observed small, mobile, and transient ld-domains in the f-PSMs, indicating a trans-to-cis-isomerization of the photo-Gb3. The mean diffusion coefficient of the ld-domains was determined to be 0.014 ± 0.009 μm2/s, from which we estimated a membrane surface viscosity of 12-21∙10-8 Pa s m, indicative of a lo-phase. Before photoisomerization, Shiga toxin B (STxB) bound homogeneously to the lo-phase in the f-PSMs harboring the photo-Gb3. Upon trans-to-cis-isomerization of the photo-Gb3, ld-lakes were again formed, and the homogeneous protein distribution turned into dynamic STxB density fluctuations, which are discussed in the context of the entry process of Shiga toxin into the host cell.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"84 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144622008","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":"Ca²⁺ increases cardiac muscle viscoelasticity independent of active force development.","authors":"Anthony J Baker, On Yeung Li, Filip Ježek, Paul C Simpson, Naomi C Chesler, Daniel A Beard","doi":"10.1016/j.bpj.2025.07.009","DOIUrl":"10.1016/j.bpj.2025.07.009","url":null,"abstract":"<p><p>In addition to activation of muscle contraction by Ca²⁺, previous studies suggest that Ca²⁺ also affects muscle passive mechanical properties. The goal of this study was to determine if Ca²⁺ regulates the stiffness of cardiac muscle, independent of active contraction. The mechanical response to stretch for mouse demembranated cardiac trabeculae was probed at different Ca²⁺ levels after eliminating active contraction using a combination of two myosin ATPase inhibitors: para-nitroblebbistatin (PNB, 50 μM), plus mavacamten (Mava, 50 μM). Myocardial force level was assessed during large stretches (≈ 20% initial muscle length) with a range of stretch velocities. For relaxed muscle, in response to stretch, muscle force rose to a peak and then decayed toward a lower steady-state level. Peak force was higher with faster stretch velocity, consistent with the presence of a viscoelastic element. However, the steady-state force was independent of stretch velocity, consistent with the presence of an elastic component. In the presence of the inhibitors PNB plus Mava, when Ca²⁺ level was increased, active contraction was completely prevented. However, the viscoelastic force response to stretch was markedly increased by high Ca²⁺ and was > 6-fold higher than at low Ca²⁺ level. The relationship of viscoelastic force to Ca²⁺ level had a similar form to the relationship of active force to Ca²⁺ (measured in the absence of inhibitors), suggesting a common regulatory mechanism is involved. As expected, Ca²⁺-activated contraction was inhibited by lowering the temperature from 21ºC to 10ºC. In contrast, the Ca²⁺-activated viscoelastic property was not inhibited at lower temperature, further suggesting that active contraction and the viscoelastic property involve distinct mechanisms. This study demonstrates that in addition to triggering activation of contraction, Ca²⁺ also increases the apparent viscoelastic property of cardiac muscle.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144616119","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":"OpenCafeMol: A coarse-grained biomolecular simulator on GPU with its application to vesicle fusion.","authors":"Yutaka Murata, Toru Niina, Shoji Takada","doi":"10.1016/j.bpj.2025.07.012","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.07.012","url":null,"abstract":"<p><p>There has been an increasing demand for longer-timescale molecular dynamics (MD) simulations of larger biomolecular systems. To meet these demands, using the C++ API of OpenMM, we developed a fast and flexible MD software, OpenCafeMol, for residue-resolution protein and lipid models that shows high performance on graphics processing unit (GPU) machines. We validated OpenCafeMol for folding small proteins, lipid membrane dynamics, and membrane protein structures. Benchmark tests of the computation times showed that OpenCafeMol with one GPU for proteins and lipid membranes can be approximately 100 and 240 times faster than the corresponding simulations on a typical CPU machine (eight cores), respectively. Taking advantage of the high speed of OpenCafeMol, we applied it to two sets of vesicle fusion simulations; one driven by force and the other coupled with conformational dynamics of a SNARE complex. In the latter, a direct MD simulation at a high temperature resulted in vesicle docking, pore formation followed by fusion, which are coupled with local folding of linkers in the SNARE complex. This opens up new avenue to study membrane-fusion mechanisms via MD simulations. The source code for OpenCafeMol is fully available. SIGNIFICANCE Recently, there has been an increasing demand for longer-timescale biomolecular dynamics simulations. To meet the demand, coarse-graining the molecular representation and using GPU are promising approaches. Here, we developed a fast and flexible MD software, OpenCafeMol, for residue-resolution protein and lipid models that shows high performance on graphics processing unit (GPU) machines. Benchmark tests showed that OpenCafeMol with one GPU can be 2 orders of magnitude faster than the corresponding simulations on a typical CPU machine. The method was applied to vesicle fusion mediated by a SNARE complex with promising results.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144625353","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":"rsRNASP1: a distance and dihedral dependent statistical potential for RNA 3D structure evaluation.","authors":"En Lou,Chen-Chen Zheng,Shixiong Yu,Ya-Lan Tan,Zhi-Jie Tan","doi":"10.1016/j.bpj.2025.07.013","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.07.013","url":null,"abstract":"Knowledge-based statistical potentials have been shown to be rather important for RNA 3-dimensional (3D) structure prediction and evaluation. Recently, several statistical potentials/scoring functions have been developed for RNA 3D structure evaluation, while their performances are still at an unsatisfied level for the datasets from various 3D structure prediction methods. In this work, we developed an all-atom distance and torsion-angle dependent statistical potential with residue separation for RNA 3D structure evaluation, named as rsRNASP1, through considering torsion angles for the backbone, sugar ring and base to involve local structure features. The extensive examinations against available RNA test datasets show that rsRNASP1 has an overall higher performance than existing top statistical potentials/scoring functions in identifying native/near-native structures and ranking the decoy structures. Especially, rsRNASP1 shows the apparently improved performance on a new dataset from the CASP15 competition. rsRNASP1 is available at https://github.com/Tan-group/rsRNASP1.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"94 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144622022","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":"Tracing the U-turns: A New Approach for Calculating the Magnetic Moment of Magnetotactic Bacteria.","authors":"Silverio Johnson,Jay X Tang","doi":"10.1016/j.bpj.2025.07.006","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.07.006","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"13 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144612850","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":"Alpha-Synuclein Fibril Structures Cluster into Distinct Classes","authors":"Moses H. Milchberg, Owen A. Warmuth, Collin G. Borcik, Dhruva D. Dhavale, Elizabeth R. Wright, Paul T. Kotzbauer, Chad M. Rienstra","doi":"10.1016/j.bpj.2025.07.007","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.07.007","url":null,"abstract":"The accumulation of Alpha-synuclein (Asyn) fibrils is the defining pathologic feature in Parkinson Disease (PD), Lewy Body Dementia (LBD), and Multiple System Atrophy (MSA). As such, the process of Asyn fibril formation has been an important research area and fibrils themselves have become attractive targets for disease diagnosis and therapeutic intervention. Due to the presence of mixed populations of fibrillar proteins associated with neurodegenerative diseases in brain tissue, high-resolution structures of Asyn fibrils are essential for the design of high-specificity imaging and therapeutic agents. Approximately one hundred high-resolution solid-state NMR (SSNMR) spectroscopy and cryo-electron microscopy (cryo-EM) structures of Asyn fibrils have been deposited to the Protein Databank (PDB); intriguingly there is significant polymorphism among them. Understanding the molecular makeup and characteristic features of each structural polymorph can determine conserved structural motifs which can be used as templates to design ligands with high specificity for clinical use. Utilizing standard alignment tools and density-based clustering approaches, we objectively classify fibril structures by tertiary structure type. We find that 84% of the structures cluster into two polymorph classes. Within each class, additional subtle variations are observed which position sidechains in specific, conserved orientations, well poised as druggable targets. Furthermore, we find that the conserved structural motifs associated with each class are found in all but one published Asyn fibril structure. We consider these classifications and conserved motifs in the context of disease-relevant fibril structures and offer a perspective on the utility of <ce:italic>in vitro</ce:italic> fibrils as substrates for drug development and models for disease pathogenesis.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"29 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144621933","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":"Dynamic Nature of Staphylococcus aureus Type I Signal Peptidases","authors":"Jesper J. Madsen, Wenqi Yu","doi":"10.1016/j.bpj.2025.07.008","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.07.008","url":null,"abstract":"Molecular dynamics simulations are used to interrogate the dynamic nature of <ce:italic>Staphylococcus aureus</ce:italic> Type I signal peptidases, SpsA and SpsB, including the impact of the P29S mutation of SpsB. Fluctuations and plasticity- rigidity characteristics vary among the proteins, particularly in the extracellular domain. Intriguingly, the P29S mutation, which influences susceptibility to arylomycin antibiotics, affects the mechanically coupled motions in SpsB. The integrity of the active site is crucial for catalytic competency, and variations in sampled structural conformations among the proteins are consistent with diverse peptidase capabilities among the two SpsB variants. We also explored the intricate interactions between the proteins and the model <ce:italic>S. aureus</ce:italic> membrane. It was observed that certain membrane-inserted residues in the loop around residue 50 (50s) and C-terminal loops, beyond the transmembrane domain, give rise to direct interactions with lipids in the bilayer membrane. Our findings are discussed in the context of functional knowledge about these signal peptidases, offering additional understanding of dynamic aspects relevant to some cellular processes with potential implications for drug targeting strategies and future experimental validation.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"47 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144621915","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 role of ester- vs. ether-linked phospholipids in the ability of biological membranes to accept protons and support proton diffusion.","authors":"Ambili Ramanthrikkovil Variyam,Mario Mencía,Nadav Amdursky","doi":"10.1016/j.bpj.2025.07.005","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.07.005","url":null,"abstract":"In biology, the distribution of ester-linked vs. ether-linked phospholipids is meaningful, such as in the abundance of ether-linked phospholipids in archaea vs. ester-linked phospholipids in bacteria/eukarya, and the presence of ether-linked phospholipids in some tissues of higher eukaryotes. Owing to biological membranes' capability of proton acceptance and supporting proton diffusion (PD) on their surface, e.g., in bioenergetics, it was envisioned that the phospholipid linkage might condition the proton transfer (PT) and PD properties. Here, we explore how and if such differences in membrane composition result in attenuation in the PT/PD properties of biological membranes by using a light-gated membrane-tethered proton donor. We reveal that the PT/PD properties differ between the membranes and between the two phases of the membranes (liquid vs. gel phase). At the liquid phase, we found that the headgroup dominates the PT/PD properties, whereas the ester-/ether-linkage has no substantial role. However, at the gel solid phase, such linkage has a significant role in determining both the PT from the probe to the membrane and the subsequent PD properties. Surprisingly, we found that the PT from the probe to the surface of the ether-linked lipid membrane was faster than that of the ester-linked lipid membrane. We explain this finding by the extracted dimensionality of PD. We show that in the gel phase, the ester-linked lipids create a proton pathway with PD dimensionality close to unity, resulting in poor PT, whereas the ether-linked lipids allow lateral PD and a faster PT. The PT/PD properties of the ether-linked lipid membranes also appear mostly insensitive to exterior bulk protons, which might be ascribed to the inner polar part of such membranes. Since bioenergetics is fundamental within cells, the different capabilities of the membranes to support PT/PD might explain the evolutionary constraints of their formation and their presence in certain mammalian tissues.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"1 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144594427","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":"A coarse-grained model for simulations of phosphorylated disordered proteins.","authors":"Arriën Symon Rauh, Gustav Stausbøll Hedemark, Giulio Tesei, Kresten Lindorff-Larsen","doi":"10.1016/j.bpj.2025.07.001","DOIUrl":"10.1016/j.bpj.2025.07.001","url":null,"abstract":"<p><p>Protein phosphorylation is a common and essential post-translational modification that affects biochemical properties and regulates biological activities. Phosphorylation is particularly common for intrinsically disordered proteins and can significantly modulate their function and potential to interact with binding partners. To understand the biophysical origins of how phosphorylation of disordered proteins influences their function, it is valuable to investigate how the modifications lead to changes in their conformational ensembles. Here, we have used a top-down data-driven approach to develop a coarse-grained molecular dynamics model compatible with the CALVADOS protein simulation model to study the effects of serine and threonine phosphorylation on the global structural properties of disordered proteins. We parameterize the model using experimental data on the effects of phosphorylation on global dimensions. By comparing with baseline models and simulations using the phosphomimetics aspartate and glutamate, we show that the effect of phosphorylation on the global dimensions of disordered proteins is mostly driven by the additional charge. We envisage that our model can be applied to study the effects of phosphorylation of disordered proteins at the proteome scale as well as to study the important roles of protein phosphorylation on phase separation.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590373","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":"Enzyme kinetics model for the coronavirus main protease including dimerization and ligand binding.","authors":"Van N T La, Lulu Kang, David D L Minh","doi":"10.1016/j.bpj.2025.06.040","DOIUrl":"10.1016/j.bpj.2025.06.040","url":null,"abstract":"<p><p>The coronavirus main protease (MPro) plays a pivotal role in viral replication and is the target of multiple antiviral drug discovery campaigns against SARS-CoV-2. In some species, CRCs of MPro enzymatic activity can exhibit biphasic behavior in which low ligand concentrations activate the enzyme, whereas higher ones inhibit it. While this behavior has been attributed to ligand-induced dimerization, quantitative enzyme kinetics models have not been fit to it. Here, we develop a kinetic model integrating dimerization and ligand binding. We perform a Bayesian regression to globally fit the model to multiple types of biochemical and biophysical data. The reversible covalent inhibitor GC376 strongly induces dimerization and binds to the dimer with positive cooperativity. In contrast, the fluorescent peptide substrate has a minor effect on dimerization but binds to the dimer with negative cooperativity. The biphasic concentration response curve occurs because, compared with substrate, the inhibitor accelerates turnover in the opposite catalytic site.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144567029","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}