bioRxiv - Biophysics最新文献_第4页

The molecular origin of body temperature in homeothermic species 恒温物种体温的分子起源

bioRxiv - Biophysics Pub Date : 2024-09-10 DOI: 10.1101/2024.09.10.612206

Gerhard Michael Artmann, Oliver H. Weiergraeber, Samar Abdullah M. Damiati, Ipek Seda Firat, Aysegul Artmann

引用次数: 0

Automated measurement of cardiomyocyte monolayer contraction using the Exeter Multiscope 使用 Exeter Multiscope 自动测量心肌细胞单层收缩力

bioRxiv - Biophysics Pub Date : 2024-09-10 DOI: 10.1101/2024.09.09.611998

Alexander D Corbett, David Horsell, Taylor Watters, Shahrum Ghasemi, Lewis Henderson, Sharika Mohanan, Caroline Mullenbroich, Gil Bub, Francis Burton, Godfrey L Smith

{"title":"Automated measurement of cardiomyocyte monolayer contraction using the Exeter Multiscope","authors":"Alexander D Corbett, David Horsell, Taylor Watters, Shahrum Ghasemi, Lewis Henderson, Sharika Mohanan, Caroline Mullenbroich, Gil Bub, Francis Burton, Godfrey L Smith","doi":"10.1101/2024.09.09.611998","DOIUrl":"https://doi.org/10.1101/2024.09.09.611998","url":null,"abstract":"We apply a novel microscope architecture, the Exeter Multiscope, to the problem of acquiring image data in rapid succession from nine wells of a 96 well plate. We demonstrate that the new microscope can detect contraction in cardiomyocyte monolayers which have been plated into these wells. Each well is sampled using 500 x 500 pixels across a 1.4 x 1.4 mm field of view, acquired in three colours at 3.7 Hz per well. The use of multiple illumination wavelengths provides post-hoc focus selection, further increasing the level of automation. The performance of the Exeter Multiscope is benchmarked against industry standard methods using a commercial microscope with a motorised stage and demonstrates that the Multiscope can acquire data almost 40 times faster. The data from both Multiscope and the commercial systems are processed by a 'pixel variance' algorithm that uses information from the pixel value variability over time to determine the timing and amplitude of tissue contraction. This algorithm is also benchmarked against an existing algorithm that employs an absolute difference measure of tissue contraction.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178211","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}

引用次数: 0

The Role of Cholesterol in M2 Clustering and Viral Budding Explained 胆固醇在 M2 聚类和病毒萌发中的作用解析

bioRxiv - Biophysics Pub Date : 2024-09-10 DOI: 10.1101/2024.09.09.611993

Dimitrios Kolokouris, Iris Elpida Kalederoglou, Anna L Duncan, Robin A. Corey, Mark Sansom, Antonios Kolocouris

{"title":"The Role of Cholesterol in M2 Clustering and Viral Budding Explained","authors":"Dimitrios Kolokouris, Iris Elpida Kalederoglou, Anna L Duncan, Robin A. Corey, Mark Sansom, Antonios Kolocouris","doi":"10.1101/2024.09.09.611993","DOIUrl":"https://doi.org/10.1101/2024.09.09.611993","url":null,"abstract":"The proton-conducting domain of the influenza A M2 homotetrameric channel (M2TM-AH; residues 22-62), consisting of four transmembrane (TM; residues 22-46) and four amphipathic helices (AHs; residues 47-62), promotes the release of viral RNA via acidification. Previous studies have also proposed the formation of clusters of M2 channels in the budding neck areas in raft-like domains of the plasma membrane, 1,2 which are rich in cholesterol, resulting in cell membrane scission and viral release. Experiments showed that cholesterol has a significant contribution to lipid bilayer undulations in viral buds suggesting a significant role for cholesterol in the budding process. However, a clear explanation of membrane curvature effect based on the distribution of cholesterol around M2TM-AH clusters is lacking. Using coarse-grained molecular dynamics simulations of M2TM-AH in bilayers, we observed that M2 channels form specific clusters with conical shapes, driven by attraction of their amphipathic helices (AHs). We showed that cholesterol stabilized the formation of M2 channel clusters, by filling and bridging the conical gap between M2 channels at specific sites in the N-terminals of adjacent channels or via the C-terminal region of TM and AHs, the latter sites displaying longer interaction time and higher stability. Potential of mean force calculations showed that when cholesterols occupy the identified interfacial binding sites between two M2 channels, the dimer is stabilized by 11 kJ/mol. This translates to the cholesterol-bound dimer being populated by almost two orders of magnitude compared to a dimer lacking cholesterol. We demonstrated that the cholesterol bridged M2 channels can exert lateral force on the surrounding membrane to induce the necessary negative Gaussian curvature profile which permits the spontaneous scission of the catenoid membrane neck and leads to viral buds and scission.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178212","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}

引用次数: 0

Elucidating the Differential Impacts of Equivalent Gating-Charge Mutations in Voltage-Gated Sodium Channels 阐明电压门控钠通道中等价门控电荷突变的不同影响

bioRxiv - Biophysics Pub Date : 2024-09-10 DOI: 10.1101/2024.09.09.612021

Eslam Elhanafy, Amin Akbari Ahangar, Rebecca Roth, Tamer M Gamal El-Din, John R Bankston, Jing Li

{"title":"Elucidating the Differential Impacts of Equivalent Gating-Charge Mutations in Voltage-Gated Sodium Channels","authors":"Eslam Elhanafy, Amin Akbari Ahangar, Rebecca Roth, Tamer M Gamal El-Din, John R Bankston, Jing Li","doi":"10.1101/2024.09.09.612021","DOIUrl":"https://doi.org/10.1101/2024.09.09.612021","url":null,"abstract":"Voltage-gated sodium (Nav) channels are pivotal for cellular signaling and mutations in Nav channels can lead to excitability disorders in cardiac, muscular, and neural tissues. A major cluster of pathological mutations localizes in the voltage-sensing domains (VSDs), resulting in either gain-of-function (GoF), loss-of-function (LoF) effects, or both. However, the mechanism behind this functional divergence of mutations at equivalent positions remains elusive. Through hotspot analysis, we identified three gating charges (R1, R2, and R3) as major mutational hotspots in VSDs. The same amino-acid substitutions at equivalent gating-charge positions in VSDI and VSDII of the cardiac sodium channel Nav1.5 show differential gating-property impacts in electrophysiology measurements. We conducted 120 μs molecular dynamics (MD) simulations on wild-type and six mutants to elucidate the structural basis of their differential impacts. Our μs-scale MD simulations with applied external electric fields captured VSD state transitions and revealed the differential structural dynamics between equivalent R-to-Q mutants. Notably, we observed transient leaky conformations in some mutants during structural transitions, offering a detailed structural explanation for gating-pore currents. Our salt-bridge network analysis uncovered VSD-specific and state-dependent interactions among gating charges, countercharges, and lipids. This detailed analysis elucidated how mutations disrupt critical electrostatic interactions, thereby altering VSD permeability and modulating gating properties. By demonstrating the crucial importance of considering the specific structural context of each mutation, our study represents a significant leap forward in understanding structure-function relationships in Nav channels. Our work establishes a robust framework for future investigations into the molecular basis of ion channel-related disorders.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178179","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}

引用次数: 0

A fluid droplet harvests the force generated by shrinking microtubules in living cells 液滴能捕捉活细胞中微管收缩产生的力

bioRxiv - Biophysics Pub Date : 2024-09-10 DOI: 10.1101/2024.09.09.612121

Katherine Morelli, Sandro M Meier, Angela Zhao, Madhurima Choudhury, M Willis, Yves Barral, Jackie Vogel

引用次数: 0

Effects of multistability, absorbing boundaries and growth on Turing pattern formation 多稳态、吸收边界和增长对图灵模式形成的影响

bioRxiv - Biophysics Pub Date : 2024-09-10 DOI: 10.1101/2024.09.09.611947

Martina Oliver Huidobro, Robert G. Endres

{"title":"Effects of multistability, absorbing boundaries and growth on Turing pattern formation","authors":"Martina Oliver Huidobro, Robert G. Endres","doi":"10.1101/2024.09.09.611947","DOIUrl":"https://doi.org/10.1101/2024.09.09.611947","url":null,"abstract":"Turing patterns are a fundamental concept in developmental biology, describing how homogeneous tissues develop into self-organized spatial patterns. However, the classical Turing mechanism, which relies on linear stability analysis, often fails to capture the complexities of real biological systems, such as multistability, non-linearities, growth, and boundary conditions. Here, we explore the impact of these factors on Turing pattern formation, contrasting linear stability analysis with numerical simulations based on a simple reaction-diffusion model, motivated by synthetic gene-regulatory pathways. We demonstrate how non-linearities introduce multistability, leading to unexpected pattern outcomes not predicted by the traditional Turing theory. The study also examines how growth and realistic boundary conditions influence pattern robustness, revealing that different growth regimes and boundary conditions can disrupt or stabilize pattern formation. Our findings are critical for understanding pattern formation in both natural and synthetic biological systems, providing insights into engineering robust patterns for applications in synthetic biology.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178209","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}

引用次数: 0

In cell NMR reveals cells selectively amplify and structurally remodel amyloid fibrils 细胞内核磁共振显示细胞会选择性地放大淀粉样蛋白纤维并对其进行结构重塑

bioRxiv - Biophysics Pub Date : 2024-09-10 DOI: 10.1101/2024.09.09.612142

Shoyab Ansari, Dominique Lagasca, Rania Dumarieh, Yiling Xiao, Sakshi Krishna, Yang Li, Kendra K Frederick

{"title":"In cell NMR reveals cells selectively amplify and structurally remodel amyloid fibrils","authors":"Shoyab Ansari, Dominique Lagasca, Rania Dumarieh, Yiling Xiao, Sakshi Krishna, Yang Li, Kendra K Frederick","doi":"10.1101/2024.09.09.612142","DOIUrl":"https://doi.org/10.1101/2024.09.09.612142","url":null,"abstract":"Amyloid forms of α-synuclein adopt different conformations depending on environmental conditions. Advances in structural biology have accelerated fibril characterization. However, it remains unclear which conformations predominate in biological settings because current methods typically not only require isolating fibrils from their native environments, but they also do not provide insight about flexible regions. To address this, we characterized α-syn amyloid seeds and used sensitivity enhanced nuclear magnetic resonance to investigate the amyloid fibrils resulting from seeded amyloid propagation in different settings. We found that the amyloid fold and conformational preferences of flexible regions are faithfully propagated in vitro and in cellular lysates. However, seeded propagation of amyloids inside cells led to the minority conformation in the seeding population becoming predominant and more ordered, and altered the conformational preferences of flexible regions. The examination of the entire ensemble of protein conformations in biological settings that is made possible with this approach may advance our understanding of protein misfolding disorders and facilitate structure-based drug design efforts.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178180","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}

引用次数: 0

LLPS REDIFINE allows the biophysical characterization of multicomponent condensates without tags or labels LLPS REDIFINE 可对多组分缩合物进行生物物理表征，无需标记或标签

bioRxiv - Biophysics Pub Date : 2024-09-10 DOI: 10.1101/2024.09.10.612223

Mihajlo Novakovic, Nina Han, Nina Chiara Kathe, Yinan Ni, Leonidas Emmanouilidis, Frederic H.-T. Allain

{"title":"LLPS REDIFINE allows the biophysical characterization of multicomponent condensates without tags or labels","authors":"Mihajlo Novakovic, Nina Han, Nina Chiara Kathe, Yinan Ni, Leonidas Emmanouilidis, Frederic H.-T. Allain","doi":"10.1101/2024.09.10.612223","DOIUrl":"https://doi.org/10.1101/2024.09.10.612223","url":null,"abstract":"Liquid-liquid phase separation (LLPS) phenomenon plays a vital role in multiple cell biology processes, providing a mechanism to concentrate biomolecules and promote cellular reactions locally. Despite its significance in biology, there is a lack of conventional techniques suitable for studying biphasic samples in their biologically relevant form. Here, we present a label-free and non-invasive approach to characterize protein, RNA and water in biomolecular condensates termed LLPS REstricted DIFusion of INvisible speciEs (REDIFINE). Relying on diffusion NMR measurements, REDIFINE exploits the exchange dynamics between the condensed and dispersed phases to allow the determination of not only diffusion constants in both phases but also the fractions of the species, the average radius of the condensed droplets and the exchange rate between the phases. We can also access the concentration of proteins in both phases. Observing proteins, RNAs, water, and even small molecules, REDIFINE analysis allows a rapid biophysical characterization of multicomponent condensates which is important to understand their functional roles. In comparing multiple systems, REDIFINE reveals that folded RNA-binding proteins form smaller and more dynamic droplets compared to the disordered ones. In addition, REDIFINE proved to be valuable beyond LLPS for the determination of binding constants in soluble protein-RNA without the need for titration.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178176","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}

引用次数: 0

The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops is Determined by Ligand Binding and Interprotomer Allostery 配体结合和原体间异构决定了 SARS-CoV-2 主蛋白酶活性位点环的构象空间

bioRxiv - Biophysics Pub Date : 2024-09-10 DOI: 10.1101/2024.09.09.612101

Ethan Lee, Sarah Rauscher

{"title":"The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops is Determined by Ligand Binding and Interprotomer Allostery","authors":"Ethan Lee, Sarah Rauscher","doi":"10.1101/2024.09.09.612101","DOIUrl":"https://doi.org/10.1101/2024.09.09.612101","url":null,"abstract":"The main protease (MPro) of SARS-CoV-2 is essential for viral replication and is, therefore, an important drug target. Here, we investigate two flexible loops in MPro that play a role in catalysis. Using all-atom molecular dynamics simulations, we analyze the structural ensemble of MPro in an apo state and substrate-bound state. We find that the flexible loops can adopt open, intermediate (partly open) and closed conformations in solution, which differs from the partially closed state observed in crystal structures of MPro. When the loops are in closed or intermediate states, the catalytic residues are more likely to be in close proximity, which is crucial for catalysis. Additionally, we find that substrate binding to one protomer of the homodimer increases the frequency of intermediate states in the bound protomer, while also affecting the structural propensity of the apo protomer's flexible loops. Using dynamic network analysis, we identify multiple allosteric pathways connecting the two active sites of the homodimer. Common to these pathways is an allosteric hotspot involving the N-terminus, a critical region that comprises part of the binding pocket. Taken together, the results of our simulation study provide detailed insight into the relationships between the flexible loops and substrate binding in a prime drug target for COVID-19.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178174","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}

引用次数: 0

Intracellular dry mass density increases under growth-induced pressure 细胞内干物质密度在生长诱导压力下增加

bioRxiv - Biophysics Pub Date : 2024-09-10 DOI: 10.1101/2024.09.10.612234

Hyojun Kim, Baptiste Alric, Nolan Chan, Julien Roul, Morgan Delarue

引用次数: 0