bioRxiv - Biophysics最新文献

Mechanical Profiling of Biopolymer Condensates through Acoustic Trapping 通过声学捕获对生物聚合物凝结物进行机械剖面分析

bioRxiv - Biophysics Pub Date : 2024-09-19 DOI: 10.1101/2024.09.16.613217

Kichitaro Nakajima, Tomas Sneideris, Lydia L. Good, Nadia Aicha Erkamp, Hirotsugu Ogi, Tuomas Knowles

{"title":"Mechanical Profiling of Biopolymer Condensates through Acoustic Trapping","authors":"Kichitaro Nakajima, Tomas Sneideris, Lydia L. Good, Nadia Aicha Erkamp, Hirotsugu Ogi, Tuomas Knowles","doi":"10.1101/2024.09.16.613217","DOIUrl":"https://doi.org/10.1101/2024.09.16.613217","url":null,"abstract":"Characterizing the mechanical properties of single colloids is a central problem in soft matter physics. It also plays a key role in cell biology through biopolymer condensates, which function as membraneless compartments. Such systems can also malfunction, leading to the onset of a number of diseases, including many neurodegenerative diseases; the functional and pathological condensates are commonly differentiated by their mechanical signature. Probing the mechanical properties of biopolymer condensates at the single particle level has, however, remained challenging. In this study, we demonstrate that acoustic trapping can be used to profile the mechanical properties of single condensates in a contactless manner. We find that acoustic fields exert the acoustic radiation force on condensates, leading to their migration to a trapping point where acoustic potential energy is minimized. Furthermore, our results show that the Brownian motion fluctuation of condensates in an acoustic potential well is an accurate probe for their bulk modulus. We demonstrate that this framework can detect the change in the bulk modulus of polyadenylic acid condensates in response to changes in environmental conditions. Our results show that acoustic trapping opens up a novel path to profile the mechanical properties of soft colloids at the single particle level in a non-invasive manner with applications in biology, materials science, and beyond.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255356","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

De-novo design of actively spinning and gyrating spherical micro-vesicles 主动旋转和回旋球形微囊的全新设计

bioRxiv - Biophysics Pub Date : 2024-09-19 DOI: 10.1101/2024.09.17.613442

Veerpal Kaur, Subhashree S. Khuntia, Charu Taneja, Abhishek Chaudhuri, K. P. Yogendran, Sabyasachi Rakshit

引用次数: 0

Localization of Albumin with Correlative Super Resolution Light- and Electron Microscopy in the Kidney 用相关超分辨光镜和电子显微镜确定肾脏中白蛋白的位置

bioRxiv - Biophysics Pub Date : 2024-09-19 DOI: 10.1101/2024.09.16.613238

Alexandra N. Birtasu, Utz H. Ermel, Johanna V. Rahm, Anja Seybert, Benjamin Flottmann, Mike Heilemann, Florian Grahammer, Achilleas S Frangakis

{"title":"Localization of Albumin with Correlative Super Resolution Light- and Electron Microscopy in the Kidney","authors":"Alexandra N. Birtasu, Utz H. Ermel, Johanna V. Rahm, Anja Seybert, Benjamin Flottmann, Mike Heilemann, Florian Grahammer, Achilleas S Frangakis","doi":"10.1101/2024.09.16.613238","DOIUrl":"https://doi.org/10.1101/2024.09.16.613238","url":null,"abstract":"The functioning of vertebrate life relies on renal filtration of surplus fluid and elimination of low-molecular-weight waste products, while keeping serum proteins in the blood. In disease, however, there is leak of serum proteins and tracing them to identify the leaking position within tissue with a nanometer resolution poses a significant challenge. Correlative microscopy integrates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Using chemical tagging of albumin with synthetic fluorophores we achieve protein-specific labeling that preserve their post-embedding fluorescence after high-pressure freezing and freeze-substitution of murine kidney tissue. Using advanced registration techniques for super-resolution correlative light and electron microscopy, we can localize the labeled albumin with a high precision in the x-y plane of electron micrographs and cartograph its distribution. Thereby we can quantify the albumin concentration and measure a linear reduction gradient across the kidney filtration barrier. Our study shows the feasibility of combining different microscopy contrasts for tracing fluorescently labeled protein markers with super resolution in various tissue samples and opens new perspectives for correlative imaging in volume electron microscopy.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255303","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

Cell-derived matrices mechanics as a functional read-out in Collagen VI-related Congenital Muscular Dystrophies 细胞衍生基质力学作为胶原蛋白 VI 相关先天性肌肉萎缩症的功能读数

bioRxiv - Biophysics Pub Date : 2024-09-18 DOI: 10.1101/2024.09.13.612824

Tom White, Aristides Lopez-Marquez, Carmen Badosa, Cecilia Jimenez-Mallebrera, Josep Samitier, Marina I Giannotti, Anna Lagunas

{"title":"Cell-derived matrices mechanics as a functional read-out in Collagen VI-related Congenital Muscular Dystrophies","authors":"Tom White, Aristides Lopez-Marquez, Carmen Badosa, Cecilia Jimenez-Mallebrera, Josep Samitier, Marina I Giannotti, Anna Lagunas","doi":"10.1101/2024.09.13.612824","DOIUrl":"https://doi.org/10.1101/2024.09.13.612824","url":null,"abstract":"Collagen VI-related congenital muscular dystrophies (COL6-RDs) are a set of neuromuscular conditions caused by pathogenic variants found in any of the three COL6 genes. The phenotypic expression of the disease does not directly correlate with the genetic background producing an overlapping spectrum of clinical phenotypes that goes from the mild Bethlem myopathy (BM) to the severe Ulrich congenital muscular dystrophy (UCMD). Diagnosis includes genetic confirmation of the disease and categorization of the phenotype based on maximum motor ability. The development of new tools able to identify phenotype traits can significantly contribute to the diagnosis and prognosis of COL6-RDs. Mutations occurring in COL6 genes result in deficiency or dysfunction of COL6 incorporated into the extracellular matrix (ECM) of connective tissues, affecting its fibrillar structure. Our research group has established personalized pre-clinical models of COL6-RDs based on cell-derived matrices (CDMs), which allowed the direct observation of the fibrillar organization of the ECM in samples derived from patients, and to compare features amongst different phenotypes. Here, we have characterized the mechanical properties of CDMs from patients using atomic force microscopy-based force spectroscopy (AFM-FS). We observed that the elastic modulus (E) varies with the phenotype, and that it correlates with COL6 organization in the CDMs. We additionally used AFM-FS to evaluate matrices derived from genetically edited cells, which resulted in E value restoration compared to control samples. Altogether, these results anticipate the potential of mechanical analysis of CDMs as a complementary clinical tool, providing phenotypic information about COL6-RDs and their response to gene therapies.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255305","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 combined approach to extract rotational dynamics of globular proteins undergoing liquid-liquid phase separation 提取发生液-液相分离的球状蛋白质旋转动力学的组合方法

bioRxiv - Biophysics Pub Date : 2024-09-18 DOI: 10.1101/2024.09.17.613388

Dominik Gendreizig, Abhishek Kalarikkal, Simon L. Holtbrügge, Saumyak Mukherjee, Laura Galazzo, Svetlana Kucher, Arnulf Rosspeintner, Lars V. Schäfer, Enrica Bordignon

{"title":"A combined approach to extract rotational dynamics of globular proteins undergoing liquid-liquid phase separation","authors":"Dominik Gendreizig, Abhishek Kalarikkal, Simon L. Holtbrügge, Saumyak Mukherjee, Laura Galazzo, Svetlana Kucher, Arnulf Rosspeintner, Lars V. Schäfer, Enrica Bordignon","doi":"10.1101/2024.09.17.613388","DOIUrl":"https://doi.org/10.1101/2024.09.17.613388","url":null,"abstract":"The formation of protein condensates (droplets) via liquid-liquid phase separation (LLPS) is a commonly observed phenomenon in vitro. Changing the environmental properties with cosolutes, molecular crowders, protein partners, temperature, pressure, etc. was shown to favour or disfavour the formation of protein droplets by fine-tuning the water-water, water-protein and protein-protein interactions. Therefore, these environmental properties and their spatiotemporal fine-tuning are likely to be important also in a cellular context at the existing protein expression levels. One of the key physicochemical properties of biomolecules impacted by molecular crowding is diffusion, which determines the viscoelastic behaviour of the condensates. Here we investigate the change in the rotational diffusion of γD-crystallin, undergoing LLPS in vitro in aqueous solutions in absence and presence of cosolutes. We studied its rotational dynamics using molecular dynamics simulations (MD), electron paramagnetic resonance (EPR) spectroscopy and fluorescence spectroscopy. MD simulations performed under dilute and crowded conditions show that the rotational diffusion of crystallin in water is retarded by one to two orders of magnitude in the condensed phase. To obtain the rotational dynamics in the dilute phase we used fluorescence anisotropy and to extract the retardation factor in in the condensed phase we used spin-labeled γD-crystallin proteins as EPR viscosity nanoprobes. Aided by a viscosity nanoruler calibrated with solutions at increasing sucrose concentrations, we validate the rotational diffusion retardation predicted by MD simulations. This study underlines the predictive power of MD simulations and showcases the use of a sensitive EPR nanoprobe to extract the viscosity of biomolecular condensates.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255150","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

Unlocking precision: How corneal cell area analysis revolutionises post-transplant stem cell monitoring 实现精准：角膜细胞面积分析如何彻底改变移植后干细胞监测

bioRxiv - Biophysics Pub Date : 2024-09-18 DOI: 10.1101/2024.09.17.612429

Patrick Parkinson, Irina Makarenko, Oliver J Baylis, Gustavo S Figueiredo, Majlinda Lako, Anvar Shukurov, Francisco C Figueiredo, Laura E Wadkin

{"title":"Unlocking precision: How corneal cell area analysis revolutionises post-transplant stem cell monitoring","authors":"Patrick Parkinson, Irina Makarenko, Oliver J Baylis, Gustavo S Figueiredo, Majlinda Lako, Anvar Shukurov, Francisco C Figueiredo, Laura E Wadkin","doi":"10.1101/2024.09.17.612429","DOIUrl":"https://doi.org/10.1101/2024.09.17.612429","url":null,"abstract":"The corneal epithelium is maintained by limbal stem cells (LSCs). Dysfunction of the LSCs, resulting from chemical and thermal burns, contact lens-related disease, congenial disorders, among other conditions, leads to limbal stem cell deficiency (LSCD), a sight-threatening condition. An effective treatment of LSCD, with 76% of patients reporting regained sight up to 24 months after the operation, consists of transplanting ex-vivo cultured LSCs from the patient's other healthy eye (i.e. autologous) or donor (i.e. allogeneic) to the affected eye. The post-operative assessment of corneal recovery is crucial but relies on ponderous and generally subjective visual inspection of a large number of microscopic images of the corneal epithelial cells, relying on the personal experience of the practitioner to interpret imprecise, qualitative diagnostic criteria. From a unique library of 100,000 cornea cell images from 34 patients, we have randomly selected 10 individuals (3,668 images) to demonstrate that the frequency distribution of the epithelial cell areas is a sensitive diagnostic tool of the corneal epithelium status. After a successful operation the distribution of cell areas is rather flat, reflecting an anomalously wide range of cell areas. As the cornea recovers, the frequency distribution becomes narrower with high statistical confidence and eventually approaches that of the healthy cornea. The corneal epithelial cell shape is independent of the cornea status despite a widespread expectation that healthy cells have a hexagonal shape. We also show that the corneal epithelial cell area distribution and its variation with the depth within the cornea are specific to each patient.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255110","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

From Monomers to Oligomers: Structural Mechanism of Receptor-Triggered MyD88 Assembly in Innate Immune Signaling 从单体到寡聚体：先天性免疫信号中受体触发 MyD88 组装的结构机制

bioRxiv - Biophysics Pub Date : 2024-09-18 DOI: 10.1101/2024.09.13.612588

Kazuki Kasai, Kayo Imamura, Masatoshi Uno, Naotaka Sekiyama, Tomoko Miyata, Fumiaki Makino, Ryusei Yamada, Yoshiki Takahashi, Noriyuki Kodera, Keiichi Namba, Hidenori Ohnishi, Akihiro Narita, Hiroki Konno, Hidehito Tochio

{"title":"From Monomers to Oligomers: Structural Mechanism of Receptor-Triggered MyD88 Assembly in Innate Immune Signaling","authors":"Kazuki Kasai, Kayo Imamura, Masatoshi Uno, Naotaka Sekiyama, Tomoko Miyata, Fumiaki Makino, Ryusei Yamada, Yoshiki Takahashi, Noriyuki Kodera, Keiichi Namba, Hidenori Ohnishi, Akihiro Narita, Hiroki Konno, Hidehito Tochio","doi":"10.1101/2024.09.13.612588","DOIUrl":"https://doi.org/10.1101/2024.09.13.612588","url":null,"abstract":"MyD88 plays a pivotal role in Toll-like receptor (TLR) and interleukin-1 family signaling through its oligomerization upon receptor activation, leading to downstream protein recruitment. The Toll/interleukin-1 receptor domain of MyD88 (TIRMyD88) is responsible for this receptor-mediated oligomerization, but the detailed mechanism involved remains elusive. We investigated the structure of TIRMyD88 oligomers and their interactions with TLRs. Cryoelectron microscopy revealed that tandemly arrayed TIRMyD88 subunits formed an antiparallel double-stranded filament that could further form rings and cylindrical filaments. Moreover, the self-assembly of TIRMyD88 in vitro was markedly accelerated by dimeric rather than monomeric receptor TIRs, possibly reflecting the signal initiation step in vivo. High-speed atomic force microscopy further captured the dynamic processes of oligomerization of TIRMyD88, in addition to its direct interaction with the receptor TIRs. Based on these results, a novel regulatory mechanism of TIRMyD88 oligomerization underlying the signal initiation step was revealed.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255304","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

Dynamics of microcompartment formation at the mitosis-to-G1 transition 有丝分裂向 G1 转变过程中微室形成的动态变化

bioRxiv - Biophysics Pub Date : 2024-09-16 DOI: 10.1101/2024.09.16.611917

Viraat Y Goel, Nicholas G Aboreden, James M Jusuf, Haoyue Zhang, Luisa Mori, Leonid A Mirny, Gerd Blobel, Edward J Banigan, Anders Sejr Hansen

{"title":"Dynamics of microcompartment formation at the mitosis-to-G1 transition","authors":"Viraat Y Goel, Nicholas G Aboreden, James M Jusuf, Haoyue Zhang, Luisa Mori, Leonid A Mirny, Gerd Blobel, Edward J Banigan, Anders Sejr Hansen","doi":"10.1101/2024.09.16.611917","DOIUrl":"https://doi.org/10.1101/2024.09.16.611917","url":null,"abstract":"As cells exit mitosis and enter G1, mitotic chromosomes decompact and transcription is reestablished. Previously, Hi-C studies showed that essentially all interphase 3D genome features including A/B-compartments, TADs, and CTCF loops, are lost during mitosis. However, Hi-C remains insensitive to features such as microcompartments, nested focal interactions between cis-regulatory elements (CREs). We therefore applied Region Capture Micro-C to cells from mitosis to G1. Unexpectedly, we observe microcompartments in prometaphase, which further strengthen in ana/telophase before gradually weakening in G1. Loss of loop extrusion through condensin depletion differentially impacts microcompartments and large A/B-compartments, suggesting that they are partially distinct. Using polymer modeling, we show that microcompartment formation is favored by chromatin compaction and disfavored by loop extrusion activity, explaining why ana/telophase likely provides a particularly favorable environment. Our results suggest that CREs exhibit intrinsic homotypic affinity leading to microcompartment formation, which may explain transient transcriptional spiking observed upon mitotic exit.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255152","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

Structure of small HBV surface antigen reveals mechanism of dimer formation 小型 HBV 表面抗原的结构揭示了二聚体的形成机制

bioRxiv - Biophysics Pub Date : 2024-09-15 DOI: 10.1101/2024.09.13.612767

Xiao He, Yunlu Kang, Weiyu Tao, Jiaxuan Xu, Xiaoyu Liu, Lei Chen

引用次数: 0

On the coupling between membrane bending and stretching in lipid vesicles 关于脂质囊泡中膜弯曲与拉伸之间的耦合关系

bioRxiv - Biophysics Pub Date : 2024-09-15 DOI: 10.1101/2024.09.13.612881

Håkan Wennerström, Emma Sparr, Joakim Stenhammar

{"title":"On the coupling between membrane bending and stretching in lipid vesicles","authors":"Håkan Wennerström, Emma Sparr, Joakim Stenhammar","doi":"10.1101/2024.09.13.612881","DOIUrl":"https://doi.org/10.1101/2024.09.13.612881","url":null,"abstract":"The formation of a lipid vesicle from a lamellar phase involves a cost in bending energy of 100-1000 times the thermal energy for values of the membrane bending rigidity κ typical for phospholipid bilayers. The bending rigidity of a bilayer is however a strongly decreasing function of its thickness h, and the bilayer can thus reduce its bending energy by stretching (and thus thinning) the bilayer. In this paper, we construct a simple model to describe this mechanism for the coupling between bending and stretching and analyse its effect on the bending energy and thermal fluctuations of spherical lipid vesicles. We show that the bilayer thinning becomes significant for small vesicles, and for a vesicle with radius R<sub>0</sub> ~ 15 nm there is a sizeable thinning of the bilayer compared to the planar state. We furthermore demonstrate how this thinning is associated with a significant decrease in free energy due to the thermally excited bending modes. We argue that this previously unexplored effect can explain the experimentally observed lower limit of achievable vesicle sizes, which eventually become unstable due to the thinning of the bilayer. We also sketch how this effect provides a potential generic mechanism for the strong curvature dependence of protein adsorption to lipid membranes.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255354","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