bioRxiv - Biophysics最新文献_第10页

Snapshots of acetyl-CoA synthesis, the final step of CO2 fixation in the Wood-Ljungdahl pathway 乙酰-CoA合成快照，伍德-荣格达尔途径中二氧化碳固定的最后一步

bioRxiv - Biophysics Pub Date : 2024-08-06 DOI: 10.1101/2024.08.05.606187

Max Dongsheng Yin, Olivier N. Lemaire, José Guadalupe Rosas-Jiménez, Mélissa Belhamri, Anna Shevchenko, Gerhard Hummer, Tristan Wagner, Bonnie J. Murphy

引用次数: 0

Cryo-EM phase-plate images reveal unexpected levels of apparent specimen damage 低温电子显微镜相位板图像显示出意想不到的试样明显损伤程度

bioRxiv - Biophysics Pub Date : 2024-08-06 DOI: 10.1101/2024.08.04.606536

Jonathan Remis, Petar N Petrov, Jessie T Zhang, Jeremy J Axelrod, Hang Cheng, Shahar Sandhaus, Holger Mueller, Robert M Glaeser

{"title":"Cryo-EM phase-plate images reveal unexpected levels of apparent specimen damage","authors":"Jonathan Remis, Petar N Petrov, Jessie T Zhang, Jeremy J Axelrod, Hang Cheng, Shahar Sandhaus, Holger Mueller, Robert M Glaeser","doi":"10.1101/2024.08.04.606536","DOIUrl":"https://doi.org/10.1101/2024.08.04.606536","url":null,"abstract":"Apoferritin (apoF) is commonly used as a test specimen in single-particle electron cryo-microscopy (cryo-EM), since it consistently produces density maps that go to 0.3 nm resolution or higher. When we imaged apoF with a laser phase plate (LPP), however, we observed more severe particle-to-particle variation in the images than we had previously thought to exist. Similarly, we found that images of ribulose bisphosphate carboxylase/oxygenase (rubisco) also exhibited a much greater amount of heterogeneity than expected. By comparison to simulations of images, we verified that the heterogeneity is not explained by the known features of the LPP, shot noise, or differences in particle orientation. We also demonstrate that our specimens are comparable to those previously used in the literature, based on using the final-reconstruction resolution as the metric for evaluation. All of this leads us to the hypothesis that the heterogeneity is due to damage that has occurred either during purification of the specimen or during preparation of the grids. It is not, however, our goal to explain the causes of heterogeneity; rather, we report that using the LPP has made the apparent damage too obvious to be ignored. In hindsight, similar heterogeneity can be seen in images of apoF and the 20S proteasome which others had recorded with a Volta phase plate. We therefore conclude that the increased contrast of phase-plate images (at low spatial frequencies) should also make it possible to visualize, on a single-particle basis, various forms of biologically functional heterogeneity in structure that had previously gone unnoticed.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141945302","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

Structures of TASK-1 and TASK-3 K2P channels provide insight into their gating and dysfunction in disease TASK-1和TASK-3 K2P通道的结构揭示了它们在疾病中的门控和功能障碍

bioRxiv - Biophysics Pub Date : 2024-08-06 DOI: 10.1101/2024.08.05.606641

Peter-Rory Hall, Thibault Jouen-Tachoire, Marcus Schewe, Peter Proks, Thomas Baukrowitz, Elisabeth P Carpenter, Simon Newstead, Karin Rodstrom, Stephen J Tucker

{"title":"Structures of TASK-1 and TASK-3 K2P channels provide insight into their gating and dysfunction in disease","authors":"Peter-Rory Hall, Thibault Jouen-Tachoire, Marcus Schewe, Peter Proks, Thomas Baukrowitz, Elisabeth P Carpenter, Simon Newstead, Karin Rodstrom, Stephen J Tucker","doi":"10.1101/2024.08.05.606641","DOIUrl":"https://doi.org/10.1101/2024.08.05.606641","url":null,"abstract":"TASK-1 and TASK-3 are pH-sensitive Two-Pore Domain (K2P/KCNK) K+ channels. Their functional roles make them promising targets for the treatment of multiple disorders including sleep apnea, pain and atrial fibrillation. Rare genetic mutations in these channels are also associated with neurodevelopmental and hypertensive disorders. A recent crystal structure of TASK-1 revealed a lower 'X-gate' that is a hotspot for missense gain-of-function mutations associated with DDSA (Developmental Delay with Sleep Apnea). However, the structural basis for gating in TASK channels and how they sense extracellular pH to regulate gating have not been fully elucidated. Here, we resolve structures for both the human TASK-1 and TASK-3 channels by cryoEM, as well as for a recurrent TASK-3 variant (G236R) associated with KCNK9 Imprinting Syndrome (formerly referred to as Birk-Barel Syndrome). Combined with functional studies of the X-gating mechanism, these structures not only provide evidence for how a highly-conserved gating mechanism becomes defective in disease, but also provide further insight into the pathway of conformational changes that underlie the pH-dependent inhibition of TASK channel activity.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141945210","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

Buzz Pollination: Investigations of Pollen Expulsion using the Discrete Element Method 嗡嗡授粉：使用离散元素法研究花粉喷出情况

bioRxiv - Biophysics Pub Date : 2024-08-06 DOI: 10.1101/2024.08.01.606085

Caelen G Boucher-Bergstedt, Mark A Jankauski, Erick Johnson

{"title":"Buzz Pollination: Investigations of Pollen Expulsion using the Discrete Element Method","authors":"Caelen G Boucher-Bergstedt, Mark A Jankauski, Erick Johnson","doi":"10.1101/2024.08.01.606085","DOIUrl":"https://doi.org/10.1101/2024.08.01.606085","url":null,"abstract":"Buzz pollination involves the release of pollen from, primarily, poricidal anthers through vibrations generated by certain bee species. Despite previous experimental and numerical studies, the intricacies of pollen dynamics within vibrating anthers remain elusive due to the challenges in observing these small-scale, opaque systems. This research employs the discrete element method (DEM) to simulate the pollen expulsion process in vibrating anthers. By exploring various frequencies and displacement amplitudes, a correlation between the maximum jerk of anther walls and the initial rate of pollen expulsion is observed under translating oscillations. This study highlights that while increased vibration intensity enhances pollen release, the rate of increase diminishes at higher intensities. Our findings also reveal the significant role of pollen-pollen interactions, which account for upwards of one-third of the total collisions. Comparisons between poricidal and pseudoporicidal anther geometries suggest that pore size and shape also influence expulsion rates. This research provides a foundation for more comprehensive models that can incorporate additional factors such as cohesion, adhesion, and Coulomb forces, paving the way for deeper insights into the mechanics of buzz pollination and its variability across different anther types and vibration parameters.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141945209","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

Exact distributions of threshold crossing times of proteins under post-transcriptional regulation by small RNAs 受小 RNA 转录后调控的蛋白质阈值跨越时间的精确分布

bioRxiv - Biophysics Pub Date : 2024-08-06 DOI: 10.1101/2024.08.05.606600

Syed Yunus Ali, Ashok Prasad, Dibyendu Das

{"title":"Exact distributions of threshold crossing times of proteins under post-transcriptional regulation by small RNAs","authors":"Syed Yunus Ali, Ashok Prasad, Dibyendu Das","doi":"10.1101/2024.08.05.606600","DOIUrl":"https://doi.org/10.1101/2024.08.05.606600","url":null,"abstract":"The timings of several cellular events like cell lysis, cell division, or pore formation in endosomes are regulated by the time taken for the relevant proteins to cross a threshold in number or concentration. Since protein synthesis is stochastic, the threshold crossing time is a first passage problem. The exact distributions of these first passage processes have been obtained recently for unregulated and auto-regulated genes. Many proteins are however regulated by post-transcriptional regulation, controlled by small non-coding RNAs (sRNAs). Certain mathematical models of gene expression with post-transcriptional sRNA regulation have been recently exactly mapped to models without sRNA regulation. Utilizing this mapping and the exact distributions, we calculate exact results on fluctuations (full distribution, all cumulants, and characteristic times) of protein threshold crossing times in the presence of sRNA regulation. We derive two interesting predictions from these exact results. We show that the size of the fluctuation of the threshold crossing times have a non-monotonic U-shaped behavior as a function of the rates of binding and unbinding of the sRNA-mRNA complex. Thus there are optimal parameters that minimize noise. Furthermore, the fluctuations in models with sRNA regulation may be higher or lower compared to the model without regulation, depending on the mean protein burst size.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141945208","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

DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study 自发缠绕组蛋白核心的 DNA 更倾向于负超螺旋：布朗动力学研究

bioRxiv - Biophysics Pub Date : 2024-08-06 DOI: 10.1101/2024.08.05.606726

Chunhong Long, Hongqiong Liang, Biao Wan

{"title":"DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study","authors":"Chunhong Long, Hongqiong Liang, Biao Wan","doi":"10.1101/2024.08.05.606726","DOIUrl":"https://doi.org/10.1101/2024.08.05.606726","url":null,"abstract":"In eukaryotes, DNA achieves a highly compact structure primarily due to its winding around the histone cores. The nature wrapping of DNA around histone core form a 1.7 left-handed superhelical turns, contributing to negative supercoiling in chromatin. On the contrary, negative supercoils generated behind the polymerase during transcription may play a role in triggering nucleosome reassembly. To elucidate how supercoils influence the dynamics of wrapping of DNA around the histone cores, we developed a novel model to simulate the intricate interplay between DNA and histone. Our simulations revealed that both positively and negatively supercoiled DNAs are capable of wrapping around histone cores to adopt the nucleosome conformation. Most of all, our findings confirmed a preference for negative supercoiled DNA during nucleosome wrapping, and revealed that the both of the negative writhe and twist are comparatively beneficial to the formation of the DNA wrapping around histone. This advancement in the understanding of spontaneously nucleosome formation may provide insights into the intricate dynamics of chromatin assembly and its diverse functions. Our model thus can be further utilized to simulate the formations of multi-nucleosomes during re-assembling of the chromatin fiber, which will significantly enhance the understanding of the fundamental mechanisms governing the structure and function of chromatin.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141945305","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 Origins of Arginine "Magic": Guanidinium Like-Charge Ion Pairing and Oligoarginine Aggregation in Water by NMR, Cryoelectron Microscopy, and Molecular Dynamics Simulations 精氨酸 "魔法 "的起源：通过核磁共振、冷冻电子显微镜和分子动力学模拟研究胍类电荷离子配对和寡精氨酸在水中的聚合作用

bioRxiv - Biophysics Pub Date : 2024-08-05 DOI: 10.1101/2024.08.04.606526

Denys Biriukov, Zuzana Osifova, Man Nguyen Thi Hong, Philip E Mason, Martin Dracinsky, Pavel Jungwirth, Jan Heyda, Mattia I Morandi, Mario Vazdar

{"title":"The Origins of Arginine \"Magic\": Guanidinium Like-Charge Ion Pairing and Oligoarginine Aggregation in Water by NMR, Cryoelectron Microscopy, and Molecular Dynamics Simulations","authors":"Denys Biriukov, Zuzana Osifova, Man Nguyen Thi Hong, Philip E Mason, Martin Dracinsky, Pavel Jungwirth, Jan Heyda, Mattia I Morandi, Mario Vazdar","doi":"10.1101/2024.08.04.606526","DOIUrl":"https://doi.org/10.1101/2024.08.04.606526","url":null,"abstract":"The phenomenon of like-charge pairing of hydrated ions is a physical manifestation of the unique solvation properties of certain ion pairs in water. Water's high dielectric constant and related ion screening capability significantly influence the interaction between like-charged ions, with the possibility to transform it - in some cases - from\u0000repulsion to attraction. Guanidinium cations (Gdm+) represent a quintessential example of such like-charge pairing due to their specific geometry and charge distribution.\u0000In this work, we present experimental quantification of Gdm+ - Gdm+ contact ion pairing in water utilizing nuclear magnetic resonance (NMR) spectroscopy experiments complemented by molecular dynamics (MD) simulations and density functional theory (DFT) calculations. The observed interaction is very weak - about -0.5 kJ mol-1 - which aligns with theoretical estimation from MD simulations. We also contrast the behavior of Gdm+ with NH4+ cations, which do no exhibit contact ion pairing in water.\u0000DFT calculations predict that the NMR chemical shift of Gdm+ dimers is smaller than that of monomers, in agreement with NMR titration curves that display a nonlinear Langmuir-like behavior. Additionally, we conducted cryo-electron microscopy experiments on oligoarginines R9, which (unlike nona-lysines K9) exhibit aggregation in water. This points again to like charge pairing of the guanidinium side chain groups, as corroborated also by molecular dynamics simulations of these peptides in water.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141945308","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

Mechanical Implications of Cellular Viscoelasticity, Cortex Polarity, Superelasticity, and Cell-Cell Junctions in Curved Tissues 弯曲组织中的细胞粘弹性、皮层极性、超弹性和细胞-细胞连接的力学影响

bioRxiv - Biophysics Pub Date : 2024-08-05 DOI: 10.1101/2024.08.01.606202

Amaury Perez-Tirado, Ulla Unkelbach, Tabea A. Oswald, Johannes Rheinlaender, Tilman E. Schaeffer, Markus Mukenhirn, Alf Honigmann, Andreas Janshoff

引用次数: 0

Site-resolved energetic information from HX/MS experiments 来自 HX/MS 实验的位点分辨能量信息

bioRxiv - Biophysics Pub Date : 2024-08-05 DOI: 10.1101/2024.08.04.606547

Chenlin Lu, Malcolm L. Wells, Andrew Reckers, Anum Glasgow

引用次数: 0

The actin cortex acts as a mechanical memory of morphology in confined migrating cells 肌动蛋白皮层是封闭迁移细胞形态的机械记忆体

bioRxiv - Biophysics Pub Date : 2024-08-05 DOI: 10.1101/2024.08.05.606589

Yohalie Kalukula, Marine Luciano, Guillaume Charras, David Brueckner, Sylvain Gabriele

引用次数: 0