bioRxiv - Biophysics最新文献_第3页

Stress-mediated growth determines E. coli division site morphogenesis 压力介导的生长决定了大肠杆菌分裂点的形态发生

bioRxiv - Biophysics Pub Date : 2024-09-12 DOI: 10.1101/2024.09.11.612282

Petr Pelech, Paula P Navarro, Andrea Vettiger, Luke H Chao, Christoph Allolio

引用次数: 0

Myosin cluster dynamics determines epithelial wound ring constriction 肌球蛋白簇动力学决定上皮伤口环收缩

bioRxiv - Biophysics Pub Date : 2024-09-12 DOI: 10.1101/2024.09.12.612715

Alka Bhat, Remi Berthoz, Simon Lo Vecchio, Coralie Spiegelhalter, Shigenobu Yonemura, Olivier Pertz, Daniel Riveline

引用次数: 0

Allosteric modulation of proton binding confers Cl- activation and glutamate selectivity to vesicular glutamate transporters 质子结合的异构调节赋予囊泡谷氨酸转运体 Cl- 激活和谷氨酸选择性

bioRxiv - Biophysics Pub Date : 2024-09-12 DOI: 10.1101/2024.09.06.609381

Bart Borghans, Daniel Kortzak, Piersilvio Longo, Jan-Philipp Machtens, Christoph Fahlke

{"title":"Allosteric modulation of proton binding confers Cl- activation and glutamate selectivity to vesicular glutamate transporters","authors":"Bart Borghans, Daniel Kortzak, Piersilvio Longo, Jan-Philipp Machtens, Christoph Fahlke","doi":"10.1101/2024.09.06.609381","DOIUrl":"https://doi.org/10.1101/2024.09.06.609381","url":null,"abstract":"Vesicular glutamate transporters (VGLUTs) fill synaptic vesicles with glutamate and remove luminal Cl- via an additional anion channel mode. Both of these transport functions are stimulated by luminal acidification, luminal-positive membrane potential, and luminal Cl-. We studied VGLUT1 transporter/channel activation using a combination of heterologous expression, cellular electrophysiology, fast solution exchange, and mathematical modeling. Cl- channel gating can be described with a kinetic scheme that includes two protonation sites and distinct opening, closing, and Cl--binding rates for each protonation state. Cl- binding promotes channel opening by modifying the pKa values of the protonation sites and rates of pore opening and closure. VGLUT1 transports glutamate and aspartate at distinct stoichiometries: H+-glutamate exchange at 1:1 stoichiometry and aspartate uniport. Neurotransmitter transport with variable stoichiometry can be described with an alternating access model that assumes that transporters without substrate translocate in the doubly protonated state to the inward-facing conformation and return with the bound amino acid substrate as either singly or doubly protonated. Glutamate, but not aspartate, promotes the release of one proton from inward-facing VGLUT1, resulting in preferential H+-coupled glutamate exchange. Cl- stimulates glutamate transport by making the glutamate-binding site accessible to cytoplasmic glutamate and by facilitating transitions to the inward-facing conformation after outward substrate release. We conclude that allosteric modification of transporter protonation by Cl- is crucial for both VGLUT1 transport functions.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178170","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

Symmetry of loop extrusion by dimeric SMC complexes is DNA-tension-dependent 二聚体 SMC 复合物挤出环的对称性取决于 DNA 张力

bioRxiv - Biophysics Pub Date : 2024-09-12 DOI: 10.1101/2024.09.12.612694

Biswajit Pradhan, Adrian Pinto, Takaharu Kanno, Damla Tetiker, Martin D. Baaske, Erin Cutt, Constantinos Chatzicharlampous, Herwig Schüler, Amar Deep, Kevin D. Corbett, Luis Aragon, Peter Virnau, Camilla Björkegren, Eugene Kim

{"title":"Symmetry of loop extrusion by dimeric SMC complexes is DNA-tension-dependent","authors":"Biswajit Pradhan, Adrian Pinto, Takaharu Kanno, Damla Tetiker, Martin D. Baaske, Erin Cutt, Constantinos Chatzicharlampous, Herwig Schüler, Amar Deep, Kevin D. Corbett, Luis Aragon, Peter Virnau, Camilla Björkegren, Eugene Kim","doi":"10.1101/2024.09.12.612694","DOIUrl":"https://doi.org/10.1101/2024.09.12.612694","url":null,"abstract":"Structural maintenance of chromosome (SMC) complexes organize and regulate genomes via DNA loop extrusion. During this process, the complexes increase the loop size by reeling in DNA from one or both sides of the loop. The factors governing this symmetry remain unclear. Here, we combine single-molecule analysis and molecular dynamic simulations to investigate the symmetry of loop extrusion of various SMC complexes. We find that whereas monomeric condensin and cohesin are one-sided extruders, the symmetry of dimeric SMCs, such as Smc5/6 and Wadjet, is DNA tension dependent. At low DNA tension (< 0.1pN), Smc5/6 and Wadjet extrude DNA from both sides of the loop. At higher tension, however, they transition to a behavior akin to one-sided extruders, yet still capable of extruding from one or the other side thereby switching the direction of extrusion. Our simulations further reveal that thermal fluctuations significantly influence loop extrusion symmetry, causing variations in DNA reeling rates between the two motors in the dimeric complexes and their direction switching at stalling tensions. Our findings challenge the previous view of loop extrusion symmetry as a fixed characteristic, revealing its dynamic nature and regulation by both intrinsic protein properties and extrinsic factors.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178168","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

Molecular basis of the urate transporter URAT1 inhibition by gout drugs 痛风药物抑制尿酸盐转运体 URAT1 的分子基础

bioRxiv - Biophysics Pub Date : 2024-09-12 DOI: 10.1101/2024.09.11.612563

Yang Suo, Justin Fedor, Han Zhang, Kalina Tsolova, Xiaoyu Shi, Kedar Sharma, Shweta Kumari, Mario J. Borgnia, Peng Zhan, Wonpil Im, Seok-Yong Lee

{"title":"Molecular basis of the urate transporter URAT1 inhibition by gout drugs","authors":"Yang Suo, Justin Fedor, Han Zhang, Kalina Tsolova, Xiaoyu Shi, Kedar Sharma, Shweta Kumari, Mario J. Borgnia, Peng Zhan, Wonpil Im, Seok-Yong Lee","doi":"10.1101/2024.09.11.612563","DOIUrl":"https://doi.org/10.1101/2024.09.11.612563","url":null,"abstract":"Hyperuricemia is a condition when uric acid, a waste product of purine metabolism, accumulates in the blood. Untreated hyperuricemia can lead to crystal formation of monosodium urate in the joints, causing a painful inflammatory disease known as gout. These conditions are associated with many other diseases and affect a significant and increasing proportion of the population. The human urate transporter 1 (URAT1) is responsible for the reabsorption of ~90% of uric acid in the kidneys back into the blood, making it a primary target for treating hyperuricemia and gout. Despite decades of research and development, clinically available URAT1 inhibitors have limitations because the molecular basis of URAT1 inhibition by gout drugs remains unknown5. Here we present cryo-electron microscopy structures of URAT1 alone and in complex with three clinically relevant inhibitors: benzbromarone, lesinurad, and the novel compound TD-3. Together with functional experiments and molecular dynamics simulations, we reveal that these inhibitors bind selectively to URAT1 in inward-open states. Furthermore, we discover differences in the inhibitor dependent URAT1 conformations as well as interaction networks, which contribute to drug specificity. Our findings illuminate a general theme for URAT1 inhibition, paving the way for the design of next-generation URAT1 inhibitors in the treatment of gout and hyperuricemia.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178167","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

Vesicle docking and fusion pore modulation by the neuronal calcium sensor Synaptotagmin-1 神经元钙传感器Synaptotagmin-1对囊泡对接和融合孔的调控

bioRxiv - Biophysics Pub Date : 2024-09-12 DOI: 10.1101/2024.09.12.612660

Maria Tsemperouli, Sudheer Kumar Cheppali, Felix Rivera Molina, David Chetrit, Ane Landajuela, Derek Toomre, Erdem Karatekin

{"title":"Vesicle docking and fusion pore modulation by the neuronal calcium sensor Synaptotagmin-1","authors":"Maria Tsemperouli, Sudheer Kumar Cheppali, Felix Rivera Molina, David Chetrit, Ane Landajuela, Derek Toomre, Erdem Karatekin","doi":"10.1101/2024.09.12.612660","DOIUrl":"https://doi.org/10.1101/2024.09.12.612660","url":null,"abstract":"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 (DCV) and synaptic vesicles (SV) to the plasma membrane (PM) 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.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178171","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

Enzyme activation by urea reveals the interplay between conformational dynamics and substrate binding: a single-molecule FRET study 尿素激活酶揭示构象动力学与底物结合之间的相互作用：单分子 FRET 研究

bioRxiv - Biophysics Pub Date : 2024-09-11 DOI: 10.1101/2024.09.01.610662

David Scheerer, Dorit Levy, Remi Casier, Inbal Riven, Hisham Mazal, Gilad Haran

{"title":"Enzyme activation by urea reveals the interplay between conformational dynamics and substrate binding: a single-molecule FRET study","authors":"David Scheerer, Dorit Levy, Remi Casier, Inbal Riven, Hisham Mazal, Gilad Haran","doi":"10.1101/2024.09.01.610662","DOIUrl":"https://doi.org/10.1101/2024.09.01.610662","url":null,"abstract":"Proteins often harness extensive motions of domains and subunits to promote their function. Deciphering how these movements impact activity is key for understanding life's molecular machinery. The enzyme adenylate kinase is an intriguing example for this relationship; it ensures efficient catalysis by large-scale domain motions that lead to the enclosure of the bound substrates ATP and AMP. At high concentrations, AMP also operates as an allosteric inhibitor of the protein. Surprisingly, the enzyme is activated by urea, a compound commonly acting as a denaturant. Combining single-molecule FRET spectroscopy and enzymatic activity studies, we find that urea interferes with two key mechanisms that contribute to enzyme efficacy. First, urea promotes the open conformation of the enzyme, aiding the proper positioning of the substrates. Second, urea decreases AMP affinity, paradoxically facilitating a more efficient progression towards the catalytically active complex. These results signify the important interplay between conformational dynamics and chemical steps, including binding, in the activity of enzymes. State-of-the-art tools, such as single-molecule fluorescence spectroscopy, offer new insights into how enzymes balance different conformations to regulate activity.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178173","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

Structural characterization of an essential lipoprotein of Mycoplasma pneumoniae 肺炎支原体必需脂蛋白的结构特征

bioRxiv - Biophysics Pub Date : 2024-09-11 DOI: 10.1101/2024.09.05.611430

Irem Keles, Sina Manger, Mbuso Siyabonga Mantanya, Achilleas S Frangakis

引用次数: 0

NMR at operational temperature for resonance assignments of a PET degrading enzyme 工作温度下的 NMR，用于 PET 降解酶的共振分配

bioRxiv - Biophysics Pub Date : 2024-09-10 DOI: 10.1101/2024.09.10.612188

Valeria Gabrielli, Jelena Grga, Sabine Gavalda, Laura Perrot, Emmanuelle Boll, Guy Lippens, Cyril Charlier, Guy Lippens

{"title":"NMR at operational temperature for resonance assignments of a PET degrading enzyme","authors":"Valeria Gabrielli, Jelena Grga, Sabine Gavalda, Laura Perrot, Emmanuelle Boll, Guy Lippens, Cyril Charlier, Guy Lippens","doi":"10.1101/2024.09.10.612188","DOIUrl":"https://doi.org/10.1101/2024.09.10.612188","url":null,"abstract":"PETases are enzymes that can break down the PET polymer in its constituent building blocks, and thereby recycle starting material for new high-quality plastics. NMR spectroscopy can help in the understanding and ultimately improvement of these PETases, but is always confronted with the lengthy step of acquisition and interpretation of triple resonance spectra for the spectral assignment. Here, we explore whether this step can be made more efficient by recording the spectra directly at high temperature, which also corresponds to more realistic working conditions for the enzyme. Taking the inactive variant of LCCICCG in which the Serine 165 has been replaced by an Alanine (LCCICCG-S165A) as an example, we evaluate spectral quality at 30C and 50C, and find that the latter condition greatly improves the Signal-to-Noise (S/N) ratio of the different spectra. As a result, we present an exhaustive backbone and side-chain assignment of LCCICCG-S165A based on a minimal set of triple resonance spectra acquired at 50C, that can act as a basis for future work on bio-structural studies on this PETase.","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":"142223568","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

Lessons learned during the journey of data: from experiment to model for predicting kinase affinity, selectivity, polypharmacology, and resistance 数据之旅中的经验教训：从实验到模型，预测激酶的亲和性、选择性、多药理学和抗药性

bioRxiv - Biophysics Pub Date : 2024-09-10 DOI: 10.1101/2024.09.10.612176

Raquel Lopez-Rios de Castro, Jaime Rodriguez-Guerra, David Schaller, Talia B. Kimber, Corey Taylor, Jessica B White, Michael Backenkohler, Alexander Payne, Ben Kaminow, Ivan Pulido, Sukrit Singh, Paula Linh Krammer, Guillermo Perez-Hernandez, Andrea Volkamer, John D. Chodera

{"title":"Lessons learned during the journey of data: from experiment to model for predicting kinase affinity, selectivity, polypharmacology, and resistance","authors":"Raquel Lopez-Rios de Castro, Jaime Rodriguez-Guerra, David Schaller, Talia B. Kimber, Corey Taylor, Jessica B White, Michael Backenkohler, Alexander Payne, Ben Kaminow, Ivan Pulido, Sukrit Singh, Paula Linh Krammer, Guillermo Perez-Hernandez, Andrea Volkamer, John D. Chodera","doi":"10.1101/2024.09.10.612176","DOIUrl":"https://doi.org/10.1101/2024.09.10.612176","url":null,"abstract":"Recent advances in machine learning (ML) are reshaping drug discovery. Structure-based ML methods use physically-inspired models to predict binding affinities from protein:ligand complexes. These methods promise to enable the integration of data for many related targets, which addresses issues related to data scarcity for single targets and could enable generalizable predictions for a broad range of targets, including mutants. In this work, we report our experiences in building KinoML, a novel framework for ML in target-based small molecule drug discovery with an emphasis on structure-enabled methods. KinoML focuses currently on kinases as the relative structural conservation of this protein superfamily, particularly in the kinase domain, means it is possible to leverage data from the entire superfamily to make structure-informed predictions about binding affinities, selectivities, and drug resistance. Some key lessons learned in building KinoML include: the importance of reproducible data collection and deposition, the harmonization of molecular data and featurization, and the choice of the right data format to ensure reusability and reproducibility of ML models. As a result, KinoML allows users to easily achieve three tasks: accessing and curating molecular data; featurizing this data with representations suitable for ML applications; and running reproducible ML experiments that require access to ligand, protein, and assay information to predict ligand affinity. Despite KinoML focusing on kinases, this framework can be applied to other proteins. The lessons reported here can help guide the development of platforms for structure-enabled ML in other areas of drug discovery.","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":"142178175","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