bioRxiv - Biophysics最新文献_第5页

Mycobacterial Topoisomerase I Energetically Suffers From C-Terminal Deletions 分枝杆菌拓扑异构酶 I 因 C 端缺失而失去活力

bioRxiv - Biophysics Pub Date : 2024-09-10 DOI: 10.1101/2024.09.09.612055

Dillon Balthrop, Deepesh Sigdel, Chunfeng Mao, Yuk-Ching Tse-Dinh, Maria Mills

引用次数: 0

Protocol for Simulating the Effect of THz Electromagnetic Field on Ion Channels 模拟太赫兹电磁场对离子通道影响的协议

bioRxiv - Biophysics Pub Date : 2024-09-10 DOI: 10.1101/2024.09.09.612012

Lingfeng Xue, Zigang Song, Qi Ouyang, Chen Song

引用次数: 0

Exploring the sequence and structural determinants of the energy landscape from thermodynamically stable and kinetically trapped subtilisins: ISP1 and SbtE 从热力学稳定和动力学受困的枯草杆菌蛋白中探索能量景观的序列和结构决定因素：ISP1和SbtE

bioRxiv - Biophysics Pub Date : 2024-09-10 DOI: 10.1101/2024.09.08.611919

Miriam Rose Hood, Susan Marqusee

{"title":"Exploring the sequence and structural determinants of the energy landscape from thermodynamically stable and kinetically trapped subtilisins: ISP1 and SbtE","authors":"Miriam Rose Hood, Susan Marqusee","doi":"10.1101/2024.09.08.611919","DOIUrl":"https://doi.org/10.1101/2024.09.08.611919","url":null,"abstract":"A protein′s energy landscape, all the accessible conformations, their populations, and their dynamics of interconversion, is encoded in its primary sequence. While we have a good understanding of how a protein′s primary sequence encodes its native state, we have a much weaker understanding of how sequence encodes the kinetic barriers such as unfolding and refolding. Here we have looked at two subtiliase homologs from the <em>Bacillus subtilis</em>, Intracellular Subtilisin Protease 1 (ISP1) and Subtilisin E (SbtE) that are expected to have very different dynamics. As an intracellular protein, ISP1 has a small pro-domain thought to act simply as a zymogen, whereas the extracellular SbtE has a large pro-domain required for folding. We examined the global and local energetics of the mature proteases and how each pro-domain impacts their landscapes. We find that ISP1′s pro-domain has limited impact on the energy landscape while the mature SbtE is thermodynamically unstable and kinetically trapped. The impact of the pro-domain has opposite effects on the flexibility of the core of the protein. ISP1′s core becomes more flexible while SbtE′s core becomes more rigid. ISP1 contains a conserved amino-acid insertion not present in extracellular subtilisin proteases, which points to a potential source for these differences. These homologs are an extreme example of how changes in the primary sequence can dramatically alter a proteins energy landscape, both stability and dynamics, and highlight the need for large scale, high throughput studies on the relationship between primary sequence and conformational dynamics.","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":"142178208","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 structural influence of the oncogenic driver mutation N642H in the STAT5B SH2 domain STAT5B SH2 结构域中致癌驱动突变 N642H 的结构影响

bioRxiv - Biophysics Pub Date : 2024-09-10 DOI: 10.1101/2024.09.09.612134

Liam Haas-Neill, Deniz Meneksedag-Erol, Ayesha Chaudhry, Masha Novoselova, Qirat F. Ashraf, Elvin D. de Araujo, Derek J. Wilson, Sarah Rauscher

{"title":"The structural influence of the oncogenic driver mutation N642H in the STAT5B SH2 domain","authors":"Liam Haas-Neill, Deniz Meneksedag-Erol, Ayesha Chaudhry, Masha Novoselova, Qirat F. Ashraf, Elvin D. de Araujo, Derek J. Wilson, Sarah Rauscher","doi":"10.1101/2024.09.09.612134","DOIUrl":"https://doi.org/10.1101/2024.09.09.612134","url":null,"abstract":"The point mutation N642H of the signal transducer and activator of transcription 5B (STAT5B) protein is associated with aggressive and drug-resistant forms of leukemia. This mutation is thought to promote cancer due to hyperactivation of STAT5B caused by increased stability of the active, parallel dimer state. However, the molecular mechanism leading to this stabilization is not well understood as there is currently no structure of the parallel dimer. To investigate the mutation's mechanism of action, we conducted extensive all-atom molecular dynamics simulations of multiple oligomeric forms of both STAT5B and STAT5B(N642H), including a model for the parallel dimer. The N642H mutation directly affects the hydrogen bonding network within the phosphotyrosine (pY)-binding pocket of the parallel dimer, enhancing the pY-binding interaction. The simulations indicate that apo STAT5B is highly flexible, exploring a diverse conformational space. In contrast, apo STAT5B(N642H) accesses two distinct conformational states, one of which resembles the conformation of the parallel dimer. The simulation predictions of the effects of the mutation on structure and dynamics are supported by the results of hydrogen-deuterium exchange (HDX) mass spectrometry measurements carried out on STAT5B and STAT5B(N642H) in which a phosphopeptide was used to mimic the effects of parallel dimerization on the SH2 domain. The molecular-level information uncovered in this work contributes to our understanding of STAT5B hyperactivation by the N642H mutation and could help pave the way for novel therapeutic strategies targeting this mutation.","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":"142178219","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

Calcium Binding Affinity in the Mutational Landscape of Troponin-C: Free Energy Calculation, Co-evolution modeling and Machine Learning 肌钙蛋白-C 突变图谱中的钙结合亲和力：自由能计算、协同进化建模和机器学习

bioRxiv - Biophysics Pub Date : 2024-09-09 DOI: 10.1101/2024.09.09.612070

Pooja, Pradipta Bandyopadhyay

{"title":"Calcium Binding Affinity in the Mutational Landscape of Troponin-C: Free Energy Calculation, Co-evolution modeling and Machine Learning","authors":"Pooja, Pradipta Bandyopadhyay","doi":"10.1101/2024.09.09.612070","DOIUrl":"https://doi.org/10.1101/2024.09.09.612070","url":null,"abstract":"Computational protein science has made substantial headway, but accurately predicting the functional effects of mutation in Calcium-binding proteins (CBPs) on Ca2+ binding affinity proves obscure. The complexity lies in the fact that only sequence features or structural information individually offer an incomplete picture on their own. To triumph over this adversity, we introduce a pioneering framework that effortlessly integrates protein sequence evolution information, structural characteristics, and Ca2+ binding interaction properties into a machine learning algorithm. This synthesis has been carried out poised to significantly enhance accuracy and precision in the prediction of the Ca2+ binding affinity towards CBP variants. In our study, we have developed a Ca2+ binding affinity prediction model for various mutants of cardiac Troponin-C protein, to uncover the molecular determinants that contribute binding affinity across protein variants. Our method combines state-of-the-art practices, including a physics-based approach that uses relative binding free-energy (BFE) calculations to assess mutations with implicit polarization. Additionally, it incorporates the impact of evolutionary factors on protein mutations through a theoretical deep mutational scan using a statistical probability model. Support Vector Regression (SVR) algorithms have been used to predict Ca2+ binding affinity based on sequence information, structural properties, and interactions of water molecules with Ca2+ in the EF-hand loop. Our model demonstrates high accuracy and can potentially be generalized for other calcium-binding proteins to predict the effects of point mutations on Ca2+ binding affinity for CBPs.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178213","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

Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering 利用小角散射对 RNA:RNA 复合物进行选择性氘化以进行结构分析

bioRxiv - Biophysics Pub Date : 2024-09-09 DOI: 10.1101/2024.09.09.612093

Aldrex Munsayac, Wellington C Leite, Jesse B Hopkins, Ian Hall, Hugh M O'Neill, Sarah C Keane

引用次数: 0

Aquavert: Imaging and Microfluidics for Vertical Swimming of Microorganisms Aquavert：用于微生物垂直游动的成像和微流体技术

bioRxiv - Biophysics Pub Date : 2024-09-08 DOI: 10.1101/2024.09.07.611807

Haley B. Obenshain, Isaias Zarate, Olivia Hedman-Manzano, Jared Goderich, Sungho Lee, Bryant A. Lopez, Emma Varela, Ga-Young Kelly Suh, Douglas A. Pace, Siavash Ahrar

{"title":"Aquavert: Imaging and Microfluidics for Vertical Swimming of Microorganisms","authors":"Haley B. Obenshain, Isaias Zarate, Olivia Hedman-Manzano, Jared Goderich, Sungho Lee, Bryant A. Lopez, Emma Varela, Ga-Young Kelly Suh, Douglas A. Pace, Siavash Ahrar","doi":"10.1101/2024.09.07.611807","DOIUrl":"https://doi.org/10.1101/2024.09.07.611807","url":null,"abstract":"Investigating aquatic microorganisms' swimming and feeding behaviors under well-controlled conditions is of great interest across multiple disciplines. Thus, broader access to resources that enable these investigations is desirable. Given the organisms' microscopic dimensions, an ideal system should combine microscopy to visualize and fluidics to control and modulate their environments. We report an integrated device (Aquavert) that combines DIY microscopy and microfluidics for biomechanical investigations of marine microorganisms, emphasizing vertical swimming. The DIY microscope was developed for modularity, and imaging chambers were secured in vertical orientations (either in portrait or landscape mode). Fluid channels were used to introduce flow and fluid segmentation while remaining upright. Fluid segmentation established two distinct environments (e.g., with and without algae) in neighboring regions inside a chamber. System application with multiple marine larvae (sand dollars, sea urchins, and starfish) and introduction of unicellular algae were demonstrated. Finally, the device's capabilities were extended to fluorescence imaging to visualize tracer beads. The role of gravity is often ignored in conventional plate or microfluidic experiments. Beyond the current application, Aquavert enables investigations of the behavior and physiology of microorganisms where the role of gravity is critical.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178248","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

Non-linear stress-softening of the bacterial cell wall confers cell shape homeostasis 细菌细胞壁的非线性应力软化使细胞形状保持稳定

bioRxiv - Biophysics Pub Date : 2024-09-08 DOI: 10.1101/2024.09.03.611099

Paola Bardetti, Felix Barber, Enrique R Rojas

引用次数: 0

Modelling mucus clearance in sinuses: thin-film flow inside a fluid-producing cavity lined with an active surface 鼻窦粘液清除模型：内衬活性表面的产液腔内的薄膜流

bioRxiv - Biophysics Pub Date : 2024-09-08 DOI: 10.1101/2024.09.08.611783

Nikhil Desai, Eric Lauga

{"title":"Modelling mucus clearance in sinuses: thin-film flow inside a fluid-producing cavity lined with an active surface","authors":"Nikhil Desai, Eric Lauga","doi":"10.1101/2024.09.08.611783","DOIUrl":"https://doi.org/10.1101/2024.09.08.611783","url":null,"abstract":"The paranasal sinuses are a group of hollow spaces within the human skull, surrounding the nose. They are lined with an epithelium that contains mucus-producing cells and tiny hairlike active appendages called cilia. The cilia beat constantly to sweep mucus out of the sinus into the nasal cavity, thus maintaining a clean mucus layer within the sinuses. This process, called mucociliary clearance, is essential for a healthy nasal environment and disruption in mucus clearance leads to diseases such as chronic rhinosinusitis, specifically in the maxillary sinuses, which are the largest of the paranasal sinuses. We present here a continuum mathematical model of mucociliary clearance inside the human maxillary sinus. Using a combination of analysis and computations, we study the flow of a thin fluid film inside a fluid-producing cavity lined with an active surface: fluid is continuously produced by a wall-normal flux in the cavity and then is swept out, against gravity, due to an effective tangential flow induced by the cilia. We show that a steady layer of mucus develops over the cavity surface only when the rate of ciliary clearance exceeds a threshold, which itself depends on the rate of mucus production. We then use a scaling analysis, which highlights the competition between gravitational retention and cilia-driven drainage of mucus, to rationalise our computational results. We discuss the biological relevance of our findings, noting that measurements of mucus production and clearance rates in healthy sinuses fall within our predicted regime of steady-state mucus layer development.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178245","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

Early Events in G-quadruplex Folding Captured by Time-Resolved Small-Angle X-Ray Scattering 通过时间分辨小角 X 射线散射捕捉 G-四链折叠的早期事件

bioRxiv - Biophysics Pub Date : 2024-09-08 DOI: 10.1101/2024.09.05.611539

Robert C. Monsen, T. Michael Sabo, Robert D. Gray, Jesse B. Hopkins, Jonathan B. Chaires

{"title":"Early Events in G-quadruplex Folding Captured by Time-Resolved Small-Angle X-Ray Scattering","authors":"Robert C. Monsen, T. Michael Sabo, Robert D. Gray, Jesse B. Hopkins, Jonathan B. Chaires","doi":"10.1101/2024.09.05.611539","DOIUrl":"https://doi.org/10.1101/2024.09.05.611539","url":null,"abstract":"Time-resolved small-angle X-ray experiments (TR-SAXS) are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in G4 folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 20.6 to 12.6 Å. The collapse is monophasic and is complete in less than 600 ms. Additional hand-mixing pH-jump kinetic studies show that slower kinetic steps follow the collapse. The folded and unfolded states at equilibrium were further characterized by SAXS studies and other biophysical tools, to show that G4 unfolding was complete at alkaline pH, but not in LiCl solution as is often claimed. The SAXS Ensemble Optimization Method (EOM) analysis reveals models of the unfolded state as a dynamic ensemble of flexible oligonucleotide chains with a variety of transient hairpin structures. These results suggest a G4 folding pathway in which a rapid collapse, analogous to molten globule formation seen in proteins, is followed by a confined conformational search within the collapsed particle to form the native contacts ultimately found in the stable folded form.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178217","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