Biophysical journal最新文献_第2页

Mechanistic basis for enhanced strigolactone sensitivity in KAI2 triple mutant KAI2三重突变体增强独角麦内酯敏感性的机制基础

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-04-23 DOI: 10.1016/j.bpj.2025.04.021

Briana L. Sobecks, Jiming Chen, Tanner J. Dean, Diwakar Shukla

{"title":"Mechanistic basis for enhanced strigolactone sensitivity in KAI2 triple mutant","authors":"Briana L. Sobecks, Jiming Chen, Tanner J. Dean, Diwakar Shukla","doi":"10.1016/j.bpj.2025.04.021","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.04.021","url":null,"abstract":"<ce:italic>Striga hermonthica</ce:italic> is a parasitic weed that destroys billions of dollars’ worth of staple crops every year. Its rapid proliferation stems from an enhanced ability to metabolize strigolactones (SLs), plant hormones that direct root branching and shoot growth. <ce:italic>Striga’s</ce:italic> SL receptor, <ce:italic>Sh</ce:italic>HTL7, bears more similarity to the staple crop karrikin receptor karrikin insensitive 2 (KAI2) than to SL receptor D14, though KAI2 variants in plants like <ce:italic>Arabidopsis thaliana</ce:italic> show minimal SL sensitivity. Recently, studies have indicated that a small number of point mutations to HTL7 residues can confer SL sensitivity to <ce:italic>At</ce:italic>KAI2. Here, we analyze both wild-type <ce:italic>At</ce:italic>KAI2 and SL-sensitive mutant Var64 through all-atom, long-timescale molecular dynamics simulations to determine the effects of these mutations on receptor function at a molecular level. We demonstrate that the mutations stabilize SL binding by about 2 kcal/mol. They also result in a doubling of the average pocket volume and eliminate the dependence of binding on certain pocket conformational arrangements. Although the probability of certain nonbinding SL-receptor interactions increases in the mutant compared with the wild-type, the rate of binding also increases by a factor of 10. All these changes account for the increased SL sensitivity in mutant KAI2 and suggest mechanisms for increasing the functionality of host crop SL receptors.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"139 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143901809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

"Poking cells: AI can help here too". “戳细胞：人工智能也能帮上忙”。

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-04-22 DOI: 10.1016/j.bpj.2025.04.019

Juanyong Li,Kristen Billiar

引用次数: 0

tRNA kinetics on the ribosome depends non-monotonically on intersubunit rotation. 核糖体上 tRNA 的动力学非单调地取决于亚基间的旋转。

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-04-18 DOI: 10.1016/j.bpj.2025.04.018

Sandra Byju,Paul C Whitford

{"title":"tRNA kinetics on the ribosome depends non-monotonically on intersubunit rotation.","authors":"Sandra Byju,Paul C Whitford","doi":"10.1016/j.bpj.2025.04.018","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.04.018","url":null,"abstract":"In order to translate messenger RNA into proteins, the ribosome must coordinate a wide range of conformational rearrangements. Some steps involve individual molecules, whereas others require synchronization of multiple collective motions. For example, the ribosomal \"small\" subunit (∼1 MDa) is known to undergo rotational motion (∼10°) that is correlated with large-scale displacements of tRNA molecules (∼50Å). While decades of biochemical, single-molecule and structural analysis have provided many insights into the timing of these motions, little is known about how these dynamical processes influence each other. To address this, we use molecular simulations to isolate specific interactions that allow tRNA kinetics to be controlled by subunit rotation. Specifically, we applied an all-atom structure-based model to simulate movement of tRNA between ribosomal binding sites (P/E hybrid formation). These calculations reveal a pronounced non-monotonic dependence of tRNA kinetics on subunit rotation, where the rate of P/E formation initially increases and then decreases as the subunit rotates. In addition, there a sharp increase in rate for low degrees of rotation, suggesting that adoption of P/E tRNA conformations may occur early in the rotation process. Together, these calculations demonstrate how molecular structure gives rise to an intricate relationship between these complex rearrangements.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"16 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bacteria Can Rotate while Body-Tethered to a Solid Surface. 细菌可以在身体附着在固体表面时旋转。

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-04-18 DOI: 10.1016/j.bpj.2025.04.012

Jordan Bell,Silverio Johnson,Brandon Pugnet,Jay X Tang

{"title":"Bacteria Can Rotate while Body-Tethered to a Solid Surface.","authors":"Jordan Bell,Silverio Johnson,Brandon Pugnet,Jay X Tang","doi":"10.1016/j.bpj.2025.04.012","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.04.012","url":null,"abstract":"The attachment of bacteria to solid surfaces has been studied primarily through the modes of pili or flagella tethering. We report on a common feature of tethering in pililess strains of three species of monotrichous bacteria-(Vibrio alginolyticus, Pseudomonas aeruginosa, and Caulobacter crescentus)-namely, that they may become tethered to the surface by their cell body rather than by their flagellum. These tethered bacteria rotate in alternating directions about a pivot point located under the cell body. Using high-intensity darkfield microscopy, we observed that, in most cases, the flagellum of a tethered Vibrio alginolyticus rotates together with the cell body. We name this distinct mode of attachment body tethering. Observing hundreds of rotating bacteria tethered to the surface, we find that body tethering is a more common mode of attachment than flagellum tethering for these three strains of bacteria. Our results confirm that body tethering is a key mechanism for the surface attachment of bacteria without pili. Recognizing body tethering as a robust mode of bacterial attachment to surfaces may have broad implications in the study of bacterial adhesion and biofilm formation.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"66 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Active and inactive pathways in the kinetic mechanism of the G51V retinitis pigmentosa mutant photoreaction. G51V色素性视网膜炎突变体光反应动力学机制的活性和非活性途径。

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-04-16 DOI: 10.1016/j.bpj.2025.04.016

Istvan Szundi,Weekie Yao,Eefei Chen,David S Kliger,David L Farrens

引用次数: 0

Exploring the structural and dynamical features of bacterial-tubulin FtsZ 细菌微管蛋白FtsZ的结构和动力学特性探讨

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-04-16 DOI: 10.1016/j.bpj.2025.04.017

Tamsuk Paul, Gregory A. Voth

{"title":"Exploring the structural and dynamical features of bacterial-tubulin FtsZ","authors":"Tamsuk Paul, Gregory A. Voth","doi":"10.1016/j.bpj.2025.04.017","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.04.017","url":null,"abstract":"FtsZ, a bacterial tubulin, plays a crucial role in the cytokinesis process. It shares structural similarities with tubulin, as it consists of two domains—N-terminal and C-terminal domains. The protein assembles to form single-stranded protofilaments that exhibit a dynamic phenomenon known as treadmilling where the FtsZ filaments appear to execute a unidirectional movement even though individual monomers constituting the filament do not move. Despite forming protofilaments, an FtsZ molecule requires a conformational switch to form stable contacts with neighboring subunits in a filament. Therefore, FtsZ has two well-characterized conformations based on its polymerization propensity: 1) R state, preferred by the monomeric FtsZ and 2) T state, preferred by the polymeric FtsZ. The treadmilling ability of FtsZ is coupled with the conformational switch and the GTPase activity of the protein as hydrolysis-deficient mutants of FtsZ do not treadmill. We employ all-atom molecular dynamics simulations to investigate certain structural and dynamical features of the protofilaments by considering FtsZ heptamers as our model system. We simulated FtsZ filaments in three nucleotide states—GTP, GDP, and GDP-Pi—to understand the conformational states of the terminal monomers, interface dynamics of the filaments, and important interactions at the protein interdomain and interface regions. Our study reveals that the γ-phosphate binding loop T3 prompts the structural rearrangements at the interface post hydrolysis.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"19 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143901812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Functional asymmetry in processivity clamp proteins. 加工钳蛋白的功能不对称。

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-04-16 DOI: 10.1016/j.bpj.2025.04.014

Sam Mahdi,Penny J Beuning,Dmitry M Korzhnev

{"title":"Functional asymmetry in processivity clamp proteins.","authors":"Sam Mahdi,Penny J Beuning,Dmitry M Korzhnev","doi":"10.1016/j.bpj.2025.04.014","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.04.014","url":null,"abstract":"Symmetric homo-oligomeric proteins comprising multiple copies of identical subunits are abundant in all domains of life. To fulfill their biological function, these complexes undergo conformational changes, binding events, or post-translational modifications leading to loss of symmetry. Processivity clamp proteins that encircle DNA and play multiple roles in DNA replication and repair are archetypical homo-oligomeric symmetric protein complexes. The symmetrical nature of processivity clamps enables simultaneous interactions with multiple protein binding partners; such interactions result in asymmetric changes that facilitate the transition between clamp loading and DNA replication, and between DNA replication and repair. The ring-shaped processivity clamps are opened and loaded onto DNA by clamp-loader complexes via asymmetric intermediates with one of the intermonomer interfaces disrupted, undergo spontaneous opening events, and bind heterogeneous partners. Eukaryotic clamp proteins are subject to ubiquitylation, SUMOylation, and acetylation affecting their biological functions. There is increasing evidence of the functional asymmetry of the processivity clamp proteins from structural, biophysical, and computational studies. Here, we review the symmetry and asymmetry of processivity clamps and their roles in regulating the various functions of the clamps.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"30 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143849584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparative Study on Efficacy of Thrombolytic Protocols: Dual Therapy against Standard tPA Regimen. 溶栓方案：双重治疗与标准tPA方案的疗效比较研究。

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-04-16 DOI: 10.1016/j.bpj.2025.04.013

Saleheh Heydari Ghasemi,Mohammad-Taghi Ahmadian,Ahmad Assempour,Seyed Hossein Ahmadi Tafti

{"title":"Comparative Study on Efficacy of Thrombolytic Protocols: Dual Therapy against Standard tPA Regimen.","authors":"Saleheh Heydari Ghasemi,Mohammad-Taghi Ahmadian,Ahmad Assempour,Seyed Hossein Ahmadi Tafti","doi":"10.1016/j.bpj.2025.04.013","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.04.013","url":null,"abstract":"When a blood clot occludes cerebral arteries, causing a stroke, a common cause of global death, thrombolytic therapy steps in as a highly effective treatment to restore the blood flow by dissolving the clot. Thrombolytic therapy is the use of plasminogen activators, including tissue plasminogen activator (tPA) and urokinase plasminogen activator (uPA), either separately or in combination. In this study, a mathematical model of thrombolysis has been developed for non-uniform fibrin clots, which have varying density levels nearer and farther from the cell surface. The non-Newtonian nature of blood flow and the viscoelasticity of vessel walls are considered. The dynamic of the pulsatile flow is described using the mass and momentum conservation laws with the Carreau viscosity model, and the generalized Maxwell model is used for the vessel wall. The transport of drugs and fibrinolytic factors involved in the dissolution process induced by convection and diffusion is considered. The developed model can predict the clot lysis pattern in combined drug therapies and can be used to optimize the drug dosage required for treatment. The model is used to evaluate the safety of dual thrombolytic therapy with tPA bolus and uPA continuous infusion in three different doses and then compared with the FDA-approved regimen and experimental studies. Results show that although dual thrombolytic therapy is safe and does not increase the risk of bleeding, it is not more effective than the FDA-approved regimen in faster clot dissolution and restoration of blood flow.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"37 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143849382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

FRET-FCS: Advancing Comprehensive Insights into Complex Biological Systems. FRET-FCS：推进复杂生物系统的综合见解。

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-04-15 DOI: 10.1016/j.bpj.2025.04.015

Anay Lazaro-Alfaro,Sterling L N Nicholas,Hugo Sanabria

引用次数: 0

Synergistic effect of PIP2 and PIP3 on membrane-induced phase separation of integrin complexes. PIP2和PIP3在膜诱导的整合素复合物相分离中的协同作用。

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-04-14 DOI: 10.1016/j.bpj.2025.04.011

Chiao-Peng Hsu,Arsenii Hordeichyk,Jonas Aretz,Reinhard Fässler,Andreas R Bausch

引用次数: 0