Biophysical journal最新文献_第8页

Electrodeformation of DMPC vesicle membranes near the main phase transition. DMPC囊泡膜在主相变附近的电变形。

IF 3.1 3区生物学

Biophysical journal Pub Date : 2025-09-01 DOI: 10.1016/j.bpj.2025.08.023

Simon Fabiunke, Petia M Vlahovska

{"title":"Electrodeformation of DMPC vesicle membranes near the main phase transition.","authors":"Simon Fabiunke, Petia M Vlahovska","doi":"10.1016/j.bpj.2025.08.023","DOIUrl":"10.1016/j.bpj.2025.08.023","url":null,"abstract":"The physical properties of lipid membranes are essential to cellular function, with membrane fluidity playing a key role in the mobility of embedded biomolecules. Fluidity is governed by the membrane's phase state, which is known to depend on composition and temperature. However, in living cells, the transmembrane electric potential may also influence membrane fluidity. In this study, we use giant unilamellar vesicles composed of dimyristoylphosphatidylcholine to examine the membrane's response to electric fields near its main phase transition temperature. Below the transition temperature, the vesicle remains undeformed, indicating a bilayer in the gel phase. However, near the transition, the vesicle elongates into an ellipsoid, and the evolution of the aspect ratio exhibits a two-step response: an initial rapid increase followed by a slower elongation. Electrodeformation experiments at various temperatures relative to the transition temperature Tm reveal that the duration of the fast step increases as the temperature approaches Tm, and the slow step vanishes for a bilayer the fluid phase. We attribute the initial rapid response to the fluid phase and the subsequent slow response to a thermal expansion induced by Joule heating from the electric field.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12503190/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The influence of 10n and 10n+5 linker lengths on chromatin fiber topologies explored by mesoscale modeling. 规则核小体连接体间距的染色质纤维拓扑结构是什么？中尺度模式探讨了10n和10n+5连接体长度的影响。

IF 3.1 3区生物学

Biophysical journal Pub Date : 2025-09-01 DOI: 10.1016/j.bpj.2025.08.030

Zilong Li, Stephanie Portillo-Ledesma, Moshe Janani, Tamar Schlick

{"title":"The influence of 10n and 10n+5 linker lengths on chromatin fiber topologies explored by mesoscale modeling.","authors":"Zilong Li, Stephanie Portillo-Ledesma, Moshe Janani, Tamar Schlick","doi":"10.1016/j.bpj.2025.08.030","DOIUrl":"10.1016/j.bpj.2025.08.030","url":null,"abstract":"The structural organization of chromatin is intricately influenced by the length of linker DNA connecting nucleosomes. Some studies have suggested preferred linker lengths of 10n and 10n+5 base pairs (bp) (n = integer). Because these lengths dictate the rotational orientation of successive nucleosomes in the fiber axis, they can markedly affect chromatin fiber compaction and topology. Using a refined mesoscale chromatin model with 5-bp resolution, we investigate the influence of linker DNA periodicity, linker histone density, salt concentration, and starting fiber topology on chromatin architecture for regular fibers versus \"life-like\" fibers, the latter with irregular spacing between nucleosomes. Our results reveal that regular fibers with 10n linkers exhibit compact zigzag configurations, whereas 10n+5 linkers generate more open and flexible structures. However, these effects are pronounced only for short linker lengths, as longer linkers are more heterogeneous. Moreover, increased linker histone density further enhances compaction for long linker lengths, and lower salt concentration modifies chromatin topologies, diminishing periodicity-driven effects. In addition, any periodicity effect in tightly packed solenoid configurations is much less pronounced. All these trends for regular fibers are reduced in life-like fibers with irregularly spaced nucleosomes, despite having the same average spacing. Moreover, the trend details depend highly on specific features of the fiber architecture as designed in experiments and simulations. Overall, our study highlights how reported differences depend on modeling details and emphasizes the role of linker DNA length in regulating chromatin fiber architecture and its potential implications for genome accessibility and expression.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941003","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

Membrane morphologies arising from multiconformational protein states. 分类：生物科学-生物物理学和计算生物学由多构象蛋白状态引起的膜形态。

IF 3.1 3区生物学

Biophysical journal Pub Date : 2025-09-01 DOI: 10.1016/j.bpj.2025.08.035

Avihay Kadosh, Tom Shemesh

{"title":"Membrane morphologies arising from multiconformational protein states.","authors":"Avihay Kadosh, Tom Shemesh","doi":"10.1016/j.bpj.2025.08.035","DOIUrl":"10.1016/j.bpj.2025.08.035","url":null,"abstract":"Dynamic compartmentalization by lipid membranes is a hallmark of living cells. The shapes of membrane surfaces are tightly coupled to their various functions, resulting in the myriad of complex membranal geometries. It has long been established by both theory and experiment that cells actively sculpt the shapes of membranes by utilizing curvature-stabilizing proteins that modulate the effective elastic properties of the membrane. Although it has also been known that many membrane proteins may transition between alternative conformational states, the implications of these conformational changes on membrane shaping are largely undetermined. Using continuum-based physical modeling, we explore how membrane proteins with multiple conformations can collectively shape biological membranes. We show that the conformational flexibility of such proteins may lead to emergent behaviors, such as mechanical bistability of the membrane and collective organization. We introduce a curvature-based shape discretization scheme that allows for efficient representation of membrane geometries and demonstrates that membranes embedded with such proteins can spontaneously adopt nonuniform shapes, driven by spatial patterning of protein conformational states, or by redistribution of the proteins in the membrane plane. Our general mechanism highlights how multistate proteins may collectively orchestrate large-scale morphological changes, providing a fundamental insight into the functional organization of diverse biological membrane systems.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144940988","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

AlphaFold2 captures conformational transitions in the voltage-gated channel superfamily. AlphaFold2捕获电压门控通道超家族中的构象转变。

IF 3.1 3区生物学

Biophysical journal Pub Date : 2025-08-29 DOI: 10.1016/j.bpj.2025.08.033

Elaine Tao, Ben Corry

{"title":"AlphaFold2 captures conformational transitions in the voltage-gated channel superfamily.","authors":"Elaine Tao, Ben Corry","doi":"10.1016/j.bpj.2025.08.033","DOIUrl":"10.1016/j.bpj.2025.08.033","url":null,"abstract":"Voltage-gated cation channels are crucial membrane proteins responsible for the electrical activity in excitable nerve, muscle, and cardiac tissue. These channels respond to changes in the membrane potential via conformational changes in their voltage-sensing domains (VSDs) that lead to the opening and closing of the ion conduction pore. Since alternative states of the VSDs are difficult to capture via experimental methods, we investigated the application of AlphaFold2 and subsampling of its multiple sequence alignment input to computationally predict structures across a range of intermediate and endpoint states. By generating 600 models for 32 members of the voltage-gated cation channel superfamily, we show that AlphaFold2 is capable of predicting diverse structures of the VSDs that could represent activated, deactivated, and intermediate conformations with more diversity seen for some VSD families compared with others. Modeling the full sequence of pseudo-tetrameric channels also produced a range of heterogeneous states in the pore and intracellular regions representative of local conformational changes and key secondary structural transitions. However, we observe that the global conformational coupling is limited across models, as different functional domains adopt physiologically incompatible states. Although short molecular dynamics simulations of a subset of the models suggest they are structurally plausible conformations, there are some incongruities between certain generated models and resolved cryo-EM structures. Further validation is required to confirm their structural and functional relevance.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941000","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

3D localization of retrovirus assembly in the presence of structured background with deep learning. 基于深度学习的结构化背景下逆转录病毒组装的三维定位。

IF 3.1 3区生物学

Biophysical journal Pub Date : 2025-08-29 DOI: 10.1016/j.bpj.2025.08.028

John Kohler, Kwang-Ho Hur, Elijah Wray, Jesse Donahue, Rayna Addabbo, Louis M Mansky, Joachim D Mueller

{"title":"3D localization of retrovirus assembly in the presence of structured background with deep learning.","authors":"John Kohler, Kwang-Ho Hur, Elijah Wray, Jesse Donahue, Rayna Addabbo, Louis M Mansky, Joachim D Mueller","doi":"10.1016/j.bpj.2025.08.028","DOIUrl":"10.1016/j.bpj.2025.08.028","url":null,"abstract":"Human immunodeficiency virus type 1 (HIV-1) particle assembly is driven by the Gag structural polyprotein and is a crucial step in the production of new virus particles. Elucidating the details of this process is necessary to fully understand the virus replication cycle. Real-time measurements of virus particle biogenesis in living cells have proved challenging, and most of our knowledge of this process to date has come from total internal fluorescence microscopy of labeled Gag at the bottom plasma membrane (PM) of adherent cells. While the glass coverslip adjacent to the bottom PM renders this an artificial environment, fluorescence measurements at the more physiologically relevant top PM are challenging due to the three-dimensional (3D) profile at the top PM as well as the large, structured background fluorescence that arises due to cytoplasmic, unassembled Gag protein. Here, we describe an approach to 3D localization microscopy and analysis to address the challenges associated with imaging virus assembly at the top PM in live cells. Specifically, we have employed the double helix point spread function for 3D imaging with an extended depth of field combined with a deep learning pipeline to analyze images that contain heterogeneous structured backgrounds. We demonstrate the power of this approach by measuring virus assembly at the top PM of adherent cells in 3D fluorescence microscopy and observe intriguing differences in the assembly kinetics and HIV-1 Gag puncta mobility between the adherent bottom PM and the nonadherent top PM.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941062","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

Surface properties of lysozyme aqueous solutions in the presence of reducing agents: The effect of disulfide bonds reshuffling. 还原剂存在下溶菌酶水溶液的表面性质：二硫键重组的影响。

IF 3.1 3区生物学

Biophysical journal Pub Date : 2025-08-28 DOI: 10.1016/j.bpj.2025.08.025

Michał Krycki, Eulalia A Levchuk, Imre Varga, Boris A Noskov

{"title":"Surface properties of lysozyme aqueous solutions in the presence of reducing agents: The effect of disulfide bonds reshuffling.","authors":"Michał Krycki, Eulalia A Levchuk, Imre Varga, Boris A Noskov","doi":"10.1016/j.bpj.2025.08.025","DOIUrl":"10.1016/j.bpj.2025.08.025","url":null,"abstract":"The influence of dithiothreitol (DTT) and β-mercaptoethanol (β-MEt) or their mixtures with a chaotropic denaturant, namely guanidine hydrochloride or urea, on the surface properties of lysozyme aqueous solutions was studied by the methods of dilatational surface rheology and ellipsometry. Adding 0.32 mM DTT to lysozyme solutions led to a considerable increase of the dynamic surface elasticity and a decrease of the dynamic surface tension compared with the results for native protein solutions. The observed effect was even more pronounced after a preliminary heating of the solutions. The rearrangement of disulfide bonds under the influence of a reducing agent and the subsequent cross-linking of lysozyme molecules resulted in the formation of a dense layer of adsorbed protein aggregates stabilized by intermolecular disulfide bridges at the liquid-gas interface. In the case of lysozyme solutions containing β-MEt, a significantly weaker effect ruled out the dense film formation, yet it also assumed some limited perturbations of the protein structure. The influence of reducing agents on the surface properties of lysozyme solutions differed from that of chaotropic denaturants and surfactants. At the same time, the simultaneous addition of both a reducing agent and a chaotropic denaturant led to a decrease of steady-state values of the dynamic surface elasticity due to the slow loosening of the cross-linked layer of lysozyme aggregates. Furthermore, unlike the protein solutions with urea, the molten globule state was not observed for solutions with both urea and a reducing agent, and the surface layer structure in the latter case was presumably similar to that in the layer in solutions containing guanidine hydrochloride where unfolded protein molecules formed loops and tails in the surface layer. The ellipsometric results corroborated these conclusions and revealed a decrease in the ellipsometric angle Δ in the case of both lysozyme/DTT/GuHCl and lysozyme/DTT/urea solutions.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941050","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

Putting a lid on it: The N-terminal helix of Arf1 inhibits switching via uniform stabilization. 把它盖上盖子：Arf1的n端螺旋通过均匀稳定抑制开关。

IF 3.1 3区生物学

Biophysical journal Pub Date : 2025-08-28 DOI: 10.1016/j.bpj.2025.08.031

Edgar V Peters, Tejaswi Koduru, Noam Hantman, Scott A McCallum, Qingqiu Huang, Jacqueline Cherfils, Catherine A Royer

{"title":"Putting a lid on it: The N-terminal helix of Arf1 inhibits switching via uniform stabilization.","authors":"Edgar V Peters, Tejaswi Koduru, Noam Hantman, Scott A McCallum, Qingqiu Huang, Jacqueline Cherfils, Catherine A Royer","doi":"10.1016/j.bpj.2025.08.031","DOIUrl":"10.1016/j.bpj.2025.08.031","url":null,"abstract":"The Arf and Arf-like GTPases, unlike all other Ras family GTPase members, exhibit a repressed conformation in their inactive, GDP-bound form. An important component of this autoinhibition is their N-terminal helix, which is missing in the other Ras family members. This helix caps a switch element called the interswitch, confining it to this repressed state. Activation by GDP/GTP exchange is primed by the dissociation of the N-terminal helix from the core of the protein, which precedes a massive conformational change and binding of GTP. An important unanswered question is how the energetics of Arf-GDP is remodeled at the initial step of activation, permitting the GDP/GTP reaction to proceed. In cells, the helix is displaced through interaction with a membrane, an effect that can be mimicked in solution by truncation mutants. Here, we used Arf1Δ17, a construct in which the N-terminal helix was deleted, to map the local stability of Arf1-GDP using high-pressure biophysical approaches, which we compared to that of full-length Arf1. Remarkably, deletion of the N-terminal helix decreased Arf1 stability across the entire structure. Thus, rather than imposing a specific allosteric pathway for repression, the N-terminal helix exercises global control of Arf1 stability to repress switching. This has important implications for understanding the energetics basis of the cooperation of membranes and guanine nucleotide exchange factors in Arf and Arf-like proteins activation.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941042","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

Atomistic modeling of lysophospholipids from the Campylobacter jejuni lipidome. 空肠弯曲杆菌脂质体溶血磷脂的原子模型。

IF 3.1 3区生物学

Biophysical journal Pub Date : 2025-08-28 DOI: 10.1016/j.bpj.2025.08.024

Astrid F Brandner, Kahlan E Newman, Jonathan W Essex, Syma Khalid

{"title":"Atomistic modeling of lysophospholipids from the Campylobacter jejuni lipidome.","authors":"Astrid F Brandner, Kahlan E Newman, Jonathan W Essex, Syma Khalid","doi":"10.1016/j.bpj.2025.08.024","DOIUrl":"10.1016/j.bpj.2025.08.024","url":null,"abstract":"Lysophospholipids are an important class of lipids in both prokaryotic and eukaryotic organisms. These lipids typically constitute a very small proportion (<1%) of the bacterial lipidome but can constitute 20%-45% of the Campylobacter jejuni lipidome under stress conditions. It is thus of importance to include these lipids in model C. jejuni membrane simulations for an accurate representation of the lipidic complexity of these systems. Here, we present atomistic models for four lysophospholipids from the C. jejuni lipidome, each derived from existing phospholipid models. Herein, we use molecular dynamics simulations to evaluate the ability of these models to reproduce the expected micellar, hexagonal, and lamellar phases at varying levels of hydration. Mixtures of phospholipids and lysophospholipids emulating the C. jejuni lipidome under ideal growth conditions were found to self-assemble into bilayers in solution. The properties of these mixed bilayers were compared with those containing only phospholipids: the presence of the selected lysophospholipids causes a subtle thinning of the bilayer and a reduction in area per lipid, but no significant change in lipid diffusion. We further test the mixed bilayer model running simulations in which a native inner membrane protein is embedded within the bilayer. Finally, we show that lysophospholipids facilitate the formation of pores in the membrane, with lysophospholipid-containing bilayers more susceptible to electroporation than those containing only phospholipids.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144940998","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

Structural and functional characterization of the Pro64Ser leptin mutant: Implications for congenital leptin deficiency. Pro64Ser瘦素突变体的结构和功能特征：对先天性瘦素缺乏的影响。

IF 3.1 3区生物学

Biophysical journal Pub Date : 2025-08-28 DOI: 10.1016/j.bpj.2025.08.026

Bao Quoc Ngo, Outi Lampela, André H Juffer

{"title":"Structural and functional characterization of the Pro64Ser leptin mutant: Implications for congenital leptin deficiency.","authors":"Bao Quoc Ngo, Outi Lampela, André H Juffer","doi":"10.1016/j.bpj.2025.08.026","DOIUrl":"10.1016/j.bpj.2025.08.026","url":null,"abstract":"Congenital leptin deficiency or dysfunction is a form of monogenic childhood obesity. The disease is primarily caused by mutations in the LEP gene, which encodes for the expression of a hormone called leptin. The mutations typically impair leptin synthesis, secretion, or binding to the leptin receptor (LepR). The Pro64Ser mutation in leptin, despite not affecting the protein's stability or its binding affinity to the LepR, completely abolishes the protein's ability to mediate intracellular signaling via the LepR. To elucidate the mechanism underlying this signal inhibition and to further understand the mechanism of leptin-mediated LepR signal transduction, we performed extensive molecular dynamics simulations of both the wild-type and mutant (MT) leptins. Our simulations reveal that the Pro64Ser mutation increases the rigidity of AB loop N-terminus and thus prevents the loop's conformational changes required for interaction with the LepR immunoglobulin-like domain (IgD). Conversely, the CD loop of the MT exhibits increased flexibility compared with the wild-type. This elevated flexibility potentially hinders the protein's transition into helical structure and subsequent interaction with the IgD. Given that the interactions between leptin and the LepR IgD are crucial for the formation of higher-order leptin-LepR assembly and the following intracellular signal transduction, the observed changes in the MT leptin loop dynamics provide a mechanistic explanation for the signaling defects.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941011","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

Role of Hsp70 chaperone in client-protein folding elucidated by Markov state modeling and NMR restraint-assisted molecular dynamics simulations. 利用马尔可夫状态模型和核磁共振抑制辅助分子动力学模拟阐明Hsp70伴侣蛋白在客户端蛋白折叠中的作用。

IF 3.1 3区生物学

Biophysical journal Pub Date : 2025-08-26 DOI: 10.1016/j.bpj.2025.08.022

Michael S O'Connor, Kirill A Konovalov, Josephine L Duvall, Jinoh Jang, Yichong Lao, Silvia Cavagnero, Xuhui Huang

{"title":"Role of Hsp70 chaperone in client-protein folding elucidated by Markov state modeling and NMR restraint-assisted molecular dynamics simulations.","authors":"Michael S O'Connor, Kirill A Konovalov, Josephine L Duvall, Jinoh Jang, Yichong Lao, Silvia Cavagnero, Xuhui Huang","doi":"10.1016/j.bpj.2025.08.022","DOIUrl":"10.1016/j.bpj.2025.08.022","url":null,"abstract":"Heat shock protein 70 (Hsp70) is a molecular chaperone that plays a key role in cellular processes by assisting protein folding and preventing aggregation. During client-protein folding, Hsp70 undergoes an ATP-dependent chaperone cycle involving the opening and closing of a flexible lid. Although the open-lid and closed-lid states of Hsp70 have been studied extensively, the specific role of the lid upon its interaction with client proteins remains unclear. In this study, we generated a Markov state model from coarse-grained molecular dynamics (MD) simulations of Hsp70 spanning from open-lid to closed-lid states and sampling a flexible lid-domain conformational ensemble. Starting from metastable Hsp70 conformations with varying degrees of lid opening, we performed nuclear magnetic resonance distance restraint-assisted all-atom MD simulations in explicit solvent to investigate the folding of the SH3 client protein bound to nucleotide-free Hsp70. All-atom MD simulations were performed with SH3 bound to and released from Hsp70, with nuclear magnetic resonance restraints applied to guide SH3 folding. Our results show that SH3 folds more effectively after having sampled conformational space within the closed-lid state of Hsp70. Further analysis reveals that the closed-lid state of Hsp70 interacts with SH3 via specific and highly conserved nonpolar residues, preventing the nonnative hydrophobic collapse of the SH3 client upon release from the chaperone. This study provides insights into specific atomic-level interactions that can be targeted by future experiments to better understand the molecular mechanism of Hsp70-assisted protein folding.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0