The Journal of Physical Chemistry B最新文献

{"title":"Microtubule Binding of a Tau Peptide Monitored through Fluorine NMR Probes","authors":"Kalyan S. Chakrabarti,&nbsp;Luigi Russo,&nbsp;Dipendu Dhar,&nbsp;Kerstin Overkamp,&nbsp;Mehdi D. Davari,&nbsp;Nasrollah Rezaei-Ghaleh","doi":"10.1021/acs.jpcb.6c04549","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c04549","url":null,"abstract":"<p>Binding of tau protein to microtubule (MT) supports thestabilityand cellular functions of MT. Aberrations in tau-MT binding are linkedto several neurodegenerative diseases. Little is known about how regionsoutside the four canonical MT-binding repeat regions of tau protein(R1–R4) are involved in MT binding. Here, we synthesize a tauprotein fragment (tau368–412, R’ domain), a flankingdomain downstream of the R4 domain, without and with fluorine labelsincorporated at its aromatic (Phe378, Tyr394) and proline (Pro397,Pro405, with 2<em>S</em>,4<em>R</em> stereochemistry)residues. The ¹H and ¹³C chemical shift datapoint to slight secondary structural propensities in tau peptide andconfirm that its predominantly disordered structure is largely preservedafter fluorination. The NMR chemical shift and NOESY data detect andquantify cis-Pro at Pro397 and Pro405 positions, and the MD simulationdata suggest that the cis/trans isomerization of these two prolinescould alter the conformational ensemble of the tau peptide. Throughcombined ¹H and ¹³C NMR chemical shift and ¹⁹F chemical shift, relaxation, and dark-state exchange saturationtransfer (DEST) analyses, we reveal a rapid exchange process betweenfree tau peptide and a lowly populated MT-bound state that occurson a submillisecond time scale (τ_ex ∼ 500μs). The ¹⁹F DEST data also demonstrate that theMT binding predominantly occurs at the N-terminal region of the taupeptide adjacent to the canonical R4 domain and that it retains alarge level of side-chain dynamics in the MT-bound state. Our studyprovides mechanistic insight into tau-MT binding and exemplifies hownovel ¹⁹F NMR-based methods enable investigating proteinsin the context of challenging large systems.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 39","pages":"10206–10221"},"PeriodicalIF":3.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149093614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Local RNA Structure, Ion Hydration Shell, and the Energy Barrier for Water Exchange from the Ion Hydration Shell Determine the Mechanism of Ion Condensation on Specific RNA Sites","authors":"Antarip Halder,&nbsp;Sunil Kumar,&nbsp;Govardhan Reddy,&nbsp;Sk Habibullah","doi":"10.1021/acs.jpcb.6c03417","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c03417","url":null,"abstract":"<p>RNAfolding and functioning require the binding of metal ions inspecific cavities of the folded structure, especially in riboswitchesthat regulate metal ion concentrations. However, the fundamental principlesgoverning the specific binding of metal ions to RNA are unclear. Weprobed the condensation mechanism of biologically relevant alkali(Na⁺ and K⁺), alkaline-earth (Mg²⁺ and Ca²⁺), and transition metals (Mn²⁺, Co²⁺, Ni²⁺, and Zn²⁺) on a part of theNi²⁺ and Co²⁺ (NiCo)-sensing riboswitch usingcomputer simulations. The selected structure has multiple secondarystructural elements and a single site for ion binding. We show thatthree factors primarily determine ion binding to the RNA site: (1)the varying structural constraints from different RNA secondary structuralelements; the mode of ion binding depends on the local structure ofthe RNA around the ion-binding pocket; (2) the arrangement of watermolecules in the ion hydration shell; and (3) the energy barrier forthe ion to lose a water molecule from its hydration shell and transitionfrom an outer- to an inner-shell interaction. These results have implicationsfor designing biocompatible sensors using riboswitches to probe theconcentrations of intracellular metal ions.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 39","pages":"10146–10160"},"PeriodicalIF":3.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149124700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chemical Feedback and Collective pH-Dynamics in Enzyme-Powered Artificial Cells","authors":"Nils Göth,&nbsp;Joachim Dzubiella","doi":"10.1021/acs.jpcb.6c03926","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c03926","url":null,"abstract":"<p>Chemical communication between artificial cells (ACs)is crucialfor the collective behavior in synthetic prototissues. Recently synthesizedACs show pH-responsive and pH-modifying behavior by an enzymatic chemicalreaction. However, the chemical interplay between pH-responsive ACsis theoretically not well studied. Here, we report a simple two-variablemodel for such ACs that couples substrate conversion, enzyme activity,membrane permeability, and pH-buffering. We calibrate the model torecent experiments of glucose oxidase- and urease-loaded ACs, andreproduce a protection mechanism against external acid or base perturbations.Building on the derived models we predict the dynamics of AC-mixturesof the two antagonistic ACs. Depending on composition and initialpH, the mixtures exhibit a stable low-pH state, a stable high-pH state,or bistability, providing a minimal route to hysteretic pH controlin AC-communities. On longer time scales, fuel depletion leads totransient states with programmable pH and lifetime. Our results demonstratethe potential of chemical communication in AC-systems and providetestable design rules for future experiments.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 39","pages":"10269–10278"},"PeriodicalIF":3.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149124879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anion Effects on Interspecies Interactions in Tris-Salt/Ethylene Glycol Deep Eutectic Solvents Revealed by Dielectric Relaxation Spectroscopy","authors":"Vira Agieienko,&nbsp;Vadim Neklyudov,&nbsp;Andrey Vorotyntsev,&nbsp;Richard Buchner","doi":"10.1021/acs.jpcb.6c04588","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c04588","url":null,"abstract":"<p>To understand the interspecies interactions in ethyleneglycol(EG)-based eutectic systems, we studied solutions of Tris [tris(hydroxymethyl)aminomethane]chloride, nitrate, and perchlorate in EG using dielectric relaxation(DR) spectroscopy over the frequency range 0.05 ≤ ν/GHz≤ 89 at concentrations from 0.1 M to the solubility limitsat 298.15 K. Among the studied systems, {Tris·HNO₃+EG} forms a deep eutectic solvent at salt mole fractions between0.08 and 0.13. The DR spectra are described by three relaxation modesassigned to reorientation of Tris-containing species, including freeTris·H⁺ cations and contact ion pairs (slow Debyeprocess), relatively unperturbed EG molecules (intermediate Cole–Davidsonmode), and fast librations. We show that the studied salts are onlyweakly solvated in EG, with solvation numbers at infinite dilutiondecreasing in the sequence Tris·HCl (2.30) &gt; Tris·HNO₃ (1.76) &gt; Tris·HClO₄ (1.04). This trendisconsistent with decreasing anion–EG interaction strength andwith the Gibbs formation energies of the corresponding anion–EGcomplexes. In contrast, ion association is governed by anion chargedensity, yielding apparent association constants of approximately120, 20, and 5 M^–1 for Tris·HCl, Tris·HNO₃, and Tris·HClO₄, respectively. Although thefraction of free Tris·H⁺ cations increases with concentration,all systems exhibit subideal Walden behavior within the studied compositionrange, suggesting that cation–cation interactions significantlyreduce ionic mobility. These findings demonstrate that ion solvation,ion association, and ionic mobility in Tris-based eutectic systemsare governed by different aspects of anion identity, highlightingtheir potential for the rational design and further application ofeutectic solvents with tunable physicochemical and transport properties.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 39","pages":"10310–10322"},"PeriodicalIF":3.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149093618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extending Observation Windows While Preserving Signal-to-Noise in Single-Molecule Spectroscopy","authors":"Quyen B. Le,&nbsp;Adrienne M. Garcia,&nbsp;Cynthia A. Taylor,&nbsp;John T. King","doi":"10.1021/acs.jpcb.6c03371","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c03371","url":null,"abstract":"<p>We introduce an approach to extend the observation windowin single-moleculespectroscopy that is generalizable to any fluorophore without relyingon chemical photostabilization. The bleaching time can be controlledthrough the repetition rate of a pulsed excitation source. We showthat reducing the excitation repetition rate from 40 to 2.5 MHz delaysphotobleaching and therefore extends the observation window of a single-moleculefluorophore by more than an order of magnitude. Furthermore, we demonstratethat photon-stream analyses that depend on emitted photon flux suffera decrease in signal-to-noise ratio with decreasing repetition rate,while analyses that depend on total photon number have a signal-to-noiseratio that is independent of excitation repetition rate.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 39","pages":"10140–10145"},"PeriodicalIF":3.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149124819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conformational Landscape of a Marginally Disordered Protein HYPK and its Charge-Variant Mutant in the Context of Folded Domains","authors":"Kari Gaalswyk,&nbsp;Martin Gruebele,&nbsp;Kingshuk Ghosh","doi":"10.1021/acs.jpcb.6c03835","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c03835","url":null,"abstract":"<p>Intrinsically disordered proteins (IDPs) can have varyingproportionsof disordered and structured regions, and various fractions of aminoacids promoting these regions. This raises the possibility that someIDPs may behave as marginal proteins, exhibiting properties of bothdisordered and folded states. HYPK is one such recently discoveredmarginal protein studied by fluorescence assays (with fluorescentproteins attached at the termini) and circular dichroism (CD) whilemodulating temperature, crowding, ionic strength and sequence (byaltering charge composition and patterning). Here, we use all-atommolecular dynamics (MD) simulations to understand the sequence-specificand structural origin of this marginality by investigating the conformationlandscape of both the wild-type and a charge-variant mutant of HYPK,with and without fluorescent proteins (FPs) attached at the N- andC- termini. We find the charge-variant mutant is more compact comparedto the wild type both with and without FPs, showing the importanceof charge patterning that is consistent with experimental observationsand theoretical predictions used for experimental characterization.The wild-type HYPK fused to FPs reveals two distinct conformationalpopulations differing in helix packing, which may account for themarginality observed experimentally. The charge-variant mutant proteinwith FPs also displays bimodal conformational populations, but througha different mechanism involving competitive electrostatic interactionsbetween different protein segments and the FPs. Bimodality is observedin the mutant without FPs under different salt conditions due to competitiveinteractions between different segments of the chain or between thechain and counterions, while it becomes less evident in the wild-typeHYPK without the crowding and surface interactions provided by theFPs. These findings offer broad insights into the origin of marginality,competing interactions, as well as the roles charge patterning andfolded domains play on IDP conformation both in vitro and in-cell.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 39","pages":"10161–10174"},"PeriodicalIF":3.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149093668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Saponin Chemistry Controls Anionic Lipid Tolerance and Divalent Metal Ion Responses in Magnetically Alignable Bicelles","authors":"Samuel D. McCalpin,&nbsp;Cletus N. Obi,&nbsp;Ayyalusamy Ramamoorthy","doi":"10.1021/acs.jpcb.6c03292","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c03292","url":null,"abstract":"<p>Saponin–phospholipid bicelles have emerged aspromisingmembrane-mimetic systems for anisotropy-based NMR studies, but theirutility depends on their ability to accommodate physiologically relevantlipid compositions and ionic environments. Here, we systematicallyinvestigated how saponin chemistry governs three key properties ofmagnetically alignable bicelles: tolerance to anionic lipid incorporation,responsiveness to lanthanide-induced alignment reorientation, andstability in the presence of divalent metal ions. Using ³¹P NMR spectroscopy as a sensitive probe of phase behavior and alignment,we compared bicelles formed with glycyrrhizic acid (GA), hederacosideC (HC), and crude quillaja saponins (CQS). While all saponins effectivelysolubilized the anionic lipid DMPG, only HC supported magneticallyaligned bicelles with high anionic lipid fractions (up to 70%), whereasGA was limited to low levels of incorporation (10%). Both GA- andHC-based bicelles underwent lanthanide-induced alignment flipping,although with significant spectral broadening and intermediate alignmentstates indicative of increased heterogeneity. Divalent cation effectswere strongly ion- and saponin-dependent; HC bicelles were robustto the presence of Ca²⁺ but were destabilized by Mg²⁺, whereas GA bicelles were disrupted by both ions at lowconcentrations. Together, these results demonstrate that saponin identitycritically determines bicelle compatibility with charged lipids andionic conditions, establishing design principles for tailoring saponin-basedbicelles as versatile, biomimetic alignment media for membrane proteinstructural studies.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 39","pages":"10256–10268"},"PeriodicalIF":3.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149093597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Learning Structure–Dynamics Relationships in Metallic Glasses from Atomic Configurations Using Machine Learning and DeepSets","authors":"Vu Bich Hanh,&nbsp;Ngo T. Que,&nbsp;Anh D. Phan","doi":"10.1021/acs.jpcb.6c04360","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c04360","url":null,"abstract":"<p>Understanding the relationship between atomic structureand relaxationdynamics is essential for revealing the physical behavior of metallicglasses. In this work, we integrate molecular dynamics simulations,Elastically Collective Nonlinear Langevin Equation theory, and artificialintelligence to investigate both the forward and inverse structure–dynamicsrelationships in four Zr-based metallic glasses. For the forward prediction,conventional machine learning models and a DeepSets neural networkwere developed to predict the structural relaxation time from atomicconfigurations with and without temperature information. Atomic structurealone provides strong predictive capability, while incorporating temperatureconsistently improves the performance. Among the conventional models,Gradient Boosting achieved the best accuracy with a test <em>R</em>² of 94.50%, whereas DeepSets further increased the accuracyto 96.35% by directly learning from atom-wise representations. Forthe inverse problem, machine learning models successfully reconstructedradial distribution functions from structural relaxation time andtemperature, reproducing the major structural characteristics of metallicglasses. These results demonstrate the complementary roles of atomicstructure and temperature in governing relaxation dynamics and establishan effective bidirectional artificial intelligence framework for studyingand inversely designing amorphous materials.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 39","pages":"10348–10360"},"PeriodicalIF":3.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149093647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Two-Stage Chemical Degradation of PTFE with H- and HO-Radicals: A DFT Study Under PEMFC Operating Conditions","authors":"Rashen Lou Omongos,&nbsp;Ichiro Minami,&nbsp;András Vernes,&nbsp;Alejandro A. Franco","doi":"10.1021/acs.jpcb.6c02909","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c02909","url":null,"abstract":"<p>Polytetrafluoroethylene (PTFE) plays a fundamental rolein protonexchange membrane fuel cells (PEMFCs) as it enhances the structuralintegrity of the gas diffusion and microporous layers and, more importantly,helps with water management. However, it is also vulnerable to differentkinds of degradation under PEMFC operating conditions. One of theprincipal degradation mechanisms is chemical degradation involvingH- andHO-radicals. In this study, we propose a two-stage degradationmechanism in which the process is initiated by H-radical attack onPTFE and subsequently propagated through reactions with the HO-radicals.To this end, a comparative density functional theory (DFT) study wasconducted to investigate six chemical degradation pathways of PTFEvia HO-radicals at the <em>ab initio</em> PBE0/def2-TZVPPlevel. The solvation model based on density (SMD) was employed asan implicit solvation model with water as the solvent to model PEMFCconditions. Reaction enthalpies, Gibbs free energies, and activationfree energies were calculated for all of the elementary steps. Amongthe competing routes, pathways initiated at secondary carbon sitesare both thermodynamically and kinetically favored, ultimately resultingin PTFE chain scission and the formation of CO₂ and water.These findings provide atomistic insight into the chemical degradationof PTFE and establish a mechanistic foundation for the developmentof more chemically durable components of PEMFCs while also providingthermodynamic and kinetic data that can support future multiscaledegradation models for fuel cell durability.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 39","pages":"10323–10336"},"PeriodicalIF":3.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149093598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Noncovalent Interaction Origins of Substrate Discrimination in LinB: A Combined QM/MM and SAPT Analysis","authors":"Agata Sowińska,&nbsp;Michał Rostkowski,&nbsp;Agnieszka Dybala-Defratyka,&nbsp;Agnieszka Krzemińska","doi":"10.1021/acs.jpcb.6c04481","DOIUrl":"https://doi.org/10.1021/acs.jpcb.6c04481","url":null,"abstract":"<p>Noncovalent interactions (NCIs) play a fundamental rolein ligandorganization within enzyme active sites and are increasingly recognizedas contributors to selective substrate recognition. The haloalkanedehalogenase LinB provides a suitable system for probing the physicochemicalorigins of selectivity, as structurally similar substrates exhibitmarkedly different reactivity. In this work, we investigated LinB-catalyzeddehalogenation pathways for 1,2-dibromopropane (DBP) and the closelyrelated 1,2-dichloropropane (DCP), considering both C1 and C2 nucleophilicattack for each enantiomer. While minimum free-energy pathway calculationsreproduced the experimentally observed DBP preference, they did notfully resolve the molecular origin of these selectivity trends withina reaction-coordinate framework. To address this limitation, we appliedsymmetry-adapted perturbation theory (SAPT) to ensembles of representativestructures sampled along the reaction pathways. This interaction-levelapproach revealed that substrate discrimination arises from a finelybalanced interplay of electrostatic attraction, dispersion stabilization,and exchange repulsion, rather than a single dominant factor. Active-siteresidues preorganize the binding pocket to favor DBP stabilization,whereas DCP experiences weaker stabilizing interactions and increasedrepulsion, resulting in higher barriers and reduced reactivity. Overall,this study demonstrates the utility of SAPT-based analysis of NCIsfor elucidating nonmechanistic contributions to enzyme selectivitybeyond conventional pathway approaches.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"130 39","pages":"10175–10191"},"PeriodicalIF":3.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149124810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}