The Journal of Physical Chemistry B最新文献

{"title":"A Roadmap of Responses to Asymmetry Stress in Lipid Membranes.","authors":"Lisa Hua, Sevda Akcesme, Kira Müller, Heiko Heerklotz","doi":"10.1021/acs.jpcb.4c05868","DOIUrl":"10.1021/acs.jpcb.4c05868","url":null,"abstract":"<p><p>The selective insertion of membrane-impermeant amphiphiles such as detergents, (lipo)peptides, drugs, etc. into the <i>cis</i> leaflet of a membrane causes an imbalance between the intrinsic areas of the <i>cis</i> and <i>trans</i> leaflet, referred to as asymmetry stress or differential stress. The literature provides individual mechanisms of how membranes respond to such stress, which are relevant to membrane remodeling processes and leakage phenomena. By studying vesicle budding, membrane leakage, and isothermal titration calorimetry of liposomes interacting with digitonin, alkyl maltosides, miltefosine, and octyl glucoside, we developed a roadmap linking the stress-response mechanisms to each other. Initially, lateral compression or stretching of the leaflets accommodates a minor asymmetry stress. Then, either molecules flip to the <i>trans</i> leaflet or the membrane bends to form buds. Fast flip leads to the classic three-stage model. Budding proceeds up to its limit at 20-40% of the lipid. Beyond, insertion of further detergent is opposed by the pressure in the overpopulated leaflet. This \"staying out\" state can persist over hours or days and up to high detergent concentrations before detergent micelles induce \"micellar solubilization\". Alternatively, the stress can be reduced by a transient failure of the membrane, allowing for \"cracking in\" of molecules, transferring them to the <i>trans</i> side.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1260-1273"},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996304","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":"Pressure Protein Denaturation Compared to Thermal and Chemical Unfolding: Analyses with Cooperative Models.","authors":"Joachim Seelig, Anna Seelig","doi":"10.1021/acs.jpcb.4c07703","DOIUrl":"10.1021/acs.jpcb.4c07703","url":null,"abstract":"<p><p>The thermodynamics of pressure-induced protein denaturation could so far not be directly compared with protein denaturation induced by temperature or chemical agents. Here, we provide a new cooperative model for pressure-induced protein denaturation that allows the quantitative comparison of all three denaturing processes based on their free energy, enthalpy, entropy, and cooperativity. As model proteins, we use apolipoprotein A-1 and lysozyme. The comparison shows that heat-induced unfolding is the most cooperative process. It is characterized by large positive enthalpies and entropies and (due to enthalpy-entropy compensation) small negative free energies. Pressure denaturation is less cooperative. The entropies and enthalpies are less positive, and the resulting free energies are more negative. Chemically induced unfolding is the least cooperative and shows the most negative free energies, in particular, if guanidinium hydrochloride (exhibiting a high binding affinity to certain proteins) is used as a denaturant. The three unfolding processes differ not only with respect to their cooperativity and the thermodynamic parameters but also with respect to the volume changes, suggesting structural differences of the denatured proteins. Using cooperative models thus yields significant new insights into the protein unfolding/folding processes.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1229-1236"},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11789134/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring Dynamics and Intermolecular Interactions in Binary Mixtures of Reline and DMSO: An Investigation Using Nuclear Magnetic Resonance and Infrared Spectroscopic Techniques.","authors":"Huan Chen, Bona Dai, Lingyun Xu, Hongchun Dong, Mei Wang, Lei Yu, Zihui Qiu, Yue Li, Qi Shi, Jie Shu, Yuan Yuan, Xiaohong Li","doi":"10.1021/acs.jpcb.4c05660","DOIUrl":"10.1021/acs.jpcb.4c05660","url":null,"abstract":"<p><p>Reline, which is composed of choline chloride and urea in a molar ratio of 1:2, is the first and most extensively studied deep eutectic solvent (DES). In certain applications, reline is blended with organic solvents, dimethyl sulfoxide (DMSO) in most cases, to gain improved properties. Therefore, it is crucial to have a profound understanding of the impact of DMSO on the dynamics and structures of the species in the binary mixtures. In this study, neat reline and ten reline/DMSO mixtures, with DMSO molar fraction ranging from 0.1 to 0.95, were investigated primarily through a combined approach utilizing nuclear magnetic resonance (NMR) and Fourier transform infrared (FT-IR) spectroscopic techniques. Based on our investigation, we probed a significant transition of the binary mixtures from large molecule solutions or viscous liquids to nonviscous small-molecule solutions at a DMSO molar fraction of 0.7. Specifically, upon analyzing the self-diffusion coefficient, ¹H <i>T</i>₁ and ¹H <i>T</i>₂, we observed a notable increase in the molecular mobility of the species within the reline/DMSO system, particularly when the DMSO molar fraction exceeded 0.7. Drawing upon the FT-IR findings, we suggest that the enhanced molecular mobility, as evidenced by NMR analysis, is correlated with the disruption of molecular hydrogen-bonding interactions involving the -NH₂ and -OH groups. Furthermore, based on 1D ¹H, 1D ¹⁵N, and 2D ¹H-¹H COSY spectra, it was revealed that the interaction between urea and choline remains relatively stable until the DMSO fraction exceeds 0.7, whereupon it exhibited a notable weakening as the DMSO fraction increases from 0.7 to 0.95. In the meantime, DMSO molecules predominantly engage in hydrogen bond interactions with urea and choline when the DMSO molar fraction exceeds 0.7. Our results align well with previous molecular dynamics (MD) simulation studies and provide profound insights into the significant transition in the reline/DMSO mixture system.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1311-1322"},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996309","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":"Single-Site Local-Density Potentials for the Mesoscopic Representation of Water Based on the SAFT-VR Mie Equation of State.","authors":"James P D O'Connor, Ian P Stott, Andrew J Masters, Carlos Avendaño","doi":"10.1021/acs.jpcb.4c06454","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06454","url":null,"abstract":"<p><p>In this article, we present three mesoscopic models for water. All three models make use of local density-dependent interaction potentials, as employed within the Pagonabarraga-Frenkel framework [Pagonabarraga, I.; Frenkel, D. <i>J. Chem. Phys.</i> 2001, 115, 5015-5026]. The forms of these three interaction potentials are based on the free energy function of the SAFT-VR Mie equation of state (EoS) [Lafitte, T. <i>J. Chem. Phys.</i> 2013, 139, 154504]. Two of these models represent the water-water interaction as a spherically symmetric Mie interaction with temperature-dependent parameters, while the third model works with a temperature-independent Mie potential, but then explicitly models the effect of hydrogen bonding. All three models provide good predictions of the vapor-liquid equilibrium of water over a wide temperature range. They also give accurate predictions of the isothermal compressibility for both sub- and supercritical conditions. To model the interfacial tension of the vapor-liquid interface with our mesoscale simulations, we added a square-gradient term to our potential energy function. We show that the addition of this term has a minimal effect on the bulk properties of water. However, by parametrizing the coefficient of this term as a function of temperature, all three models again provide excellent predictions of water's interfacial tension over a wide temperature range. Of the three models, our preference is for the model that includes an association term, as this model can operate successfully over a wider range of conditions.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062540","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":"Fluoxetine Alters the Biophysics of DPPC and DPPG Bilayers through Phase-Dependent and Electrostatic Interactions.","authors":"Tho H Ho, Khai G Tran, Lam K Huynh, Trang T Nguyen","doi":"10.1021/acs.jpcb.4c04631","DOIUrl":"10.1021/acs.jpcb.4c04631","url":null,"abstract":"<p><p>Lipid membranes can control the permeability of a pharmaceutical drug, whereas the drug can induce changes in the structural and biophysical properties of the membranes. Understanding this interplay of drug-lipid membrane interactions can be of great importance in drug design. Here, we present a molecular dynamics study to provide insights into the interactions between the antidepressant fluoxetine and 1,2-dipalmitoyl-<i>sn</i>-glycero-3-phosphocholine (DPPC) or 1,2-dipalmitoyl-<i>sn</i>-glycero-3-phosphoglycerol (DPPG) bilayers. It was found that, due to the electrostatic interaction, the headgroup of the zwitterionic DPPC lipid is more stable than that of the negatively charged DPPG lipid, allowing the gel phase to persist even at the elevated temperature. At 25 °C, fluoxetine cannot penetrate into the gel-phase DPPC bilayer, while the electrostatic interaction between positively charged fluoxetine and negatively charged DPPG bilayer retains the drug within the lipid headgroup domain. When the temperature is increased to 45 °C, both neutral and charged forms of fluoxetine can partition into the DPPC and DPPG bilayers spontaneously. Analysis of the biophysical and structural changes in both DPPC and DPPG bilayers in the presence of fluoxetine revealed a phase-dependent effect. The binding of fluoxetine to the lipid bilayers limits the movement and orientation of the drug. These findings shed light on the interactions between a commonly prescribed antidepressant and lipid membranes, and such information can be beneficial to the development of potential therapeutic agents.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1248-1259"},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833169","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":"IR Fingerprint of the Intermolecular Hydrogen Bond on Amino Acids and Its Relevance to Chaperone Activity of αB-Crystallin.","authors":"Guohong Liao, Meixia Ruan, Yingjie Wang, Hailong Chen, Yuxiang Weng","doi":"10.1021/acs.jpcb.4c07865","DOIUrl":"10.1021/acs.jpcb.4c07865","url":null,"abstract":"<p><p>Intermolecular hydrogen bonds between carboxyl (COO^-) and amino groups are a common weak interaction in proteins. Infrared (IR) spectral assignment of such an intermolecular hydrogen bond provides a fingerprint for studying protein-protein interactions as its absorption frequency is affected by the molecular electrostatic environment. Temperature-dependent FTIR and temperature-jump time-resolved IR absorbance difference spectra of several typical amino acids and those of wild type and single-site mutated αB-crystallin were performed. It was found that the antisymmetric vibrational frequency of the COO^- groups in amino acids decreases from approximately 1626 to 1610 cm^-1 upon the formation of intermolecular hydrogen bonds, which was further supported by DFT calculations, while the IR frequency of the intermolecular hydrogen bonds on the formation of intermolecular hydrogen bonds, which was further supported by DFT calculations, while the IR frequency of the intermolecular hydrogen bonded COO^- groups at the αB-crystallin dimeric interface was also observed around 1610 cm^-1. With this spectral label, the active site of αB-crystallin, a heat shock molecular chaperone against the UV-light-damaged γD-crystallin was investigated. The active site was found to be localized at an arch loop structure connecting the two β-strands locked by intermolecular hydrogen bonds at the dimeric interface. It is the liberated arch loop after breaking of the intermolecular hydrogen bond locks that binds the damaged γD-crystallin, leading to the observed chaperone-like activity of αB-crystallin.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1237-1247"},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996340","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":"Proton Transfer Equilibrium in Pseudoprotic Ionic Liquids: Inferences on Ionic Populations.","authors":"Mark N Kobrak, Dmytro Nykypanchuk, Ankit Jain, Eddie Louz, Andrzej A Jarzecki","doi":"10.1021/acs.jpcb.4c07150","DOIUrl":"10.1021/acs.jpcb.4c07150","url":null,"abstract":"<p><p>Nonstoichiometric pseudoprotic ionic liquids (NPPILs) are an emerging class of ionic liquids with interesting physical properties and intriguing prospects for technological applications. However, fundamental questions remain about the proton transfer equilibria that underlie their ionic character. We use a combination of nuclear magnetic resonance spectroscopy, infrared spectroscopy, and small-angle X-ray scattering to characterize the equilibria of trihexylamine/butyric acid and water/butyric acid mixtures. This combination of techniques offers considerable insight into how proton transfer changes with the composition of the mixture. Further, we construct a model based on information from ¹H and ¹³C NMR, which yields numerical values for the concentrations of all ions present in the trihexylamine/butyric acid mixture, and demonstrate that the results of the model are supported by data from other physical measurements. This is the first quantitative calculation of ionic concentrations in an NPPIL.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1376-1386"},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11789136/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating Solvent Effects on the Stability of the Diethylnitroxyl Radical via Electron Paramagnetic Resonance.","authors":"Xinyu Wang, Yongtao Wang, Jia Yao, Haoran Li","doi":"10.1021/acs.jpcb.4c08026","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08026","url":null,"abstract":"<p><p>Operando electron paramagnetic resonance is used to monitor the light-initiated generation of the diethylnitroxyl radical from diethylhydroxylamine (DEHA) and its decay kinetics, thereby unveiling solvent effects on both the electronic structure and stability of the nitroxyl radical. The observed trends in hyperfine coupling constants (<i>A</i>_N and <i>A</i>_H) across different solvents align with previously reported values of the 4-amino-2,2,6,6-tetramethylpiperidoxyl radical (ATEMPO). Regarding the stability of the DEHA radical in various solvents, the obtained decay-kinetic constants (<i>k</i>) correlated more strongly with <i>A</i>_N than with the permittivity of the solvents. Moreover, distinguishing between protic and aprotic solvents leads to a better relationship between <i>A</i>_N and <i>k</i>, and a positive and constant correction of the nitroxyl radical's <i>A</i>_N supports the hydrogen-bonding effect in protic solvents. These findings indicate that mere hydrogen-bonding interaction does not enhance the stability of radicals. <i>A</i>_N of ATEMPO may serve as a superior metric for assessing the impact of solvent effects on both the electronic structure and stability of nitroxyl radicals. The data presented in this study will offer substantiation for the judicious selection of suitable solvents in reactions involving radicals.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062526","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":"Automated-Screening Oriented Electric Sensing of Vitamin B1 Using a Machine Learning Aided Solid-State Nanopore.","authors":"Sneha Mittal, Milan Kumar Jena, Biswarup Pathak","doi":"10.1021/acs.jpcb.4c05619","DOIUrl":"10.1021/acs.jpcb.4c05619","url":null,"abstract":"<p><p>Micronutrient detection and identification at the single-molecule level are paramount for both clinical and home diagnostics. Analytical tools such as high-performance liquid chromatography and liquid chromatography-tandem mass spectrometry have been widely used but include a high instrument cost and prolonged analysis time. Here, as a model system, by merging nanopore signatures with machine learning algorithms, we propose an automated electric sensing strategy to identify vitamin B1 and its phosphorylated derivatives with good accuracy. Further, the relationship between vitamin B1 dynamics and nanopore signatures is examined. To understand the machine-decision-making process, Shapley additive explanations are made. Using a machine learning aided solid-state nanopore, we pave the way for next-generation micronutrient detection.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1301-1310"},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542920","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":"Therapeutic Advantages of Nanoparticle-Impregnated Lysozyme Conjugates toward Amyloid-β Fibrillation and Antimicrobial Activity.","authors":"Jahnabi Upadhyaya, Imocha Rajkumar Singh, Bishal Pun, Hirak Jyoti Baishya, Sugam Kumar, S R Joshi, Sivaprasad Mitra","doi":"10.1021/acs.jpcb.4c07261","DOIUrl":"10.1021/acs.jpcb.4c07261","url":null,"abstract":"<p><p>The interaction of protein with nanoparticles (NPs) of varying shape and/or size boosts our understanding on their bioreactivity and establishes a comprehensive database for use in medicine, diagnosis, and therapeutic applications. The present study explores the interaction between lysozyme (LYZ) and different NPs like graphene oxide (GO) and zinc oxide (ZnO) having various shapes (spherical, 's', and rod-shaped, 'r') and sizes, focusing on their binding dynamics and subsequent effects on both the protein fibrillation and antimicrobial properties. Typically, GO is considered a promising medium due to its apparent inhibition and prolonged lag phase for LYZ fibrillation. However, the present results showed that spherical ZnO NPs (sZnO) offer superior efficacy in modulating fibrillation with an extended lag time of about 158.70 h, further emphasizing the importance of detailed investigation on the nanomaterial characteristics and fibril formation kinetics beyond initial observations. The experimental findings further confirmed a strong correlation between the binding affinity of NPs to the native protein and their effective inhibition of protein denaturation, ultimately preventing fibril formation. Interestingly, the lysozyme nanoconjugates showed intriguing bactericidal effects, as confirmed through the agar plate assay and SEM imaging, over the native protein. Overall, this study shows that appropriate bionanomaterials can exhibit multifunctional properties, which paves the way for a deeper investigation of NP characteristics, ultimately benefiting a wide array of intriguing research.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"1274-1288"},"PeriodicalIF":2.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982053","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}