The Journal of Physical Chemistry B最新文献_第3页

Improving Aqueous Metal Salt Interactions Using Machine-Learned Interatomic Potentials. 利用机器学习原子间电位改善金属盐水溶液相互作用。

IF 2.9 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-09-26 DOI: 10.1021/acs.jpcb.5c04022

Feranmi V Olowookere, C Heath Turner

{"title":"Improving Aqueous Metal Salt Interactions Using Machine-Learned Interatomic Potentials.","authors":"Feranmi V Olowookere, C Heath Turner","doi":"10.1021/acs.jpcb.5c04022","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c04022","url":null,"abstract":"Accurate modeling of aqueous metal salt solutions is essential for understanding processes relevant to environmental safety, energy storage, and separation technologies. Trace metals such as As3+ at low concentrations pose significant health and environmental risks. They are challenging to simulate due to limitations in both classical force fields (CFFs), which lack accuracy, and ab initio methods, which are restricted to short trajectories. In this study, we develop machine-learned interatomic potentials (MLIPs) to model aqueous AsCl3 and MgCl2 using the NequIP/Allegro equivariant graph neural network architecture trained on ab initio molecular dynamics (AIMD) and density functional theory data. Our MLIP models accurately reproduce ab initio energies and forces while capturing solvation structure, ion diffusion, and hydration dynamics more effectively than CFFs (AMBER and UFF models). Our MLIPs achieve energy MAEs < 1 meV/atom and force RMSEs < 40 meV/Å, while providing an O(104) speedup over AIMD. These MLIPs offer a reliable and efficient alternative for modeling trace metal speciation and transport, with implications for improved separation and environmental processes.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147193","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}

引用次数: 0

Impact of Force Field Polarization on Correlated Motions of Proteins. 力场极化对蛋白质相关运动的影响。

IF 2.9 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-09-26 DOI: 10.1021/acs.jpcb.5c03537

Ana Milinski, Annick Dejaegere, Roland H Stote

{"title":"Impact of Force Field Polarization on Correlated Motions of Proteins.","authors":"Ana Milinski, Annick Dejaegere, Roland H Stote","doi":"10.1021/acs.jpcb.5c03537","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c03537","url":null,"abstract":"Correlated motions of proteins underpin many physiological mechanisms, such as substrate binding, signal transduction, enzymatic activity, and allostery. These motions arise from low-frequency collective movements of biomolecules and have mostly been studied using molecular dynamics simulations. Here, we present the effects of two different empirical energy force fields used for molecular dynamics simulations on correlated motions─the nonpolarizable CHARMM36m additive force field and the polarizable Drude-2019 force field. The study was conducted on two proteins, ubiquitin─a small protein with well-described dynamics─and the nuclear receptor protein─peroxisome proliferator-activated receptor gamma (PPARγ). The ligand binding domain of PPARγ was of particular interest since its function is to regulate transcription through ligand and coregulator protein binding. It has been previously shown that a dynamical network of correlated motions ensures the transmission of information related to PPARγ ligand binding. We present the results of classical MD simulations where we analyze the results in terms of residue fluctuations, residue correlation maps, community network analysis, and hydrophobic cluster analysis. We find that RMS fluctuations tend to be greater and correlated motions are less intense with the Drude-2019 force field than with the nonpolarizable all atom additive force field. Analysis of large hydrophobic clusters in the respective proteins shows a greater loss of native contacts in the simulations using the Drude-2019 force field than in the simulations using the all atom additive force field. Our results provide the first quantification of the impact of using a polarizable force field in computational studies that focus on correlated motions.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147144","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}

引用次数: 0

Polycyclic Aromatic Hydrocarbons: Solvation, Solubility, and Hydrophobic Effects from Monte Carlo Simulations. 多环芳烃：溶解度、溶解度和蒙特卡罗模拟的疏水效应。

IF 2.9 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-09-25 DOI: 10.1021/acs.jpcb.5c05354

William L Jorgensen, Julian Tirado-Rives

{"title":"Polycyclic Aromatic Hydrocarbons: Solvation, Solubility, and Hydrophobic Effects from Monte Carlo Simulations.","authors":"William L Jorgensen, Julian Tirado-Rives","doi":"10.1021/acs.jpcb.5c05354","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c05354","url":null,"abstract":"Free energies of solvation in water and liquid cyclohexane have been computed for 20 arenes ranging in size from cyclobutadiene to coronene. Monte Carlo statistical mechanics (MC) was used with free-energy perturbation theory (FEP) and the OPLS-AA force field. The computed results for free energies of hydration are in close agreement with experimental data giving an average error of 0.4 kcal/mol. Some discrepancies are found for larger arenes for which the experimental data have greater uncertainties owing to low solubility. The free energies of solvation and free energy of transfer from cyclohexane to water all display strong correlations with the solvent-accessible surface area (SASA) or volume of the arene. In contrast to the hydration of alkanes, the free energies of hydration of arenes become much more favorable with increasing size covering an 11 kcal/mol range. The free energies of solvation in cyclohexane are still more favorable, resulting in a 5 kcal/mol range for the resistance to transfer of arenes from cyclohexane to aqueous solution. Strong correlations are also found between the aqueous solubility of arenes and the free energies of solvation in cyclohexane and water. The reported results provide fundamental thermodynamic data for solution-phase properties of arenes, with relevance to materials and environmental science.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147306","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}

引用次数: 0

Protein-Lipid Interactions in a Three-Component POPC-Cholesterol-Sphingomyelin Modulated Membrane. 三组分popc -胆固醇-鞘磷脂调节膜中的蛋白质-脂质相互作用。

IF 2.9 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-09-25 DOI: 10.1021/acs.jpcb.4c08395

Akanksha Kumari, Sugam Kumar, V K Aswal, Jaydeep Bhattacharya, Sobhan Sen, Ranjita Ghosh Moulick

{"title":"Protein-Lipid Interactions in a Three-Component POPC-Cholesterol-Sphingomyelin Modulated Membrane.","authors":"Akanksha Kumari, Sugam Kumar, V K Aswal, Jaydeep Bhattacharya, Sobhan Sen, Ranjita Ghosh Moulick","doi":"10.1021/acs.jpcb.4c08395","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c08395","url":null,"abstract":"Biomolecules and excipients can modulate membrane properties, initiate a string of events, and regulate their functionality. To elucidate these phenomena ex vivo, we prepared a three-component lipid model system that consisted of varying proportions of cholesterol, sphingomyelin, and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). To decipher the membrane dynamics, we included a nonmembranous protein, hemoglobin, in our study. Our initial investigation revealed the formation of self-assembled structures and phase separation in a pure POPC-based synthetic membrane when hemoglobin was reconstituted via a detergent-mediated method. A slight unfolding helped the protein adapt to the huge hydrophobic stress of the lipid environment and led to the formation of these self-assembled structures. To identify an optimal lipid composition that mimics the biological membrane, we employed three varying proportions of lipid mixtures: POPC, sphingomyelin, and cholesterol. We examine events like the formation of lipid bilayers, supramolecular structures, and phase separation using techniques like FRAP, FCS, AFM, Z-stacking, and rheology. We observed the variation in condensate formation and its distribution within the membrane, which differs upon an increase in concentration of sphingomyelin and cholesterol. Such membrane behavior is important for raft formation and signaling.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147284","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}

引用次数: 0

The Role of Hydrogen Bonds in Thermodynamic and Structural Properties in Binary Mixtures of Amino Acid Ionic Liquid-H₂O: A Combined Experimental and Computational Study. 氨基酸离子液体-水二元混合物中氢键在热力学和结构性质中的作用：实验与计算相结合的研究。

IF 2.9 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-09-25 DOI: 10.1021/acs.jpcb.5c02525

Ying Chen, Yan Qi, Deqi Peng, Jianying Qu, Ying Ma, Zhiliang Ou, Xiang Wang

{"title":"The Role of Hydrogen Bonds in Thermodynamic and Structural Properties in Binary Mixtures of Amino Acid Ionic Liquid-H2O: A Combined Experimental and Computational Study.","authors":"Ying Chen, Yan Qi, Deqi Peng, Jianying Qu, Ying Ma, Zhiliang Ou, Xiang Wang","doi":"10.1021/acs.jpcb.5c02525","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02525","url":null,"abstract":"Amino acid ionic liquids (AAILs) have attracted attention due to their excellent biocompatibility and degradability. In order to better understand the effect of water on the thermodynamic properties and nanomicrostructures of AAILs, we synthesized choline alanine ([Ch][Ala]) and measured the density of [Ch][Ala]-H2O with different water mass fractions at 298.15 K-348.15 K. The excess molar volumes (VmE) were calculated from the density data and compared with 3-aminopropyl-tri-n-butylphosphonium alanine aqueous solutions ([aP4443][Ala]-H2O), and it was found that the VmE of both AAILs-H2O mixtures were negative. The transport properties and nanomicrostructures of AAILs-H2O mixtures were then investigated by MD simulations and DFT calculations. The results showed that the microstructures and transport properties of both AAILs and H2O mixtures changed significantly upon the addition of water. Hydrogen bonds between anions slow down the dynamic properties of the mixtures. With the addition of water molecules, the anions and cations of both AAILs form hydrogen bonds with H2O, reducing the structural correlation of the anion-cation and destroying the polar ionic network and nonpolar structural domains. In addition, there were different aggregation states of water molecules in AAILs at different water concentrations.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147314","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}

引用次数: 0

Inhibition of Insulin Amyloid Fibrillation by the Putative Anticancer Alkaloid Chelerythrine: Spectroscopic, Imaging, and Theoretical Investigations. 假定的抗癌生物碱车车蓟碱对胰岛素淀粉样蛋白颤动的抑制：光谱、成像和理论研究。

IF 2.9 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-09-25 DOI: 10.1021/acs.jpcb.5c03665

Shukdeb Sing, Arindam Das, Gouranga Jana, Anirban Basu

{"title":"Inhibition of Insulin Amyloid Fibrillation by the Putative Anticancer Alkaloid Chelerythrine: Spectroscopic, Imaging, and Theoretical Investigations.","authors":"Shukdeb Sing, Arindam Das, Gouranga Jana, Anirban Basu","doi":"10.1021/acs.jpcb.5c03665","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c03665","url":null,"abstract":"Type-2 diabetes (T2D) is a major issue in the public health sector due to its high incidence and lack of global therapeutic options. The self-assembly behavior of human insulin (INS) can lead to membrane damage and cell dysfunction, which is directly linked to T2D ailment. The development of a potential therapeutic that can prevent the formation of amyloid fibrils is a promising strategy for the treatment of T2D ailment. Herein, we have used a natural alkaloid, chelerythrine, and explored its antiamyloidogenic function against INS fibrillation. Thioflavin T fluorescence and Congo red absorbance analysis revealed that chelerythrine can significantly suppress the INS fibrillation process. Circular dichroism and FTIR studies demonstrated that chelerythrine markedly reduced the β-sheet content of the INS fibrillar samples, indicating that chelerythrine inhibited the fibrillogenesis process. Tyrosine fluorescence analysis, Nile red analysis, and 8-anilino-1-napthalenesulfonic acid analysis also revealed that chelerythrine arrested the INS fibrillation, and the hydrophobic interaction between INS and chelerythrine played a critical role in this inhibitory process. Apart from the hydrophobic interaction, polar interaction and some other interactions may also be responsible for the inhibitory action of chelerythrine, which was revealed from molecular docking results. AFM imaging analysis strongly supported that the quantity of fibrils in the presence of chelerythrine was markedly less. Furthermore, chelerythrine has the potential to defibrillate existing fibrillar assemblies. Our work clearly elaborated the inhibitory effect of chelerythrine on INS fibrillation.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145135917","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}

引用次数: 0

Multiscale Analysis of Lubricating Grease: Molecular Self-Assembly, Shear Behavior, and Machine Learning-Assisted Viscosity Prediction. 润滑脂的多尺度分析：分子自组装，剪切行为和机器学习辅助粘度预测。

IF 2.9 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-09-25 DOI: 10.1021/acs.jpcb.5c05894

Dongjie Liu, Jingyi Wang, Zilu Liu, Wenjun Yuan, Jinjia Wei, Fei Chen

{"title":"Multiscale Analysis of Lubricating Grease: Molecular Self-Assembly, Shear Behavior, and Machine Learning-Assisted Viscosity Prediction.","authors":"Dongjie Liu, Jingyi Wang, Zilu Liu, Wenjun Yuan, Jinjia Wei, Fei Chen","doi":"10.1021/acs.jpcb.5c05894","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c05894","url":null,"abstract":"Lubricating grease is a semisolid material widely used in various mechanical systems, composed of base oil, thickeners, and additives. The network structures formed by thickeners offer grease special rheological properties. The viscosity of grease, a key indicator of its lubricating performance, is affected by the combined influence of temperature, shear rate, and thickener ratio. In this research, via molecular dynamics simulations and quantum chemistry calculations, combined with machine learning methods, we first demonstrate the self-assembly behavior of the three-dimensional network structure of lithium-based lubricating grease and identify three structural components crucial for network formation: COO--Li+-COO-, COO--Li+-OH, and OH-OH. Electrostatic interactions mainly drive the self-assembly of thickeners, with hydrogen bonds also playing a role. Nonequilibrium molecular dynamics simulations are conducted to calculate viscosities under different shear rates, temperatures, and thickener ratios. The results show significant shear thinning with increasing shear rate and temperature, and the viscosity increases with increasing thickener ratios. Machine learning algorithms are applied to predict grease viscosities, with ensemble models using the boosting method providing the most accurate prediction performance (coefficients of determination over 0.985). Feature importance and Shapley additive explanation analysis indicate that the order of feature importance is shear rate > temperature > thickener ratio, in which shear rate and temperature have negative effects on the predicted values , whereas thickener ratio has a positive effect. This research offers molecular insights into the formation of lithium-based grease networks, helps us understand its rheological behavior, which is affected by multiple factors, and provides guidance for designing lubricating grease.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147221","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}

引用次数: 0

Conformational Transition and Recognition Mechanism of Eukaryotic Riboswitches Powered by Thiamine Pyrophosphate Analogues: An Elucidation through Multiple Short Molecular Dynamics Simulations and Markov Model. 焦磷酸硫胺素类似物驱动的真核核糖开关的构象转变和识别机制：通过多个短分子动力学模拟和马尔可夫模型的阐明。

IF 2.9 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-09-25 DOI: 10.1021/acs.jpcb.5c04050

Jianzhong Chen, Jian Wang, Wei Wang, Wanchun Yang, Lu Zhao, Jing Su

{"title":"Conformational Transition and Recognition Mechanism of Eukaryotic Riboswitches Powered by Thiamine Pyrophosphate Analogues: An Elucidation through Multiple Short Molecular Dynamics Simulations and Markov Model.","authors":"Jianzhong Chen, Jian Wang, Wei Wang, Wanchun Yang, Lu Zhao, Jing Su","doi":"10.1021/acs.jpcb.5c04050","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c04050","url":null,"abstract":"Understanding the ligand-mediated conformational changes in eukaryotic riboswitches is crucial for elucidating their functional roles. In this study, multiple short molecular dynamics simulations, followed by Markov model analysis, were conducted to investigate how the binding of ligands such as three thiamine pyrophosphate analogues (TPP, PYI, and D2X) influences the conformational transitions of eukaryotic riboswitches. Our findings indicate that the presence of these ligands induces a greater number of conformational states and alters the relative orientation of ligands to key nucleotides, thereby impacting ligand-riboswitch recognition. The ligands TPP, PYI, and D2X were found to exert distinct effects on the conformations of specific structural regions, including P1, P4, P5, and L3 and junctions J23 and J45. This suggests that the dynamic nature of the riboswitch of eukaryotic riboswitches is highly dependent on the conformational responses within these regions, also supported by our principal component analysis. Additionally, changes in π-π interactions of ligands with nucleotides G30 and A31, hydrogen bonds formed between ligands and nucleotide, as well as those of a magnesium ion (Mg2+) with nucleotides G48, G66, and ligands, may play a significant role in mediating the conformational transitions of eukaryotic riboswitches. Overall, this research is expected to provide valuable theoretical insights into the functions and target roles of riboswitches.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147101","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}

引用次数: 0

Exploring Protic and Aprotic Solvent Effects on the Molecular Properties of Furfurals in Ionic Liquids. 探索质子和非质子溶剂对离子液体中糠醛分子性质的影响。

IF 2.9 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-09-25 DOI: 10.1021/acs.jpcb.5c03227

Sweta Jha, Praveenkumar Sappidi

{"title":"Exploring Protic and Aprotic Solvent Effects on the Molecular Properties of Furfurals in Ionic Liquids.","authors":"Sweta Jha, Praveenkumar Sappidi","doi":"10.1021/acs.jpcb.5c03227","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c03227","url":null,"abstract":"Furfurals serve as a pivotal, suitable biomass-derived platform chemicals for producing assorted value-added chemicals, biofuels, and biochemicals. Ionic liquids (ILs) are used to form various furfurals from lignocellulosic biomass (LCB). However, different forms of furfurals interact differently with imidazolium-based ionic liquids (IMILs), making their separation from the ILs difficult. In this study, we perform molecular dynamics simulations to investigate the performance of different furfurals in the presence of 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4], the protic solvent formic acid (FA), and the aprotic solvent hexamethylphosphoramide (HMPA). We consider seven different furfurals with distinct physiochemical properties, such as 2,5-bis(hydroxymethyl)furan (2BHF), 2,5-diformylfuran (2DFF), 2,5-dimethylfuran (2DMF), 2-methylfuran (2MF), furan-2,5-carboxylic acid (FCA), 2-furoic acid (FUA), and furan (FUR). We performed various structural, dynamic, and detailed thermodynamic analyses to understand their fundamental molecular behavior. In-depth atomic-level insights indicate that furfurals exhibit significant interaction with the solvent HMPA compared to FA. Based on the solvation free energy (ΔGsolv) and partition coefficient (log P) values, HMPA enhances the extraction ability of furfurals from the ILs. Overall, the results presented in this article provide guidance on furfural interaction behavior in the presence of protic and aprotic solvents for effective extraction.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147190","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}

引用次数: 0

Statistical Physics-Based Approaches to Model the Function and Complexation of Disordered Proteins. 基于统计物理的方法来模拟无序蛋白质的功能和络合。

IF 2.9 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-09-25 DOI: 10.1021/acs.jpcb.5c05422

Austin Haider, Kari Gaalswyk, Lilianna Houston, Nicholas J Ose, S Banu Ozkan, Kingshuk Ghosh

{"title":"Statistical Physics-Based Approaches to Model the Function and Complexation of Disordered Proteins.","authors":"Austin Haider, Kari Gaalswyk, Lilianna Houston, Nicholas J Ose, S Banu Ozkan, Kingshuk Ghosh","doi":"10.1021/acs.jpcb.5c05422","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c05422","url":null,"abstract":"Functional classification of intrinsically disordered proteins (IDP) is a challenge due to their low sequence homology and lack of stable tertiary structure. We embrace this challenge to classify a model system of two IDPs─NCBD and CID─that have coevolved and for which both ancestral and extant sequences are available, along with quantitative binding data. One of these sequences, NCBD, exhibits partial secondary structure, while the other (CID) remains highly disordered and is highly charged. We classify these sequences using statistical physics-derived sequence-dependent interaction maps that predict distance maps (ensemble average distances between arbitrary residue pairs). We also use sequence-specific dynamic profiles for further comparison. Our findings show that CID proteins can be classified into two major groups due to two distinct types of patterns in their electrostatic interaction maps. Classification of CIDs using nonelectrostatic patterning yields diverging predictions, illustrating the importance of accurately modeling long-range electrostatic interactions. Conversely, the classification of NCBD sequences generally reaches a consensus when physics-based noncharge patterning metrics are applied, along with the dynamical profiles. Furthermore, we used these sequence-dependent metrics and dynamical profiles to quantitatively model the binding affinities between the two IDPs. Surprisingly, we find that multiple physics-based sequence metrics quantitatively recapitulate the binding affinities between CID and NCBD variants, linking sequence composition and patterning to their emergent function. This integrated framework provides a generalizable strategy for classifying IDPs and predicting complexation behavior, offering new avenues for probing sequence-function relationships in disordered protein systems.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147269","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}

引用次数: 0