The Journal of Physical Chemistry B最新文献

{"title":"Free Energy Landscape of Lesion Recognition by Human 8-Oxoguanine DNA N-Glycosylase 1: Mechanistic Insights into Detection and Processing of 8-Oxoguanine in DNA.","authors":"Hyeonjun Kim, Youngshang Pak","doi":"10.1021/acs.jpcb.4c07073","DOIUrl":"10.1021/acs.jpcb.4c07073","url":null,"abstract":"<p><p>Human 8-oxoguanine DNA <i>N</i>-glycosylase 1 (hOGG1) is an essential enzyme in DNA repair, responsible for recognizing and excising 8-oxoguanine (8OG), the lesion resulting from oxidative damage to guanine (G). By removing 8OG, hOGG1 prevents mutations like G-to-T transversions, maintains genomic stability, and reduces the risk of cancer and other diseases. Structural studies of hOGG1 bound to DNA have shown that lesion recognition occurs through base eversion from the DNA helix and hOGG1 finger residue insertion into the DNA helix. To better understand this complex process, enhanced sampling molecular dynamics simulations were used to map two-dimensional free energy surfaces that describe lesion recognition in terms of base eversion and finger residue insertion. The resulting free energy profiles reveal one major SN2-like and two minor SN1-like pathways for 8OG and normal G and show that hOGG1 has kinetic and thermodynamic advantages in terms of recognizing 8OG over G. Based on these data, simple kinetic models were utilized to provide a quantitative view of lesion recognition kinetics of 8OG versus G. The most favorable kinetic scenario identified was that the scanning rate of hOGG1 falls between the initial interrogation rates of 8OG and G. According to this scenario, hOGG1 rapidly scans normal Gs at its intrinsic diffusion speed, bypassing unnecessary interrogations. However, when hOGG1 encounters 8OG, the enzyme significantly slows down during lesion recognition until the damaged base is excised from its catalytic pocket. This highly selective mechanism ensures that hOGG1 efficiently repairs oxidative DNA damage by carefully regulating how it scans the DNA, thus optimizing the balance between speed and accuracy during the scanning process.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"12133-12142"},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764501","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":"Balancing Group 1 Monoatomic Ion-Polar Compound Interactions in the Polarizable Drude Force Field: Application in Protein and Nucleic Acid Systems.","authors":"Yiling Nan, Prabin Baral, Asuka A Orr, Haley M Michel, Justin A Lemkul, Alexander D MacKerell","doi":"10.1021/acs.jpcb.4c06354","DOIUrl":"10.1021/acs.jpcb.4c06354","url":null,"abstract":"<p><p>An accurate force field (FF) is the foundation of reliable results from molecular dynamics (MD) simulations. In our recently published work, we developed a protocol to generate atom pair-specific Lennard-Jones (known as NBFIX in CHARMM) and through-space Thole dipole screening (NBTHOLE) parameters in the context of the Drude polarizable FF based on readily accessible quantum mechanical (QM) data to fit condensed phase experimental thermodynamic benchmarks, including the osmotic pressure, diffusion coefficient, ionic conductivity, and solvation free energy, when available. In the present work, the developed protocol is applied to generate NBFIX and NBTHOLE parameters for interactions between monatomic ions (specifically Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺, and Cl^-) and common functional groups found in proteins and nucleic acids. The parameters generated for each ion-functional group pair were then applied to the corresponding functional groups within proteins or nucleic acids followed by MD simulations to analyze the distribution of ions around these biomolecules. The modified FF successfully addresses the issue of overbinding observed in a previous iteration of the Drude FF. Quantitatively, the model accurately reproduces the effective charge of proteins and demonstrates a level of charge neutralization for a double-helix B-DNA in good agreement with the counterion condensation theory. Additionally, simulations involving ion competition correlate well with experimental results, following the trend Li⁺ > Na⁺ ≈ K⁺ > Rb⁺. These results validate the refined model for group 1 ion-biomolecule interactions that will facilitate the application of the polarizable Drude FF in systems in which group 1 ions play an important role.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"12078-12091"},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11646484/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764544","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":"Balance between Association and Dissociation Rate Constants Determines Morphology and Property of Amyloid Fibrils.","authors":"Taiga Nakagawa, Daisuke Tsuri, Ichiro Nishii, Naoko Kajimura, Katsumi Matsuzaki, Masaru Hoshino","doi":"10.1021/acs.jpcb.4c07654","DOIUrl":"10.1021/acs.jpcb.4c07654","url":null,"abstract":"<p><p>A parallel dimeric Aβ(1-40) peptide was prepared, and its structural and fibrillogenic characteristics were examined. The covalent linking of the peptide strongly facilitated the spontaneous formation of thioflavin-T-active, fibrillar aggregates rich in β strands without a lag phase. However, the aggregates formed by the dimeric peptide did not exhibit \"seeding activity\" to catalyze the formation of amyloid fibrils by wild-type Aβ(1-40) molecules. Heteronuclear NMR analysis revealed that an isolated dimeric molecule in reverse micelles lacked ordered secondary structures. It was therefore considered that excessively high hydrophobicity caused by dimerization was the major reason for the rapid formation of amorphous aggregates without seeding activity. A hundred-fold dilution of the concentration of dimeric peptides reproduced the aggregation kinetics with a preceding lag phase of several hours, similar to that of wild-type molecules. The resulting aggregates exhibited a typical amyloid fibril-like morphology and, importantly, possessed seeding activity for wild-type peptides. The present results emphasize the importance of an appropriate balance between association and dissociation rate constants for the formation of \"one-dimensional crystalline\" amyloid fibrils.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"12325-12332"},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749403","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":"Dual Nature of Large and Anisotropic Glass-Forming Molecules in Terms of Debye-Stokes-Einstein Relation Revealed.","authors":"Abin Raj, Marzena Rams-Baron, Kajetan Koperwas, Żaneta Wojnarowska, Marian Paluch","doi":"10.1021/acs.jpcb.4c04757","DOIUrl":"10.1021/acs.jpcb.4c04757","url":null,"abstract":"<p><p>The fundamental Debye-Stokes-Einstein (DSE) relation between rotational relaxation times and shear viscosity attracts longstanding research interest as one of the most important characteristics of many glass-forming liquids. Here, we provide strong evidence, missing so far, for the relevance of anisotropy for DSE-related behavior. Dielectric spectroscopy and shear viscosity measurements were employed to get insight into the decoupling between reorientation relaxation times and viscosity for anisotropic glass-formers with dipole moments oriented parallel or perpendicular to the long molecular axis. We found that in the case of large and anisotropic molecules, the breakdown of DSE relation depends on the component of anisotropic rotation contributing to the dielectric response. Specifically, for glass-formers with dipole moment perpendicular to the long molecular axis, the DSE relation was found to be valid throughout the supercooled regime. Contrary, a departure from the DSE predictions in the intermediate supercooled regime, was observed for glass-formers where only short-axes contributions were relevant in dielectric response. MD simulations revealed differences in the mechanism of short and long axes reorientations suggesting that for anisotropic objects, not the reorientation mechanism itself, but the aspect of anisotropic motion, is the key to understanding the behavior of these systems in the context of DSE relation.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"12154-12160"},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764567","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":"Spectroscopic Insight on Neodymium Solvation in Lithium Borohydride-Supported Electrolyte.","authors":"Abderrahman Atifi, Corey D Pilgrim, Christopher A Zarzana","doi":"10.1021/acs.jpcb.4c06917","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06917","url":null,"abstract":"<p><p>Borohydride-based electrolytes have recently emerged as promising media for the electrodeposition of electropositive metals, including rare earth (RE) elements. While the presence of supporting alkali metal cations and RE counteranions provides essential electrochemical conductivity for achieving fast metal electrodeposition, interactions between the host ligand and solvated neodymium (Nd) complexes remain unclear. This study provides insights into the coordination structure of a concentrated and directly solvated Nd salt in a lithium borohydride-supported electrolyte. Our spectroscopic results indicate that the RE coordination environment is significantly influenced by the solvation mechanism, which can vary between metathesis and complexation pathways, primarily dictated by stoichiometric factors. Under dilute conditions, nearly complete metathesis of anions leads to a high coordination number for the host ligand (borohydride), consistent with the previously reported solvated Nd speciation in chlorine-free electrolytes. In contrast, concentrated dissolution of the Nd salt in the supported electrolyte is dominated by a complexation pathway featuring a Li-ion-paired complex with a low coordination number of the host ligand. Density functional theory (DFT) calculations indicated that the observed blue shift in the borohydride vibration was the result of an increase in electron density drawn into the terminal B-H interbond region from the hydride as the coordination changed from Li to Nd. In conjunction with DFT results, vibrational analyses allowed correlation of the experimental shifts associated with changes in Nd ligation and coordination spheres, further consolidating the prevalence of highly chloride-coordinated species under concentrated conditions. The outcomes of this work illuminate the distinctive and heterogeneous coordination structures that the electroactive RE species can adopt at high concentrations in lithium borohydride-supported electrolytes, as a key step to comprehend the reported metal electrodeposition performance in these media.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811549","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":"Continuous Tuning of Intersystem Crossing Times in Rose Bengal Water/Methanol Solutions.","authors":"Onno Strolka, Pascal Rauthe, Tim Muschik, Philipp Frech, André Niebur, Andreas-N Unterreiner, Jannika Lauth","doi":"10.1021/acs.jpcb.4c07449","DOIUrl":"10.1021/acs.jpcb.4c07449","url":null,"abstract":"<p><p>We use femtosecond transient broadband absorption spectroscopy (TAS) to characterize Rose Bengal in water/methanol solutions and reveal a continuous tunability of intersystem crossing (ISC) times by changing the mole fraction of the solvents. We find that the transients of excited state absorptions (ESAs) in Rose Bengal at ∼430 nm can be attributed to transitions from the singlet state S₁, with decay times of 74 ps via ISC in pure water and up to 405 ps in pure methanol. TA measurements at near-infrared wavelengths, on the other hand, reveal the rise of an ESA at ∼1080 nm from the triplet state T₁ with time constants of 68 and 491 ps in pure water and methanol, respectively, strongly supporting the associated UV-vis TAS data. Solvent mixtures show a quasi-linear rise of the ISC times with increasing mole fractions of methanol and indicate that Rose Bengal in varying solvent mixtures can be used as a model system to study their influence on excited state photophysics.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"12189-12196"},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724287","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":"Thermal Stability and Photostability of Highly Confined Molecular Nanocomposites.","authors":"Cindy Yueli Chen, Haonan Wang, Ahmad Arabi Shamsabadi, Zahra Fakhraai","doi":"10.1021/acs.jpcb.4c06713","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06713","url":null,"abstract":"<p><p>Capillary rise infiltration of molecular glasses into self-assembled layers of rigid nanoparticles (NPs) can produce highly confined molecular nanocomposite films (MNCFs). Here, we investigate the thermal stability and photostability of MNCFs made by confining indomethacin glasses in silica NPs. We demonstrate increasing confinement decreases the rate of thermal degradation and increases the activation energy of degradation (up to ∼70 kJ/mol in 11 nm NPs, ∼3 nm pore size). Upon UV exposure under nitrogen, photodegradation is only observed at the near-surface region of MNCFs, with a thickness of one NP diameter. However, no further degradation is observed, even after prolonged UV exposure. The dramatically improved thermal stability and photostability of MNCFs can be attributed to the slower transport of reaction products, corresponding to the increased <i>T</i>_g (up to ∼30 K in 11 nm NPs). These findings demonstrate that extreme nanoconfinement can prolong the durability of molecular glasses in applications such as coatings and organic electronics.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811433","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":"Cataractous Eye Protein Isolate Stabilized Gold Nanoparticles Prevent Their Ethanol-Induced Aggregation.","authors":"Prasun Chowdhury, Sreshtha Chaki, Atri Sen, Swagata Dasgupta","doi":"10.1021/acs.jpcb.4c07076","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c07076","url":null,"abstract":"<p><p>Due to their distinctive optical, electrical, and catalytic characteristics, gold nanoparticles (AuNPs) have found increasing use for a wide range of applications, including biomedicine and catalysis. Inherent agglomeration propensities impair their functional qualities, stability, and biocompatibility. This work investigates the potential applications of the cataractous eye protein isolate (CEPI), a waste product rich in proteins from cataract surgery, as a novel AuNP stabilizing agent. It was found that CEPI can successfully stabilize AuNPs under a variety of situations, preventing ethanol-induced aggregation and preserving their structural integrity. Using spectroscopic and analytical techniques, including UV-Vis spectroscopy, dynamic light scattering (DLS), circular dichroism (CD) spectroscopy, and fluorescence quenching studies, we confirmed the successful binding of CEPI to AuNPs and the enhanced stability of the conjugates. A shift in the localized surface plasmon resonance (LSPR) peak and modifications to the secondary structure of the CEPI were indicative of strong binding and protective effects between CEPI and AuNPs. These findings suggest that CEPI, an underutilized biomaterial, can serve as an effective and biocompatible stabilizer for AuNPs, with potential applications in biomedical and therapeutic fields.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142816724","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":"Machine Learning Models for Predicting Polymer Solubility in Solvents across Concentrations and Temperatures.","authors":"Mona Amrihesari, Joseph Kern, Hilary Present, Sofia Moreno Briceno, Rampi Ramprasad, Blair Brettmann","doi":"10.1021/acs.jpcb.4c06500","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c06500","url":null,"abstract":"<p><p>Artificial intelligence and machine learning have become essential tools in predicting material properties to aid in the accelerated design of new materials. Polymer solubility, critical for new formulations and solution processing, is one such property. However, current models are limited by inadequate experimental data sets that cannot capture the complexity and detail for many features contributing to polymer solubility. Here, we provide a data set for polymer solution behavior based on Crystal16 turbidity measurements that includes high quality percent transmission data for polymer solutions for a variety of polymers, solvents, concentrations and temperatures. We use this data set to train a model that predicts the experimental transmission data at many temperatures and multiple concentrations. From this, we are able to classify the polymer/solvent pairs into three solubility categories providing a level of granularity to predictions beyond prior binary classification models considering only solvent/nonsolvent classes. The inclusion of multiple concentrations, temperatures and partially soluble data expands solubility prediction capability beyond prior work into predictions more attractive for use by formulators and process designers working with industrial polymer solutions.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142816729","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":"Phenolic -OH-Induced Fluorescence and Chemoselectivity in a Triptycene-Based <i>trans</i>-Azo Oligomer for Sensing Applications.","authors":"Meha Bhargava, Sonia Ali, Mamta Guleria, Jyoti Agarwal","doi":"10.1021/acs.jpcb.4c05081","DOIUrl":"10.1021/acs.jpcb.4c05081","url":null,"abstract":"<p><p>A novel triptycene-based <i>trans</i>-azo fluorescent oligomer exhibiting phenolic groups has been designed. The presence of phenolic -OH in conjugation with the azo group rendered the oligomer fluorescence active by keto-enol tautomerism, which was evidenced by quenching the fluorescence intensity of <b>TP1</b> in 1 M aq. NaOH. A green synthetic protocol was employed to synthesize this oligomer as a dark-brown solid, and it was characterized by using diverse analytical tools such as FTIR, ¹³C-CPMAS NMR, GPC, FESEM, EDS, TGA, and PXRD techniques. FESEM and PXRD confirmed its existence as amorphous nanoclusters. The oligomer displayed efficient chemosensing properties toward the detection of picric acid with the LOD value of 391 nM. The specific recognition of PA in the presence of other explosives and the results of real water sample analysis further indicated the high efficacy of the <b>TP1</b> as a chemosensor.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"12227-12236"},"PeriodicalIF":2.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724288","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}