Alexander Moriarty, Takeshi Kobayashi, Teng Dong, Kristo Kotsi, Panagiota Angeli, Matteo Salvalaglio, Ian McRobbie, Alberto Striolo
{"title":"New Coarse-Grained Models to Describe the Self-Assembly of Aqueous Aerosol-OT.","authors":"Alexander Moriarty, Takeshi Kobayashi, Teng Dong, Kristo Kotsi, Panagiota Angeli, Matteo Salvalaglio, Ian McRobbie, Alberto Striolo","doi":"10.1021/acs.jpcb.5c00472","DOIUrl":"10.1021/acs.jpcb.5c00472","url":null,"abstract":"<p><p>Aerosol-OT (AOT) is a very versatile surfactant that exhibits a plethora of self-assembly behaviors. In particular, due to its double-tail structure, it is capable of forming vesicles in water. However, the size of these structures, and the time scales over which they form, make them difficult to study using traditional all-atomistic molecular dynamics simulations. Here, three coarse-grained models are developed for AOT with different levels of detail. The models take advantage of the Martini 3 force field, which enables 2:1 mappings to be employed for the tail groups. It is shown that these models are able to reproduce the self-assembly behavior of AOT in water at three concentrations: below the critical vesicle concentration (CVC), above the CVC, and in the lamellar phase. The results also demonstrate the formation of vesicles from bicelles above the critical vesicle concentration, which is an important milestone for the continued study of vesicle behavior.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"5299-5310"},"PeriodicalIF":2.8,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12128036/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109134","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":"Molecular Dynamics Simulations of Concentrated and Dilute Aqueous Solutions of Poly(<i>N</i>-Isopropylacrylamide) Using a Modified OPLS-AA Model.","authors":"Takuma Yagasaki, Nobuyuki Matubayasi","doi":"10.1021/acs.jpcb.5c00789","DOIUrl":"10.1021/acs.jpcb.5c00789","url":null,"abstract":"<p><p>We perform molecular dynamics (MD) simulations of aqueous poly(<i>N</i>-isopropylacrylamide) (PNIPAM) solutions using the OPLS-AA model and its modified version in combination with the TIP4P/2005 water model. The original OPLS-AA model underestimates the demixing temperature of concentrated solutions and the coil-globule transition temperature in dilute solutions, whereas the modified model reproduces both. It was reported that the transition from the globule state to the coil state never occurred in MD simulations with the original OPLS-AA model. This problem is avoided by using the modified model because of the fast dynamics near the coil-globule transition temperature, which is higher for the modified model than for the original model by ∼60 K. The distribution functions of two structural order parameters calculated from well equilibrated trajectories of the modified model clearly show that the coil-globule transition is not a discontinuous first-order transition, as suggested in previous MD studies, but a continuous transition as predicted from mean field theory. We also find that the effect of polymer-polymer hydrogen bonding on the dynamics of aggregated polymer chains is less significant than assumed in experimental studies.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"5234-5244"},"PeriodicalIF":2.8,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074943","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}
Maciej Banaszek, Barbara Golec, Renata Rybakiewicz-Sekita, Jarosław Kowalski, Piotr Szczodry, Natalia Dutkiewicz, Jacek Waluk and Aleksander Gorski*,
{"title":"Enhancing Photostability by Thermodynamic and Kinetic Factors: Free-Base and Palladium meso-Aryl-octaethylporphyrins","authors":"Maciej Banaszek, Barbara Golec, Renata Rybakiewicz-Sekita, Jarosław Kowalski, Piotr Szczodry, Natalia Dutkiewicz, Jacek Waluk and Aleksander Gorski*, ","doi":"10.1021/acs.jpcb.5c0242310.1021/acs.jpcb.5c02423","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02423https://doi.org/10.1021/acs.jpcb.5c02423","url":null,"abstract":"<p >Photostability is a crucial parameter in applications based on light–matter interactions. In this work, we demonstrate that photodegradation efficiency can be strongly decreased by altering the thermodynamic and kinetic characteristics of a chromophore. Photobleaching quantum yields have been determined for a series of free-base octaethylporphyrins and their palladium metallocomplexes gradually substituted by phenyl groups at the <i>meso</i> positions. Due to increased oxidation potential of palladium porphyrins, photostability is improved in comparison with zinc or magnesium derivatives. A spectacular effect is observed for nonplanar palladium derivatives in which the triplet lifetime in deoxygenated solution is shortened by 3 orders of magnitude with respect to planar porphyrins. Comparison of photodestruction efficiencies in oxygen-containing and degassed toluene samples shows a hundred-fold decrease of photobleaching quantum yields for nonplanar palladium porphyrins, reaching an extremely low value of less than 10<sup>–9</sup>. In contrast, free-base, nonplanar porphyrins are less stable than the planar analogues in nondegassed toluene. Finally, planar free-base and palladium porphyrins become significantly less photostable in the degassed solution because the triplet decay time increases by 3 orders of magnitude compared to oxygen-containing samples.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 22","pages":"5491–5500 5491–5500"},"PeriodicalIF":2.8,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jpcb.5c02423","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144211748","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}
Thor van Heesch, Sudhanshu Sharma, Bert van Erp, Alberto Pérez de Alba Ortíz, Remus T Dame, Jocelyne Vreede, Krishna Gavvala
{"title":"Adaptation of DNA to Protein Binding Revealed by Spectroscopy and Molecular Simulation.","authors":"Thor van Heesch, Sudhanshu Sharma, Bert van Erp, Alberto Pérez de Alba Ortíz, Remus T Dame, Jocelyne Vreede, Krishna Gavvala","doi":"10.1021/acs.jpcb.5c00189","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00189","url":null,"abstract":"<p><p>DNA demonstrates remarkable structural diversity, transitioning between conformations such as B-DNA and A-DNA under specific environmental or protein-binding conditions. These transitions are relevant for mediating cellular processes such as gene regulation, DNA organization, and stress response. In bacteria, the histone-like nucleoid structuring protein (H-NS) exemplifies the interaction between sequence-dependent DNA conformational adaptability and protein-mediated regulatory mechanisms. Despite evidence for the strong affinity of H-NS for AT-rich DNA, the specific molecular and structural interactions driving this recognition remain largely unclear. Combining fluorescence spectroscopy, circular dichroism (CD), molecular dynamics (MD) simulations, and enhanced sampling techniques, we show that H-NS exhibits a 10-fold higher affinity for ApT repeats compared to that of GpC repeats. Interestingly, selective binding of H-NS to AT-rich DNA causes a structural adaptation in the DNA, including increased bending flexibility, minor groove widening, and localized A-like DNA features, while GC-rich DNA remains closer to the canonical B-form. Our approach yielded detailed insights into how H-NS exploits the intrinsic conformational plasticity of DNA to achieve sequence-dependent binding. More broadly, this work illustrates how DNA-binding proteins can harness the structural adaptability of the DNA double helix, which may modulate regulatory outcomes, and provides insight into how the intrinsic properties of DNA shape protein-DNA interactions in diverse biological systems.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172037","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":"Assessment of Anticancer and Antibacterial Activities of Patchouli Essential Oil Nanoemulsion","authors":"Irom Ragish Singh, Ajmal Koya Pulikkal*, Malsawmdawngkima Hnamte, Laldingliani Tlau Bualchhuak and Awadhesh Kumar, ","doi":"10.1021/acs.jpcb.5c0165410.1021/acs.jpcb.5c01654","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01654https://doi.org/10.1021/acs.jpcb.5c01654","url":null,"abstract":"<p >Patchouli essential oil (PEO) obtained from <i>Pogostemon cablin</i>, acclaimed for its therapeutic properties and aroma, has gained increased attention for its potential applications in the food, pharmaceutical, and cosmeceutical industries. However, the application of PEO is modest due to its hydrophobicity, poor solubility in aqueous media, and high volatility. Nanoemulsions (NEs) rescue these inconsistencies with their proficiency in encapsulating PEO as nanosized droplets, thus providing a new dimension to the modern-day drug delivery of PEO. The present work reports the preparation of patchouli essential oil-based nanoemulsions (PNEs) by ultrasonication using Tween 80 as an emulsifier and water as the continuous medium. Twelve PNEs were prepared with 1:1, 1:2, and 1:3 oil-to-surfactant ratios (OSRs) and sonication times of 5, 10, 15, and 20 min. An increase in the sonication time and a decrease in the level of the OSR reduced the average droplet diameter (<i>Z</i><sub>avg</sub>) of the PNEs. PNE with 1:3 OSR and 20 min sonication was optimized for biological studies as it displayed the minimum <i>Z</i><sub>avg</sub> (∼14 nm), maximum stability upon centrifugation (5000 rpm), thermal treatment (30, 60, and 90 °C), and storage (4 weeks), where it showed a slowest Ostwald ripening rate (ω) of ∼6.7 × 10<sup>–6</sup> nm<sup>3</sup> s<sup>–1</sup>. The optimized PNE showed <i>in vitro</i> anticancer activity against A549 lung cancer cells by showing cell cytotoxicity and inducing apoptosis. The observation of a lower IC<sub>50</sub> of the optimized PNE (0.71 μL mL<sup>–1</sup>) than that of PEO (1.13 μL mL<sup>–1</sup>) confirmed improved anticancer activity. The first evidence of anticancer activity of PNE against the A549 lung cancer cell line is presented. Moreover, the optimized PNE also showed antibacterial activity against <i><i>Vibrio cholerae</i></i>, <i>Bacillus cereus</i>, <i><i>Escherichia coli</i></i>, <i>Staphylococcus aureus</i>, and <i><i>Salmonella typhimurium</i></i> with minimum inhibitory concentration (MIC) values of 3.12, 3.12. 6.25, 6.25, and 3.12 μg mL<sup>–1</sup>, respectively.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 22","pages":"5630–5641 5630–5641"},"PeriodicalIF":2.8,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144211760","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":"Linear Discriminant Analysis-Based Machine Learning and All-Atom Molecular Dynamics Simulations for Probing Electro-Osmotic Transport in Cationic-Polyelectrolyte-Brush-Grafted Nanochannels.","authors":"Raashiq Ishraaq, Siddhartha Das","doi":"10.1021/acs.jpcb.5c01072","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01072","url":null,"abstract":"<p><p>Deciphering the correct mechanisms governing certain phenomena in polyelectrolyte (PE) brush grafted systems, revealed through atomistic simulations, is an extremely challenging problem. In a recent study, our all-atom molecular dynamics (MD) simulations revealed a nonlinearly large electroosmotic (EOS) flow (in the presence of an applied electric field) in nanochannels grafted with PMETAC [poly(2-(methacryloyloxy)ethyl trimethylammonium chloride] brushes. Given the lack of any formal procedure that would have directed us to identify the correct factors responsible for such an occurrence, we needed to devote several months to unraveling the involved mechanisms. In this letter, we propose a linear discriminant analysis (LDA)-based machine learning (ML) approach to address this gap. At first, we obtained data on certain basic features from the all-atom MD data. These basic features represent the number of atoms of a certain species around one atom of another (or the same) species. We obtain such data on basic features for a reference case (case of an EOS flow in PMETAC-brush-grafted nanochannels with a smaller electric field) and a perturbed case (case of an EOS flow in PMETAC-brush-grafted nanochannels with a larger electric field) in bins into which the nanochannel half height has been divided. These data sets are high-dimensional data sets to which the LDA is applied. This leads to the projection of the data (between the reference and the perturbed states) in a highly separated form on a 1D line. From such LDA calculations, we can identify the relative importance of the different basic features in ensuring this separation of the data (between the reference and the perturbed states) on the 1D line. The relative importance of the different basic features is quantified as \"importance scores\" for the different features, which, in turn, tell us what to study and where to study. Such knowledge enables us to rapidly identify the key factors responsible for the nonlinearly large EOS transport in PMETAC-brush-grafted nanochannels.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172040","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":"Mechanisms of CO<sub>2</sub> Absorption in Amino Acid-Based Deep Eutectic Solvents: Insights from Molecular Dynamics and DFT Calculations.","authors":"Hung-Yi Chi, Heng-Kwong Tsao, Yu-Jane Sheng","doi":"10.1021/acs.jpcb.5c00558","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00558","url":null,"abstract":"<p><p>This study explores the mechanisms of CO<sub>2</sub> absorption in two amino acid-containing deep eutectic solvents (DESs) through molecular dynamics (MD) simulations and density functional theory (DFT) calculations. The MD simulations, which focus mainly on physical absorption, reveal that alanine-based DES (Ala DES) exhibits higher CO<sub>2</sub> solubility than l-arginine-based DES (l-arg DES), attributed to stronger physical absorption. Furthermore, the hydrogen bond donor paired with the amino acids is identified as a critical factor for enhancing physical absorption efficiency. DFT calculations, which account for chemical absorption, investigate two reaction pathways: single-molecule reactions involving intramolecular proton transfer and two-molecule reactions involving intermolecular proton exchange. While Ala DES does not exhibit spontaneous chemical absorption, l-arg DES demonstrates such reactions, leading to the formation of carbamic acid or carbamate (Δ<i>G</i> < 0), indicative of CO<sub>2</sub> capture through chemical interactions. Consequently, Ala DES primarily relies on physical absorption, whereas l-arg DES utilizes multiple reactive sites for chemical absorption. These results are consistent with experimental findings, which show that l-arg DES achieves higher CO<sub>2</sub> solubility under atmospheric conditions. Overall, our study highlights the interplay between DES components and reactivity in enhancing CO<sub>2</sub> capture efficiency.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172041","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":"Mechanistic Insights into Choline Degradation Catalyzed by the Choline Trimethylamine-Lyase CutC","authors":"Yi-Qian Yang, Wen-Hao Deng and Rong-Zhen Liao*, ","doi":"10.1021/acs.jpcb.5c0149610.1021/acs.jpcb.5c01496","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c01496https://doi.org/10.1021/acs.jpcb.5c01496","url":null,"abstract":"<p >Choline trimethylamine-lyase (CutC) is a prominent glycyl radical enzyme that catalyzes the degradation of choline into nitrogenous metabolites trimethylamine (TMA) and acetaldehyde. Choline and TMA are crucial nitrogen-containing compounds and play essential roles in various biological pathways, including neurotransmission and global metabolic functions. Although many experimental studies have been dedicated to elucidating the function of CutC, its exact catalytic mechanism remains elusive. Herein, we employed molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) methodologies to investigate the reaction mechanism of CutC in detail. Our calculation results reveal that the enzymatic reaction is initiated by a two-step hydrogen atom transfer (HAT) mechanism, a typical process mediated by a cysteine radical in glycyl radical enzymes (GREs). Significantly, in our suggested reaction mechanism, unlike the previously proposed 1,2-elimination pathway, a more favorable stepwise 1,2-migration of the TMA group occurs after the formation of a substrate radical. This migration of the TMA group leads to the formation of a hemiaminal intermediate, which is likely to be eliminated outside of CutC. Furthermore, our mechanistic investigations indicate that the residue Glu440, adjacent to the choline substrate, plays a pivotal role in helping substrate binding through a hydrogen bond rather than serving as a general base for proton abstraction. These findings provide deeper insights into the catalytic strategy that CutC employs for C–N bond cleavage in choline metabolism and broaden the mechanistic repertoire documented for glycyl radical enzymes in mediating elimination reactions.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 22","pages":"5438–5448 5438–5448"},"PeriodicalIF":2.8,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144211883","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":"Effective Control of Thermal Transfer in Nanoconfined Water by Applying an Electric Field: A Molecular Dynamics Study","authors":"Bing-Bing Wang, Wen-Qing Guo and Jie-Wen Deng*, ","doi":"10.1021/acs.jpcb.5c0092810.1021/acs.jpcb.5c00928","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00928https://doi.org/10.1021/acs.jpcb.5c00928","url":null,"abstract":"<p >Thermal properties of water confined at the nanoscale exhibit variations compared with bulk water. The dynamics of water molecules is altered when an electric field is applied, which influences the thermal transport in nanoconfined water. To explore this phenomenon, we conducted molecular dynamics simulations to investigate the thermal transport of confined water in nanochannels under a uniform electric field. The findings indicate that the thermal conductivity of nanoconfined water decreases when the electric field strength is below 4 V nm<sup>–1</sup> in the direction parallel to the solid–liquid interface of the nanochannel or below 9 V nm<sup>–1</sup> in the direction perpendicular to the solid–liquid interface. This decrease can be attributed to the limited thermal diffusion of water molecules caused by the electric force. On the contrary, when the electric field strength surpasses 4 V nm<sup>–1</sup> or 9 V nm<sup>–1</sup>, the thermal conductivity of nanoconfined water experiences a substantial increase due to the freezing of water molecules induced by the strong electric field. The interfacial thermal resistance decreases on the heat source side, while it increases with increasing electric field strength on the cold source side. Furthermore, applying an electric field parallel to the nanochannel facilitates the electro-freezing of water molecules more effectively, resulting in a greater enhancement of thermal transport in nanoconfined water.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 22","pages":"5550–5560 5550–5560"},"PeriodicalIF":2.8,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144211898","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}
Lianxin Wang, Yuanfei Xue, Jia-Ning Wang, Yan Mo and Ye Mei*,
{"title":"Rational Enzyme Evolution by Facilitating Correlated Motion along the Reaction","authors":"Lianxin Wang, Yuanfei Xue, Jia-Ning Wang, Yan Mo and Ye Mei*, ","doi":"10.1021/acs.jpcb.5c0213310.1021/acs.jpcb.5c02133","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c02133https://doi.org/10.1021/acs.jpcb.5c02133","url":null,"abstract":"<p >Enzymes are highly efficient and specific protein catalysts that play an essential role in regulating metabolic processes in living organisms. By modulating the rates of chemical reactions, enzymes tune fundamental crucial biological functions. Directed evolution is a widely used strategy to enhance protein functionality by selecting variants with desirable traits through random mutation and recombination. However, this approach relies heavily on chemical intuition and demands substantial experimental resources, including labor-intensive mutagenesis. In contrast, rational enzyme engineering leverages mechanistic insights to enhance efficiency and reduce costs. This study presents a mutation strategy guided by the correlated motion of protein during enzymatic reactions, validated through four mutations across two proteins. The results underscore the potential of this physics-based approach to streamline and advance enzyme evolution.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":"129 22","pages":"5591–5600 5591–5600"},"PeriodicalIF":2.8,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144211841","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}