The Journal of Physical Chemistry B最新文献

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Structural Features of the Thymol-Carvacrol Equimolar Mixture: X-Ray Scattering and Molecular Dynamics.
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-03-27 Epub Date: 2025-03-12 DOI: 10.1021/acs.jpcb.4c07674
Emanuela Mangiacapre, Fabrizio Lo Celso, Alessandro Triolo, Fabio Ramondo, Daniel J M Irving, Ahmad Alhadid, Mirjana Minceva, Olga Russina
{"title":"Structural Features of the Thymol-Carvacrol Equimolar Mixture: X-Ray Scattering and Molecular Dynamics.","authors":"Emanuela Mangiacapre, Fabrizio Lo Celso, Alessandro Triolo, Fabio Ramondo, Daniel J M Irving, Ahmad Alhadid, Mirjana Minceva, Olga Russina","doi":"10.1021/acs.jpcb.4c07674","DOIUrl":"10.1021/acs.jpcb.4c07674","url":null,"abstract":"<p><p>We present a structural characterization of a low-transition-temperature mixture (LTTM), consisting of thymol and carvacrol, at an equimolar ratio. Carvacrol and thymol are natural regioisomers of terpenes. When combined at an equimolar ratio, they form a liquid mixture at room temperature, with supercooling capability and glass transition at ca. 210 K. Using small- and wide-angle X-ray scattering and molecular dynamics, we describe the structural complexity within this system. X-ray scattering reveals a low-Q peak at around 0.6 Å<sup>-1</sup>, indicating the existence of mesoscale structural heterogeneities, likely related to the segregation of polar moieties engaged in hydrogen bond (HB) interactions within an aromatic, apolar matrix. These polar interactions are predominantly a result of HBs involving thymol as the HB donor species. The liquid structure is also driven by O-H···π interactions, prevalently due to the ability of the carvacrol π-site to engage in this type of weak interaction as a HB acceptor. Besides, dispersive interactions affect the local arrangement of molecules, with a propensity of carvacrol rings to orient their first neighbors with a perpendicular orientation, while thymol tends to induce a closer approach of other thymol molecules with a preferential parallel alignment. Overall, we observed a complex structural arrangement driven by the interplay of both conventional and weak hydrogen bond interactions, with the aromatic nature of the compounds playing a pivotal role in shaping the system's architecture. Carvacrol and thymol, despite being very similar compounds, are characterized by distinctly different behavior in terms of the interactions they engage in with their neighbors, likely due to the different steric hindrance experienced by their hydroxyl groups, which are close to either a small methyl or a bulky isopropyl group, respectively. Such observations can provide useful hints to develop new solvents with tailored properties.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3224-3236"},"PeriodicalIF":2.8,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143612848","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
Microscopic Significance of Hydrophobic Residues for Protein Stability in Ionic Liquids.
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-03-27 Epub Date: 2025-03-17 DOI: 10.1021/acs.jpcb.5c00236
Guochao Sun, Bing Fang, Yanmei Yang, Yuanyuan Qu, Qingmeng Zhang, Weifeng Li
{"title":"Microscopic Significance of Hydrophobic Residues for Protein Stability in Ionic Liquids.","authors":"Guochao Sun, Bing Fang, Yanmei Yang, Yuanyuan Qu, Qingmeng Zhang, Weifeng Li","doi":"10.1021/acs.jpcb.5c00236","DOIUrl":"10.1021/acs.jpcb.5c00236","url":null,"abstract":"<p><p>It is well-known that ionic liquids (ILs) can alter the structural stability of proteins. The change in protein conformation is closely related to the interaction between the protein residue and ILs. To probe the impact of hydrophobic interactions on protein stability in ILs, we conducted molecular dynamic simulations and compared the unfolding process of two proteins, the wild-type villin headpiece protein HP35 and its doubly mutant form HP35NN which contains two hydrophobic norleucine (NLE) substitutions at Lys24/29, in hydrated 1-butyl-3-methylimidazolium chloride ([BMIM]Cl). By sampling at a long time scale, the denaturation ability of ILs was well captured. Specifically, HP35NN exhibits greater structural instability than HP35, characterized by the unfolding of helix-3 where the mutated hydrophobic residues are located. These findings highlight the thermodynamic instability of the protein caused by the mutation of two hydrophobic residues in the ILs. By evaluating the hydration kinetics of helix-3 with ILs, we found that the intramolecular hydrogen bonds of HP35NN were broken. At the same time, HP35NN binds to more ILs through hydrophobic interactions. Therefore, we propose that the hydrophobic interaction between ILs and the mutated hydrophobic residue plays a crucial role in the denaturation of HP35NN. The stability comparison and verification of the alkyl chain model of hydrophobic residues in ILs also further prove the instability of hydrophobic residue mutation in ILs. These findings may provide valuable basic information for understanding the effect of ILs on the conformational stability of proteins.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3244-3252"},"PeriodicalIF":2.8,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646555","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
Photochemistry upon Charge Separation in Triphenylamine Derivatives from fs to μs.
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-03-27 Epub Date: 2025-03-12 DOI: 10.1021/acs.jpcb.4c07199
Hendrik J Brockmann, Letao Huang, Felix Hainer, Danyellen Galindo, Angelina Jocic, Jie Han, Milan Kivala, Andreas Dreuw, Tiago Buckup
{"title":"Photochemistry upon Charge Separation in Triphenylamine Derivatives from fs to μs.","authors":"Hendrik J Brockmann, Letao Huang, Felix Hainer, Danyellen Galindo, Angelina Jocic, Jie Han, Milan Kivala, Andreas Dreuw, Tiago Buckup","doi":"10.1021/acs.jpcb.4c07199","DOIUrl":"10.1021/acs.jpcb.4c07199","url":null,"abstract":"<p><p>Quantum chemical methods and time-resolved laser spectroscopy are employed to elucidate ultrafast charge-separation processes in triphenylamine (TPA) derivatives upon photoexcitation. When changing the ambient solvent from non-electron-accepting to electron-acceptor solvents, such as chloroform, a vastly extended and multifaceted photochemistry of TPA derivatives is observed. Following initial excitation, two concurrent charge-transfer processes are identified. When the TPA derivative and solvent molecules are arranged in a configuration that favors efficient electron transfer, charge separation occurs immediately, leading to the formation of a radical cation of the TPA derivative. This highly reactive species can subsequently combine with other TPA derivative molecules to yield a dimeric species. Alternatively, if the molecular positioning upon photoexcitation is not optimal, relaxation back to the S<sub>1</sub> state occurs. From this state, an electron transfer process leads to the formation of a charge-transfer complex, where the negatively charged solvent molecule remains closely associated with the positively charged TPA derivative. Within 30 ps, charge recombination occurs in this complex, resulting in the formation of triplet states. This transition to the triplet state is driven by a lower reaction barrier for charge separation compared to that for the formation of the singlet state.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3207-3215"},"PeriodicalIF":2.8,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603048","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
d-Limonene and 1-Pentanol Mixtures: Vapor-Liquid Equilibrium Analysis Using Molecular Dynamics.
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-03-27 Epub Date: 2025-03-17 DOI: 10.1021/acs.jpcb.4c07478
Suguru Nishikawa, Hitoshi Washizu
{"title":"<i>d</i>-Limonene and 1-Pentanol Mixtures: Vapor-Liquid Equilibrium Analysis Using Molecular Dynamics.","authors":"Suguru Nishikawa, Hitoshi Washizu","doi":"10.1021/acs.jpcb.4c07478","DOIUrl":"10.1021/acs.jpcb.4c07478","url":null,"abstract":"<p><p>Vapor-liquid equilibrium (VLE) data of fragrance components are crucial for product development and separation processes. However, experimentally obtaining these data can often be a high-cost and challenging task. In order to address this issue, simulations of VLE data using molecular dynamics (MD) methods have gained attention, though there are still relatively few studies about the vapor-liquid equilibrium calculations of fragrance components using MD. In this study, we focused on a mixture of <i>d</i>-limonene and 1-pentanol as representative components and conducted MD simulations. The VLE data obtained by varying the molar fraction of <i>d</i>-limonene, including x-y phase diagrams and activity coefficients, showed a high degree of agreement with the experimental data. Additionally, an analysis of the density profiles on a molecular level revealed a slight increase in the concentration of 1-pentanol at the vapor-liquid interface.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3216-3223"},"PeriodicalIF":2.8,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646550","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
Functional Connectivity of Red Chlorophylls in Cyanobacterial Photosystem I Revealed by Fluence-Dependent Transient Absorption.
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-03-27 Epub Date: 2025-03-18 DOI: 10.1021/acs.jpcb.5c00198
Sara H Sohail, Siddhartha Sohoni, Po-Chieh Ting, Lexi R Fantz, Sami M Abdulhadi, Craig MacGregor-Chatwin, Andrew Hitchcock, C Neil Hunter, Gregory S Engel, Sara C Massey
{"title":"Functional Connectivity of Red Chlorophylls in Cyanobacterial Photosystem I Revealed by Fluence-Dependent Transient Absorption.","authors":"Sara H Sohail, Siddhartha Sohoni, Po-Chieh Ting, Lexi R Fantz, Sami M Abdulhadi, Craig MacGregor-Chatwin, Andrew Hitchcock, C Neil Hunter, Gregory S Engel, Sara C Massey","doi":"10.1021/acs.jpcb.5c00198","DOIUrl":"10.1021/acs.jpcb.5c00198","url":null,"abstract":"<p><p>External stressors modulate the oligomerization state of photosystem I (PSI) in cyanobacteria. The number of red chlorophylls (Chls), pigments lower in energy than the P<sub>700</sub> reaction center, depends on the oligomerization state of PSI. Here, we use ultrafast transient absorption spectroscopy to interrogate the effective connectivity of the red Chls in excitonic energy pathways in trimeric PSI in native thylakoid membranes of the model cyanobacterium <i>Synechocystis</i> sp. PCC 6803, including emergent dynamics, as red Chls increase in number and proximity. Fluence-dependent dynamics indicate singlet-singlet annihilation within energetically connected red Chl sites in the PSI antenna but not within bulk Chl sites on the picosecond time scale. These data support picosecond energy transfer between energetically connected red Chl sites as the physical basis of singlet-singlet annihilation. The time scale of this energy transfer is faster than predicted by Förster resonance energy transfer calculations, raising questions about the physical mechanism of the process. Our results indicate distinct strategies to steer excitations through the PSI antenna; the red Chls present a shallow reservoir that direct excitations away from P<sub>700</sub>, extending the time to trapping by the reaction center.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3191-3197"},"PeriodicalIF":2.8,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956136/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655457","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}
引用次数: 0
rCGMM: A Coarse-Grained Force Field Embedding Elastic Network for Studying Small Noncoding RNA Dynamics.
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-03-27 Epub Date: 2025-03-18 DOI: 10.1021/acs.jpcb.4c07286
Subhasree Majumder, Debnath Pal
{"title":"rCGMM: A Coarse-Grained Force Field Embedding Elastic Network for Studying Small Noncoding RNA Dynamics.","authors":"Subhasree Majumder, Debnath Pal","doi":"10.1021/acs.jpcb.4c07286","DOIUrl":"10.1021/acs.jpcb.4c07286","url":null,"abstract":"<p><p>Short noncoding RNA molecules play significant roles in catalysis, biological regulation, and disease pathways. Their assessment through sequence-based approaches has been a challenge, compounded by the significant structural flexibility accrued from six free backbone torsions per nucleotide. To efficiently study the structure and dynamics of an extensive repertoire of these molecules in a high throughput mode, we have built a coarse-grained force field using one, two, three, and four pseudoatoms to represent the phosphate, sugar, pyrimidines, and purines, respectively. The Boltzmann inversion method was applied to structures of 5 piRNA, 8 miRNA, and 13 siRNA from the Nucleic Acid Database (NDB) to estimate the initial force field parameters and iteratively optimized through 1 μs molecular dynamics run by comparing against an equivalent all-atom simulation using the CHARMM36 force field. We applied an elastic net to model the hydrogen bond network stabilizing the local structure for double-stranded cases. A spine using pseudoatoms was calculated for the same from the coarse-grain beads, and all beads within a threshold radial distance were constrained using soft distance potentials. Lennard-Jones and Coulomb's potential function modeled the nonbonded interaction. Benchmarks on 26 molecules compared through root-mean-square deviation graphs against all-atom simulation show close concurrence for single- and double-stranded small noncoding RNA molecules. The rCGMM force field is available for download at https://github.com/majumderS/rCGMM.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3159-3170"},"PeriodicalIF":2.8,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655459","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
Weak Organic Acid Effect of Bacterial Light-Driven Proton-Pumping Rhodopsin.
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-03-27 Epub Date: 2025-03-19 DOI: 10.1021/acs.jpcb.4c06891
Zikun Lyu, Shunki Takaramoto, Keiichi Inoue
{"title":"Weak Organic Acid Effect of Bacterial Light-Driven Proton-Pumping Rhodopsin.","authors":"Zikun Lyu, Shunki Takaramoto, Keiichi Inoue","doi":"10.1021/acs.jpcb.4c06891","DOIUrl":"10.1021/acs.jpcb.4c06891","url":null,"abstract":"<p><p>Microbial rhodopsins are photoreceptor proteins that utilize light to elicit various biological functions. The best-studied microbial rhodopsins are outward proton (H<sup>+</sup>)-pumping rhodopsins, which transport H<sup>+</sup> from the cytoplasmic to the extracellular side. Recently, the weak organic acid (WOA) effect, specifically the enhancement of pumping activity by WOAs such as acetic acid and indole-3-acetic acid (IAA), was discovered in outward H<sup>+</sup>-pumping rhodopsins from fungi. However, it remains unclear whether the WOA effect exists in nonfungal H<sup>+</sup>-pumping rhodopsins. Here, we revealed that the H<sup>+</sup>-pumping activity of a bacterial outward H<sup>+</sup> pump rhodopsin, <i>Psp</i>R, from the rhizobacterium <i>Pseudomonas putida</i>, is also enhanced by extracellular acetic acid and IAA. Using transient absorption measurements on purified <i>Psp</i>R protein, we found that extracellular WOAs accelerate cytoplasmic H<sup>+</sup> uptake and extracellular H<sup>+</sup> release from a protonated counterion during its photocycle. Furthermore, acetic acid applied on the cytoplasmic side has an inhibitory effect on the H<sup>+</sup> pump activity of <i>Psp</i>R, which is less significant for IAA and can be mitigated by increasing the H<sup>+</sup> concentration or introducing a cytoplasmic donor residue. These findings on the WOA effect in a bacterial rhodopsin provide new insights into the physiological function of outward H<sup>+</sup>-pumping rhodopsins in bacteria, particularly in their interaction with plants.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3198-3206"},"PeriodicalIF":2.8,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655537","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
Molecular Structure Refinement of a ß-Heptapeptide Based on Residual Dipolar Couplings: The Challenge of Extracting Structural Information from Measured RDCs.
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-03-27 Epub Date: 2025-03-13 DOI: 10.1021/acs.jpcb.4c06955
Maria Pechlaner, Wilfred F van Gunsteren, Lorna J Smith, Niels Hansen
{"title":"Molecular Structure Refinement of a ß-Heptapeptide Based on Residual Dipolar Couplings: The Challenge of Extracting Structural Information from Measured RDCs.","authors":"Maria Pechlaner, Wilfred F van Gunsteren, Lorna J Smith, Niels Hansen","doi":"10.1021/acs.jpcb.4c06955","DOIUrl":"10.1021/acs.jpcb.4c06955","url":null,"abstract":"<p><p>The experimental determination of residual dipolar couplings (RDCs) rests on sampling the rotational motion of a molecule in an environment that induces a slightly nonuniform, unfortunately immeasurable, orientation distribution of the molecule in solution. Averaging over this slightly nonuniform, anisotropic distribution reduces the size of the dipolar couplings (DCs) from the kHz range to the Hz range for the resulting RDCs by a factor of 10<sup>3</sup> to 10<sup>4</sup>. These features hamper the use of measured RDCs to contribute to the structure determination or refinement of (bio)molecules. The commonly used alignment-tensor (<i>AT</i>) methodology assumes that the immeasurable, unknown orientation distribution of the molecule can be expressed in terms of five spherical harmonic functions of order 2. Staying close to experiment, RDCs can, alternatively, be calculated from a molecular simulation by sampling the rotational motion of the molecule (<i>MRS</i> method) or, instead, of a vector (<i>mfv</i>) representing the magnetic field (<i>HRS</i> method). The <i>AT</i> and <i>HRS</i> methods were applied to a β-heptapeptide solvated in methanol, for which 131 NOE atom-atom distance upper bounds and 21 <sup><i>3</i></sup><i>J</i>-couplings derived from NMR experiments are available and, in addition, 39 RDC values obtained for the molecule solvated in methanol with polyvinyl acetate added. In methanol at room temperature and pressure, the molecule adopts a relatively stable helical fold. It appears that MD simulation of the molecule in methanol using the GROMOS biomolecular force field already satisfies virtually all experimental data. Application of RDC restraining shows the limitations caused by the assumptions on which the <i>AT</i> and <i>HRS</i> methods rest and suggests that experimentally measured RDCs are less useful for molecular structure determination or refinement than other observable quantities that can be measured by NMR techniques. The results illustrate that in structure determination or refinement of a (bio)molecule based on experimentally measured data, it is mandatory (i) to refrain from the vacuum boundary condition and (ii) from torsional-angle restraints that do not account for the multiplicity of the inverse function of the Karplus relation expressing <sup>3</sup><i>J</i>-couplings in terms of molecular torsional angles, (iii) to allow for Boltzmann-weighted time- or molecule-averaging and, not the least, (iv) to use a force field that has an adequate basis in thermodynamic data of biomolecules.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3131-3158"},"PeriodicalIF":2.8,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956018/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622895","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}
引用次数: 0
Investigating the Therapeutic Ability of Novel Antimicrobial Peptide Dendropsophin 1 and Its Analogues through Membrane Disruption and Monomeric Pore Formation.
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-03-27 Epub Date: 2025-02-12 DOI: 10.1021/acs.jpcb.4c07758
Fahmida Rahman, Sujit Halder, Shamo Rahman, Md Lokman Hossen
{"title":"Investigating the Therapeutic Ability of Novel Antimicrobial Peptide Dendropsophin 1 and Its Analogues through Membrane Disruption and Monomeric Pore Formation.","authors":"Fahmida Rahman, Sujit Halder, Shamo Rahman, Md Lokman Hossen","doi":"10.1021/acs.jpcb.4c07758","DOIUrl":"10.1021/acs.jpcb.4c07758","url":null,"abstract":"<p><p>Antimicrobial peptides (AMPs) are an alternative source of antibiotics that fight worldwide antibiotic-resistant catastrophes. Dendropsophin 1 (Dc1) is a recently invented novel AMP with 17 amino acid residues obtained from the screen secretion of a frog named <i>Dendropsophus columbianus</i>. Dc1 has two slightly mutated analogues, namely, Dc1.1 and Dc1.2, with improved cationicity and mean amphipathic moment to enhance the selective toxicity against microorganisms. Experimental results indicate that Dc1 and Dc1.1 have similar antimicrobial activity against Gram-negative bacteria <i>Escherichia coli</i> and Gram-positive bacteria <i>Staphylococcus aureus</i>, whereas the synthesized peptide Dc1.2 has shown antimicrobial activity against a wide range of microorganisms. However, the molecular level details of the peptide-membrane interaction and the corresponding changes in the peptide structure remain elusive. In this study, we investigate the bacterial membrane disruption capability of these AMPs by running a total of 14.2 μs long molecular dynamics (MD) simulations. Our findings suggest that all three peptides affect the upper layer of the membrane with different degrees of disruption. After penetration, Dc1 and Dc1.2 retain stable α-helices in the core region, indicating the potential to disrupt the second layer. However, secondary structure analysis shows that Dc1.2 attains extended helical regions on the C-terminus, suggesting it as the superior candidate among the analogues to have the potential of stable pore formation, leading to bacterial cell death. To speed up our study, we adopt a one-transmembrane configuration of Dc1, Dc1.1, and Dc1.2 and find toroidal pores with subsequent water leakage for Dc1.2.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3171-3182"},"PeriodicalIF":2.8,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397499","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 Polydispersity on Phase Separation: Insights from Polyethylene Glycol and Dextran Mixtures.
IF 2.8 2区 化学
The Journal of Physical Chemistry B Pub Date : 2025-03-27 Epub Date: 2025-03-13 DOI: 10.1021/acs.jpcb.4c08640
Akari Kamo, Arash Nikoubashman, Miho Yanagisawa
{"title":"Impact of Polydispersity on Phase Separation: Insights from Polyethylene Glycol and Dextran Mixtures.","authors":"Akari Kamo, Arash Nikoubashman, Miho Yanagisawa","doi":"10.1021/acs.jpcb.4c08640","DOIUrl":"10.1021/acs.jpcb.4c08640","url":null,"abstract":"<p><p>The dynamic formation of (bio)molecular condensates has emerged as a key regulatory mechanism in cellular processes. Concepts from polymer physics can provide valuable insights into the underlying mechanisms and properties of these condensates. While stoichiometric interactions between chemically distinct molecules have traditionally been the primary focus for understanding and predicting the equilibrium behavior, recent attention has turned to the role of molecular diversity, particularly the interplay between molecules of similar types but varying chain lengths. To mimic such cellular conditions, we investigated the impact of molecular weight polydispersity using polyethylene glycol (PEG) and dextran (Dex) solutions through experiments and molecular simulations. Our findings reveal that polydisperse systems, which contain a higher fraction of short-chain components, exhibit a narrower two-phase region, along with reduced concentration differences and interfacial tension between the coexisting polymer-rich and polymer-poor phases. In these systems, the Dex-rich phase is enriched with longer Dex chains compared to the PEG-rich phase, with a gradual transition in chain length across their interface. However, polydispersity has no significant effects on the critical concentration and critical exponents. Finally, our study of condensation kinetics demonstrates that phase separation is not limited by the nucleation rate but instead by the diffusion-driven aggregation of polymers.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"3263-3271"},"PeriodicalIF":2.8,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622893","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
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