Pub Date : 2024-07-03DOI: 10.1021/acs.jpcb.4c02255
Piotr Ciura, Pamela Smardz, Marta Spodzieja, Adam K Sieradzan, Pawel Krupa
The herpesvirus entry mediator (HVEM) and its ligand LIGHT play crucial roles in immune system regulation, including T-cell proliferation, B-cell differentiation, and immunoglobulin secretion. However, excessive T-cell activation can lead to chronic inflammation and autoimmune diseases. Thus, inhibiting the HVEM-LIGHT interaction emerges as a promising therapeutic strategy for these conditions and in preventing adverse reactions in organ transplantation. This study focused on designing peptide inhibitors, targeting the HVEM-LIGHT interaction, using molecular dynamics (MD) simulations of 65 peptides derived from HVEM. These peptides varied in length and disulfide-bond configurations, crucial for their interaction with the LIGHT trimer. By simulating 31 HVEM domain variants, including the full-length protein, we assessed conformational changes upon LIGHT binding to understand the influence of HVEM segments and disulfide bonds on the binding mechanism. Employing multitrajectory microsecond-scale, all-atom MD simulations and molecular mechanics with generalized Born and surface area (MM-GBSA) binding energy estimation, we identified promising CRD2 domain variants with high LIGHT affinity. Notably, point mutations in these variants led to a peptide with a single disulfide bond (C58-C73) and a K54E substitution, exhibiting the highest binding affinity. The importance of the CRD2 domain and Cys58-Cys73 disulfide bond for interrupting HVEM-LIGHT interaction was further supported by analyzing truncated CRD2 variants, demonstrating similar binding strengths and mechanisms. Further investigations into the binding mechanism utilized steered MD simulations at various pulling speeds and umbrella sampling to estimate the energy profile of HVEM-based inhibitors with LIGHT. These comprehensive analyses revealed key interactions and different binding mechanisms, highlighting the increased binding affinity of selected peptide variants. Experimental circular dichroism techniques confirmed the structural properties of these variants. This study not only advances our understanding of the molecular basis of HVEM-LIGHT interactions but also provides a foundation for developing novel therapeutic strategies for immune-related disorders. Furthermore, it sets a gold standard for peptide inhibitor design in drug development due to its systematic approach.
{"title":"Multilayered Computational Framework for Designing Peptide Inhibitors of HVEM-LIGHT Interaction.","authors":"Piotr Ciura, Pamela Smardz, Marta Spodzieja, Adam K Sieradzan, Pawel Krupa","doi":"10.1021/acs.jpcb.4c02255","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c02255","url":null,"abstract":"<p><p>The herpesvirus entry mediator (HVEM) and its ligand LIGHT play crucial roles in immune system regulation, including T-cell proliferation, B-cell differentiation, and immunoglobulin secretion. However, excessive T-cell activation can lead to chronic inflammation and autoimmune diseases. Thus, inhibiting the HVEM-LIGHT interaction emerges as a promising therapeutic strategy for these conditions and in preventing adverse reactions in organ transplantation. This study focused on designing peptide inhibitors, targeting the HVEM-LIGHT interaction, using molecular dynamics (MD) simulations of 65 peptides derived from HVEM. These peptides varied in length and disulfide-bond configurations, crucial for their interaction with the LIGHT trimer. By simulating 31 HVEM domain variants, including the full-length protein, we assessed conformational changes upon LIGHT binding to understand the influence of HVEM segments and disulfide bonds on the binding mechanism. Employing multitrajectory microsecond-scale, all-atom MD simulations and molecular mechanics with generalized Born and surface area (MM-GBSA) binding energy estimation, we identified promising CRD2 domain variants with high LIGHT affinity. Notably, point mutations in these variants led to a peptide with a single disulfide bond (C58-C73) and a K54E substitution, exhibiting the highest binding affinity. The importance of the CRD2 domain and Cys58-Cys73 disulfide bond for interrupting HVEM-LIGHT interaction was further supported by analyzing truncated CRD2 variants, demonstrating similar binding strengths and mechanisms. Further investigations into the binding mechanism utilized steered MD simulations at various pulling speeds and umbrella sampling to estimate the energy profile of HVEM-based inhibitors with LIGHT. These comprehensive analyses revealed key interactions and different binding mechanisms, highlighting the increased binding affinity of selected peptide variants. Experimental circular dichroism techniques confirmed the structural properties of these variants. This study not only advances our understanding of the molecular basis of HVEM-LIGHT interactions but also provides a foundation for developing novel therapeutic strategies for immune-related disorders. Furthermore, it sets a gold standard for peptide inhibitor design in drug development due to its systematic approach.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490008","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}
Pub Date : 2024-07-03DOI: 10.1021/acs.jpcb.4c03222
Guilherme Volpe Bossa, Erik Hobbie, Sylvio May
Macroions such as nanoparticles, polyelectrolytes, ionic gels, and amphiphiles can form condensed, often self-assembled, phases that are embedded in a solvent region. The condensed phase contains not only the partially or fully immobile charges of their macroions but also corresponding counterions that are mobile and thus free to migrate out of their confinement into the solvent region where they benefit from high translational entropy. Based on the nonlinear Poisson-Boltzmann model for monovalent ions, we quantify the corresponding fraction of released counterions for a planar slab geometry of the macroion phase. Slab thickness, extension of the solvent phase, fixed background charge density provided by the macroions, and dielectric constants inside slab and solvent combine into three dimensionless parameters that the fraction of released counterions depends on. We calculate that fraction and analyze the limits of a thin macroion phase, a large solvent phase, and linearized theory, where simple analytic results become available. Of particular interest is the presence of a single-planar interface that separates a bulk macroion phase from an extended solvent region. We calculate the apparent surface charge density that emerges due to the released counterions. Our model yields a comprehensive description of counterion partitioning between a planar macroion phase and a solvent region on the level of mean-field electrostatics in the absence of added salt ions.
{"title":"Counterion Release from Macroion Assemblies of Planar Geometry.","authors":"Guilherme Volpe Bossa, Erik Hobbie, Sylvio May","doi":"10.1021/acs.jpcb.4c03222","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c03222","url":null,"abstract":"<p><p>Macroions such as nanoparticles, polyelectrolytes, ionic gels, and amphiphiles can form condensed, often self-assembled, phases that are embedded in a solvent region. The condensed phase contains not only the partially or fully immobile charges of their macroions but also corresponding counterions that are mobile and thus free to migrate out of their confinement into the solvent region where they benefit from high translational entropy. Based on the nonlinear Poisson-Boltzmann model for monovalent ions, we quantify the corresponding fraction of released counterions for a planar slab geometry of the macroion phase. Slab thickness, extension of the solvent phase, fixed background charge density provided by the macroions, and dielectric constants inside slab and solvent combine into three dimensionless parameters that the fraction of released counterions depends on. We calculate that fraction and analyze the limits of a thin macroion phase, a large solvent phase, and linearized theory, where simple analytic results become available. Of particular interest is the presence of a single-planar interface that separates a bulk macroion phase from an extended solvent region. We calculate the apparent surface charge density that emerges due to the released counterions. Our model yields a comprehensive description of counterion partitioning between a planar macroion phase and a solvent region on the level of mean-field electrostatics in the absence of added salt ions.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490005","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}
Pub Date : 2024-07-02DOI: 10.1021/acs.jpcb.4c02065
Laurell F Kessler, Ashwin Balakrishnan, Tanja Menche, Dongni Wang, Yunqing Li, Maximilian Mantel, Marius Glogger, Marina S Dietz, Mike Heilemann
Protein labeling through transient and repetitive hybridization of short, fluorophore-labeled DNA oligonucleotides has become widely applied in various optical super-resolution microscopy methods. The main advantages are multitarget imaging and molecular quantification. A challenge is the high background signal originating from the presence of unbound fluorophore-DNA labels in solution. Here, we report the self-quenching of fluorophore dimers conjugated to DNA oligonucleotides as a general concept to reduce the fluorescence background. Upon hybridization, the fluorescence signals of both fluorophores are restored. We expand the toolbox of fluorophores suitable for self-quenching and report their spectra and hybridization equilibria. We apply self-quenched fluorophore-DNA labels to stimulated emission depletion microscopy and single-molecule localization microscopy and report improved imaging performances.
通过荧光团标记的 DNA 短寡核苷酸的瞬时和重复杂交进行蛋白质标记,已广泛应用于各种光学超分辨率显微镜方法。其主要优点是多目标成像和分子定量。但溶液中存在未结合的荧光团-DNA 标记会产生高背景信号,这是一个挑战。在此,我们报告了荧光团二聚体与 DNA 寡核苷酸共轭的自淬灭方法,这是减少荧光背景的一般概念。杂交时,两种荧光团的荧光信号都会恢复。我们扩展了适合自淬灭的荧光团工具箱,并报告了它们的光谱和杂交平衡。我们将自淬火荧光团-DNA 标签应用于受激发射耗尽显微镜和单分子定位显微镜,并报告了改进的成像性能。
{"title":"Self-Quenched Fluorophore-DNA Labels for Super-Resolution Fluorescence Microscopy.","authors":"Laurell F Kessler, Ashwin Balakrishnan, Tanja Menche, Dongni Wang, Yunqing Li, Maximilian Mantel, Marius Glogger, Marina S Dietz, Mike Heilemann","doi":"10.1021/acs.jpcb.4c02065","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c02065","url":null,"abstract":"<p><p>Protein labeling through transient and repetitive hybridization of short, fluorophore-labeled DNA oligonucleotides has become widely applied in various optical super-resolution microscopy methods. The main advantages are multitarget imaging and molecular quantification. A challenge is the high background signal originating from the presence of unbound fluorophore-DNA labels in solution. Here, we report the self-quenching of fluorophore dimers conjugated to DNA oligonucleotides as a general concept to reduce the fluorescence background. Upon hybridization, the fluorescence signals of both fluorophores are restored. We expand the toolbox of fluorophores suitable for self-quenching and report their spectra and hybridization equilibria. We apply self-quenched fluorophore-DNA labels to stimulated emission depletion microscopy and single-molecule localization microscopy and report improved imaging performances.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490010","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}
Pub Date : 2024-07-02DOI: 10.1021/acs.jpcb.4c01906
Cristian M O Lépori, M Alejandra Luna, Cecilia Challier, Paola R Beassoni, N Mariano Correa, R Dario Falcone
Two ionic liquids (ILs) with amphiphilic properties composed of 1-butyl-3-methylimidazolium dioctylsulfosuccinate (bmim-AOT) and 1-hexyl-3-methylimidazolium dioctylsulfosuccinate (hmim-AOT) form unilamellar vesicles spontaneously simply by dissolving the IL-like surfactant in water. These novel vesicles were characterized using two different and highly sensitive fluorescent probes: 6-propionyl-2-(dimethylaminonaphthalene) (PRODAN) and trans-4-[4-(dimethylamino)-styryl]-1-methylpyridinium iodide (HC). These fluorescent probes provide information about the physicochemical properties of the bilayer, such as micropolarity, microviscosity, and electron-donor capacity. In addition, the biocompatibility of these vesicles with the blood medium was evaluated, and their toxicity was determined using Dictyostelium discoideum amoebas. First, using PRODAN and HC, it was found that the bilayer composition and the chemical structure of the ions at the interface produced differences between both amphiphiles, making the vesicles different. Thus, the bilayer of hmim-AOT vesicles is less polar, more rigid, and has a lower electron-donor capacity than those made by bmim-AOT. Finally, the results obtained from the hemolysis studies and the growth behavior of unicellular amoebas, particularly utilizing the D. discoideum assay, showed that both vesicular systems do not produce toxic effects up to a concentration of 0.02 mg/mL. This elegant assay, devoid of animal usage, highlights the potential of these newly organized systems for the delivery of drugs and bioactive molecules of different polarities.
由 1-丁基-3-甲基咪唑鎓二辛基磺基琥珀酸盐(bmim-AOT)和 1-己基-3-甲基咪唑鎓二辛基磺基琥珀酸盐(hmim-AOT)组成的两种具有两亲特性的离子液体(IL),只需将类似 IL 的表面活性剂溶解在水中,就能自发形成单酰胺囊泡。使用两种不同的高灵敏度荧光探针对这些新型囊泡进行了表征:6-丙酰基-2-(二甲氨基萘)(PRODAN)和反式-4-[4-(二甲基氨基)-苯乙烯基]-1-甲基吡啶鎓碘化物(HC)。这些荧光探针可提供双分子层的理化性质信息,如微泼度、微粘度和电子供体能力。此外,还评估了这些囊泡与血液培养基的生物相容性,并使用盘基变形虫测定了它们的毒性。首先,利用 PRODAN 和 HC 发现,这两种双亲化合物的双分子层组成和界面上离子的化学结构产生了差异,从而使囊泡有所不同。因此,与 bmim-AOT 相比,hmim-AOT 囊泡的双分子层极性更弱、刚性更大、电子供体能力更低。最后,从溶血研究和单细胞变形虫的生长行为(特别是利用 D. discoideum 试验)中获得的结果表明,这两种囊泡系统在 0.02 毫克/毫升的浓度下都不会产生毒性作用。这种无需使用动物的优雅检测方法,凸显了这些新组织系统在递送不同极性的药物和生物活性分子方面的潜力。
{"title":"Exploring the Properties of Unilamellar Vesicle Bilayers Formed by Ionic Liquid Surfactants for Future Applications in Nanomedicine.","authors":"Cristian M O Lépori, M Alejandra Luna, Cecilia Challier, Paola R Beassoni, N Mariano Correa, R Dario Falcone","doi":"10.1021/acs.jpcb.4c01906","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c01906","url":null,"abstract":"<p><p>Two ionic liquids (ILs) with amphiphilic properties composed of 1-butyl-3-methylimidazolium dioctylsulfosuccinate (bmim-AOT) and 1-hexyl-3-methylimidazolium dioctylsulfosuccinate (hmim-AOT) form unilamellar vesicles spontaneously simply by dissolving the IL-like surfactant in water. These novel vesicles were characterized using two different and highly sensitive fluorescent probes: 6-propionyl-2-(dimethylaminonaphthalene) (PRODAN) and <i>trans</i>-4-[4-(dimethylamino)-styryl]-1-methylpyridinium iodide (HC). These fluorescent probes provide information about the physicochemical properties of the bilayer, such as micropolarity, microviscosity, and electron-donor capacity. In addition, the biocompatibility of these vesicles with the blood medium was evaluated, and their toxicity was determined using <i>Dictyostelium discoideum</i> amoebas. First, using PRODAN and HC, it was found that the bilayer composition and the chemical structure of the ions at the interface produced differences between both amphiphiles, making the vesicles different. Thus, the bilayer of hmim-AOT vesicles is less polar, more rigid, and has a lower electron-donor capacity than those made by bmim-AOT. Finally, the results obtained from the hemolysis studies and the growth behavior of unicellular amoebas, particularly utilizing the <i>D. discoideum</i> assay, showed that both vesicular systems do not produce toxic effects up to a concentration of 0.02 mg/mL. This elegant assay, devoid of animal usage, highlights the potential of these newly organized systems for the delivery of drugs and bioactive molecules of different polarities.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490006","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}
Pub Date : 2024-07-02DOI: 10.1021/acs.jpcb.4c02359
Yanlin Li, Sangjun Yoo, Wei Bu, Honghu Zhang, Pulak Dutta
Specific ion effects in the interactions of monovalent anions with amine groups─one of the hydrophilic moieties found in proteins─were investigated using octadecylamine monolayers floating at air-aqueous solution interfaces. We find that at solution pH 5.7, larger monovalent anions induce a nonzero pressure starting at higher areas/molecules, i.e., a wider "liquid expanded" region in the monolayer isotherms. Using X-ray fluorescence at near total reflection (XFNTR), an element- and surface-specific technique, ion adsorption to the amines at pH 5.7 is confirmed to be ion-specific and to follow the conventional Hofmeister series. However, at pH 4, this ion specificity is no longer observed. We propose that at the higher pH, the amine headgroups are only partially protonated, and large polarizable ions such as iodine are better able to boost amine protonation. At the lower pH, on the other hand, the monolayer is fully protonated, and electrostatic interactions dominate over ion specificity. These results demonstrate that ion specificity can be modified by changing the experimental conditions.
{"title":"Modifying Specific Ion Effects: Studies of Monovalent Ion Interactions with Amines.","authors":"Yanlin Li, Sangjun Yoo, Wei Bu, Honghu Zhang, Pulak Dutta","doi":"10.1021/acs.jpcb.4c02359","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c02359","url":null,"abstract":"<p><p>Specific ion effects in the interactions of monovalent anions with amine groups─one of the hydrophilic moieties found in proteins─were investigated using octadecylamine monolayers floating at air-aqueous solution interfaces. We find that at solution pH 5.7, larger monovalent anions induce a nonzero pressure starting at higher areas/molecules, i.e., a wider \"liquid expanded\" region in the monolayer isotherms. Using X-ray fluorescence at near total reflection (XFNTR), an element- and surface-specific technique, ion adsorption to the amines at pH 5.7 is confirmed to be ion-specific and to follow the conventional Hofmeister series. However, at pH 4, this ion specificity is no longer observed. We propose that at the higher pH, the amine headgroups are only partially protonated, and large polarizable ions such as iodine are better able to boost amine protonation. At the lower pH, on the other hand, the monolayer is fully protonated, and electrostatic interactions dominate over ion specificity. These results demonstrate that ion specificity can be modified by changing the experimental conditions.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490007","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}
Pub Date : 2024-07-02DOI: 10.1021/acs.jpcb.4c01171
Ning Wu, Yingguang Liu, Zhibo Xing, Shuo Wang, Cheng Zhang
One-dimensional van der Waals (vdWs) heterostructures are celebrated for their exceptional thermal management capabilities, garnering significant research interest. Consequently, our research focused on the one-dimensional vdWs heterojunction comprising carbon nanotube half-wrapped in boron nitride nanotube (BNCNT), specifically their thermal rectification (TR) properties. We employed non-equilibrium molecular dynamics to explore the TR mechanism and assess the impacts of temperature, strain, and coupling strength on heat flux and TR ratio. Our findings reveal that the backward heat flux demonstrates greater atomic vibration instability, as indicated by mean square displacement (MSD), compared to forward heat flux. This instability leads to a higher concentration of localized phonons, thereby diminishing the backward heat flux and enhancing TR. Additionally, we utilized MSD to shed light on the negative differential thermal resistance phenomenon and the influence of stress on forward and backward heat fluxes. Remarkably, TR ratios reached 344% at 3% strain and 400% at -1% strain. Calculations of phonon density of states revealed a competitive mechanism between in-plane and out-of-plane phonons coupling in the inner carbon nanotube and an overlap degree of out-of-plane phonon spectra between the inner carbon nanotube and outer boron nitride nanotube. This accounts for the differing trends in forward and backward heat fluxes as coupling strength χ increases, with TR ratios exceeding 1000% at χ = 7.5. This study provides vital insights for advancing one-dimensional vdWs thermal rectifiers.
{"title":"One-Dimensional van der Waals Heterojunction Comprising Carbon Nanotube Half-Wrapped in Boron Nitride Nanotube: Deep Investigation of Thermal Rectification.","authors":"Ning Wu, Yingguang Liu, Zhibo Xing, Shuo Wang, Cheng Zhang","doi":"10.1021/acs.jpcb.4c01171","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c01171","url":null,"abstract":"<p><p>One-dimensional van der Waals (vdWs) heterostructures are celebrated for their exceptional thermal management capabilities, garnering significant research interest. Consequently, our research focused on the one-dimensional vdWs heterojunction comprising carbon nanotube half-wrapped in boron nitride nanotube (BNCNT), specifically their thermal rectification (TR) properties. We employed non-equilibrium molecular dynamics to explore the TR mechanism and assess the impacts of temperature, strain, and coupling strength on heat flux and TR ratio. Our findings reveal that the backward heat flux demonstrates greater atomic vibration instability, as indicated by mean square displacement (MSD), compared to forward heat flux. This instability leads to a higher concentration of localized phonons, thereby diminishing the backward heat flux and enhancing TR. Additionally, we utilized MSD to shed light on the negative differential thermal resistance phenomenon and the influence of stress on forward and backward heat fluxes. Remarkably, TR ratios reached 344% at 3% strain and 400% at -1% strain. Calculations of phonon density of states revealed a competitive mechanism between in-plane and out-of-plane phonons coupling in the inner carbon nanotube and an overlap degree of out-of-plane phonon spectra between the inner carbon nanotube and outer boron nitride nanotube. This accounts for the differing trends in forward and backward heat fluxes as coupling strength χ increases, with TR ratios exceeding 1000% at χ = 7.5. This study provides vital insights for advancing one-dimensional vdWs thermal rectifiers.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490009","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}
A combined experimental and simulation study of dielectric relaxation (DR) of a deep eutectic solvent (DES) composed of betaine, urea, and water with the composition [Betaine:Urea:Water = 11.7:12:1 (weight ratio) and 9:18:5 (molar ratio)] was performed to explore and understand the interaction and dynamics of this system. Temperature-dependent (303 ≤ T/K ≤ 343) measurements were performed over 9 decades of frequency, combining three different measurement setups. Measured DR, comprising four distinct steps with relaxation times spreading over a few picoseconds to several nanoseconds, was found to agree well with simulations. The simulated total DR spectra, upon dissection into three self (intraspecies) and three cross (interspecies) interaction contributions, revealed that the betaine-betaine self-term dominated (∼65%) the relaxation, while the urea-urea and water-water interactions contributed only ∼7% and ∼1%, respectively. The cross-terms (betaine-urea, betaine-water, and urea-water) together accounted for <30% of the total DR. The slowest DR component with a time constant of ∼1-10 ns derived dominant contribution from betaine-betaine interactions, where betaine-water and urea-water interactions also contributed. The subnanosecond (0.1-0.6 ns) time scale originated from all interactions except betaine-water interaction. An extensive interaction of water with betaine and urea severely reduced the average number of water-water H-bonds (∼0.7) and heavily decreased the static dielectric constant of water in this DES (εs ∼ 2). Furthermore, simulated first rank collective single particle reorientational relaxations (C1(t)) and the structural H-bond fluctuation dynamics (CHB (t)) exhibited multiexponential kinetics with time scales that corresponded well with those found both in the simulated and measured DR.
为了探索和理解该系统的相互作用和动力学,我们对甜菜碱、尿素和水组成的深共晶溶剂(DES)的介电弛豫(DR)进行了实验和模拟相结合的研究,其组成为[甜菜碱:尿素:水 = 11.7:12:1(重量比)和 9:18:5(摩尔比)]。结合三种不同的测量设置,在 9 个十年频率范围内进行了随温度变化(303 ≤ T/K ≤ 343)的测量。测量到的 DR 包括四个不同的步骤,弛豫时间从几皮秒到几纳秒不等,与模拟结果十分吻合。将模拟的总弛豫光谱分解为三个自身(种内)和三个交叉(种间)相互作用贡献后发现,甜菜碱-甜菜碱自身项主导了弛豫(∼65%),而尿素-尿素和水-水相互作用分别只贡献了∼7%和∼1%。交叉作用(甜菜碱-尿素、甜菜碱-水和尿素-水)共占 s ∼ 2)。此外,模拟的第一级集体单粒子重取向弛豫(C1(t))和结构 H 键波动动力学(CHB(t))表现出多指数动力学,其时间尺度与模拟和测量的 DR 中发现的时间尺度十分吻合。
{"title":"Temperature-Dependent Dielectric Relaxation Measurements of (Betaine + Urea + Water) Deep Eutectic Solvent in Hz-GHz Frequency Window: Microscopic Insights into Constituent Contributions and Relaxation Mechanisms.","authors":"Jayanta Mondal, Dhrubajyoti Maji, Sudipta Mitra, Ranjit Biswas","doi":"10.1021/acs.jpcb.4c02784","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c02784","url":null,"abstract":"<p><p>A combined experimental and simulation study of dielectric relaxation (DR) of a deep eutectic solvent (DES) composed of betaine, urea, and water with the composition [Betaine:Urea:Water = 11.7:12:1 (weight ratio) and 9:18:5 (molar ratio)] was performed to explore and understand the interaction and dynamics of this system. Temperature-dependent (303 ≤ <i>T</i>/<i>K</i> ≤ 343) measurements were performed over 9 decades of frequency, combining three different measurement setups. Measured DR, comprising four distinct steps with relaxation times spreading over a few picoseconds to several nanoseconds, was found to agree well with simulations. The simulated total DR spectra, upon dissection into three self (intraspecies) and three cross (interspecies) interaction contributions, revealed that the betaine-betaine self-term dominated (∼65%) the relaxation, while the urea-urea and water-water interactions contributed only ∼7% and ∼1%, respectively. The cross-terms (betaine-urea, betaine-water, and urea-water) together accounted for <30% of the total DR. The slowest DR component with a time constant of ∼1-10 ns derived dominant contribution from betaine-betaine interactions, where betaine-water and urea-water interactions also contributed. The subnanosecond (0.1-0.6 ns) time scale originated from all interactions except betaine-water interaction. An extensive interaction of water with betaine and urea severely reduced the average number of water-water H-bonds (∼0.7) and heavily decreased the static dielectric constant of water in this DES (ε<sub>s</sub> ∼ 2). Furthermore, simulated first rank collective single particle reorientational relaxations (<i>C</i><sub>1</sub>(<i>t</i>)) and the structural H-bond fluctuation dynamics (<i>C</i><sub>HB</sub> (<i>t</i>)) exhibited multiexponential kinetics with time scales that corresponded well with those found both in the simulated and measured DR.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141464336","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}
Pub Date : 2024-07-01DOI: 10.1021/acs.jpcb.4c02823
Zixin Hu, Tiedong Sun, Wenwen Chen, Lars Nordenskiöld, Lanyuan Lu
Coarse-grained models designed for intrinsically disordered proteins and regions (IDP/Rs) usually omit some bonded potentials (e.g., angular and dihedral potentials) as a conventional strategy to enhance backbone flexibility. However, a notable drawback of this approach is the generation of inaccurate backbone conformations. Here, we addressed this problem by introducing residue-specific angular, refined dihedral, and correction map (CMAP) potentials, derived based on the statistics from a customized coil database. These bonded potentials were integrated into the existing Mpipi model, resulting in a new model, denoted as the "Mpipi+" model. Results show that the Mpipi+ model can improve backbone conformations. More importantly, it can markedly improve the secondary structure propensity (SSP) based on the experimental chemical shift and, consequently, succeed in capturing transient secondary structures. Moreover, the Mpipi+ model preserves the liquid-liquid phase separation (LLPS) propensities of IDPs.
{"title":"Refined Bonded Terms in Coarse-Grained Models for Intrinsically Disordered Proteins Improve Backbone Conformations.","authors":"Zixin Hu, Tiedong Sun, Wenwen Chen, Lars Nordenskiöld, Lanyuan Lu","doi":"10.1021/acs.jpcb.4c02823","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c02823","url":null,"abstract":"<p><p>Coarse-grained models designed for intrinsically disordered proteins and regions (IDP/Rs) usually omit some bonded potentials (e.g., angular and dihedral potentials) as a conventional strategy to enhance backbone flexibility. However, a notable drawback of this approach is the generation of inaccurate backbone conformations. Here, we addressed this problem by introducing residue-specific angular, refined dihedral, and correction map (CMAP) potentials, derived based on the statistics from a customized coil database. These bonded potentials were integrated into the existing Mpipi model, resulting in a new model, denoted as the \"Mpipi+\" model. Results show that the Mpipi+ model can improve backbone conformations. More importantly, it can markedly improve the secondary structure propensity (SSP) based on the experimental chemical shift and, consequently, succeed in capturing transient secondary structures. Moreover, the Mpipi+ model preserves the liquid-liquid phase separation (LLPS) propensities of IDPs.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141475465","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}
Proton (H+) motive force (PMF) serves as the energy source for the flagellar motor rotation, crucial for microbial motility. Here, to control PMF using light, we introduced light-driven inward and outward proton pump rhodopsins, RmXeR and AR3, into Escherichia coli. The motility of E. coli cells expressing RmXeR and AR3 significantly decreased and increased upon illumination, respectively. Tethered cell experiments revealed that, upon illumination, the torque of the flagellar motor decreased to nearly zero (28 pN nm) with RmXeR, while it increased to 1170 pN nm with AR3. These alterations in PMF correspond to +146 mV (RmXeR) and -140 mV (AR3), respectively. Thus, bidirectional optical control of PMF in E. coli was successfully achieved by using proton pump rhodopsins. This system holds a potential for enhancing our understanding of the roles of PMF in various biological functions.
{"title":"Bidirectional Optical Control of Proton Motive Force in <i>Escherichia coli</i> Using Microbial Rhodopsins.","authors":"Kotaro Nakanishi, Keiichi Kojima, Yoshiyuki Sowa, Yuki Sudo","doi":"10.1021/acs.jpcb.4c03027","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c03027","url":null,"abstract":"<p><p>Proton (H<sup>+</sup>) motive force (PMF) serves as the energy source for the flagellar motor rotation, crucial for microbial motility. Here, to control PMF using light, we introduced light-driven inward and outward proton pump rhodopsins, <i>Rm</i>XeR and AR3, into <i>Escherichia coli</i>. The motility of <i>E. coli</i> cells expressing <i>Rm</i>XeR and AR3 significantly decreased and increased upon illumination, respectively. Tethered cell experiments revealed that, upon illumination, the torque of the flagellar motor decreased to nearly zero (28 pN nm) with <i>Rm</i>XeR, while it increased to 1170 pN nm with AR3. These alterations in PMF correspond to +146 mV (<i>Rm</i>XeR) and -140 mV (AR3), respectively. Thus, bidirectional optical control of PMF in <i>E. coli</i> was successfully achieved by using proton pump rhodopsins. This system holds a potential for enhancing our understanding of the roles of PMF in various biological functions.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141464414","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}
Pub Date : 2024-07-01DOI: 10.1021/acs.jpcb.4c02699
Maria Carolina P Lima, Braxten D Hornsby, Carol S Lim, Thomas E Cheatham
The chimeric oncoprotein Bcr-Abl is the causative agent of virtually all chronic myeloid leukemias and a subset of acute lymphoblastic leukemias. As a result of the so-called Philadelphia chromosome translocation t(9;22), Bcr-Abl manifests as a constitutively active tyrosine kinase, which promotes leukemogenesis by activation of cell cycle signaling pathways. Constitutive and oncogenic activation is mediated by an N-terminal coiled-coil oligomerization domain in Bcr (Bcr-CC), presenting a therapeutic target for inhibition of Bcr-Abl activity toward the treatment of Bcr-Abl+ leukemias. Previously, we demonstrated that a rationally designed Bcr-CC mutant, CCmut3, exerts a dominant negative effect upon Bcr-Abl activity by preferential oligomerization with Bcr-CC. Moreover, we have shown that conjugation to a leukemia-specific cell-penetrating peptide (CPP-CCmut3) improves intracellular delivery and activity. However, our full-length CPP-CCmut3 construct (81 aa) is encumbered by an intrinsically high degree of conformational variability and susceptibility to proteolytic degradation relative to traditional small-molecule therapeutics. Here, we iterate a new generation of CCmut3 inhibitors against Bcr-CC-mediated Bcr-Abl assembly designed to address these constraints through incorporation of all-hydrocarbon staples spanning i and i + 7 positions in α-helix 2 (CPP-CCmut3-st). We utilize computational modeling and biomolecular simulation to evaluate single- and double-stapled CCmut3 candidates in silico for dynamics and binding energetics. We further model a truncated system characterized by the deletion of α-helix 1 and the flexible loop linker, which are known to impart high conformational variability. To study the impact of the N-terminal cyclic CPP toward model stability and inhibitor activity, we also model the full-length and truncated systems devoid of the CPP, with a cyclized CPP, and with an open-configuration CPP, for a total of six systems that comprise our library. From this library, we present lead-stapled peptide candidates to be synthesized and evaluated experimentally as our next iteration of inhibitors against Bcr-Abl.
{"title":"Molecular Modeling of Single- and Double-Hydrocarbon-Stapled Coiled-Coil Inhibitors against Bcr-Abl: Toward a Treatment Strategy for CML.","authors":"Maria Carolina P Lima, Braxten D Hornsby, Carol S Lim, Thomas E Cheatham","doi":"10.1021/acs.jpcb.4c02699","DOIUrl":"https://doi.org/10.1021/acs.jpcb.4c02699","url":null,"abstract":"<p><p>The chimeric oncoprotein Bcr-Abl is the causative agent of virtually all chronic myeloid leukemias and a subset of acute lymphoblastic leukemias. As a result of the so-called Philadelphia chromosome translocation t(9;22), Bcr-Abl manifests as a constitutively active tyrosine kinase, which promotes leukemogenesis by activation of cell cycle signaling pathways. Constitutive and oncogenic activation is mediated by an N-terminal coiled-coil oligomerization domain in Bcr (Bcr-CC), presenting a therapeutic target for inhibition of Bcr-Abl activity toward the treatment of Bcr-Abl<sup>+</sup> leukemias. Previously, we demonstrated that a rationally designed Bcr-CC mutant, CCmut3, exerts a dominant negative effect upon Bcr-Abl activity by preferential oligomerization with Bcr-CC. Moreover, we have shown that conjugation to a leukemia-specific cell-penetrating peptide (CPP-CCmut3) improves intracellular delivery and activity. However, our full-length CPP-CCmut3 construct (81 aa) is encumbered by an intrinsically high degree of conformational variability and susceptibility to proteolytic degradation relative to traditional small-molecule therapeutics. Here, we iterate a new generation of CCmut3 inhibitors against Bcr-CC-mediated Bcr-Abl assembly designed to address these constraints through incorporation of all-hydrocarbon staples spanning <i>i</i> and <i>i</i> + 7 positions in α-helix 2 (CPP-CCmut3-st). We utilize computational modeling and biomolecular simulation to evaluate single- and double-stapled CCmut3 candidates <i>in silico</i> for dynamics and binding energetics. We further model a truncated system characterized by the deletion of α-helix 1 and the flexible loop linker, which are known to impart high conformational variability. To study the impact of the N-terminal cyclic CPP toward model stability and inhibitor activity, we also model the full-length and truncated systems devoid of the CPP, with a cyclized CPP, and with an open-configuration CPP, for a total of six systems that comprise our library. From this library, we present lead-stapled peptide candidates to be synthesized and evaluated experimentally as our next iteration of inhibitors against Bcr-Abl.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141475464","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}