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Binding of SARS-CoV-2 Nonstructural Protein 1 to 40S Ribosome Inhibits mRNA Translation. SARS-CoV-2 非结构蛋白 1 与 40S 核糖体的结合抑制了 mRNA 翻译。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-07-15 DOI: 10.1021/acs.jpcb.4c01391
Hung Nguyen, Hoang Linh Nguyen, Mai Suan Li

Experimental evidence has established that SARS-CoV-2 NSP1 acts as a factor that restricts cellular gene expression and impedes mRNA translation within the ribosome's 40S subunit. However, the precise molecular mechanisms underlying this phenomenon have remained elusive. To elucidate this issue, we employed a combination of all-atom steered molecular dynamics and coarse-grained alchemical simulations to explore the binding affinity of mRNA to the 40S ribosome, both in the presence and absence of SARS-CoV-2 NSP1. Our investigations revealed that the binding of SARS-CoV-2 NSP1 to the 40S ribosome leads to a significant enhancement in the binding affinity of mRNA. This observation, which aligns with experimental findings, strongly suggests that SARS-CoV-2 NSP1 has the capability to inhibit mRNA translation. Furthermore, we identified electrostatic interactions between mRNA and the 40S ribosome as the primary driving force behind mRNA translation. Notably, water molecules were found to play a pivotal role in stabilizing the mRNA-40S ribosome complex, underscoring their significance in this process. We successfully pinpointed the specific SARS-CoV-2 NSP1 residues that play a critical role in triggering the translation arrest.

实验证据证明,SARS-CoV-2 NSP1 是一种限制细胞基因表达的因子,会阻碍核糖体 40S 亚基内的 mRNA 翻译。然而,这种现象背后的确切分子机制仍然难以捉摸。为了阐明这一问题,我们采用了全原子导向分子动力学和粗粒度炼金术模拟相结合的方法,探讨了在 SARS-CoV-2 NSP1 存在和不存在的情况下,mRNA 与 40S 核糖体的结合亲和力。我们的研究发现,SARS-CoV-2 NSP1 与 40S 核糖体结合会显著增强 mRNA 的结合亲和力。这一观察结果与实验结果一致,有力地表明 SARS-CoV-2 NSP1 具有抑制 mRNA 翻译的能力。此外,我们还发现 mRNA 与 40S 核糖体之间的静电相互作用是 mRNA 翻译背后的主要驱动力。值得注意的是,我们发现水分子在稳定 mRNA-40S 核糖体复合物方面起着关键作用,这突出了水分子在这一过程中的重要性。我们成功地确定了在引发翻译停止过程中起关键作用的特定 SARS-CoV-2 NSP1 残基。
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引用次数: 0
Flanking Effect on the Structure and Stability of Human Telomeric G-Quadruplex in Varying Salt Concentrations. 侧翼对不同盐浓度下人类端粒 G-四重链结构和稳定性的影响
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-07-15 DOI: 10.1021/acs.jpcb.4c02969
Asim Bisoi, Sunipa Sarkar, Prashant Chandra Singh

The stability of the human telomere G-quadruplex (G4) is directly linked to cancer disease. The human telomere is mostly associated with the flanking nucleobases, which can affect the stability of G4. Hence, in this study, the effect of the flanking nucleobases in the context of their chemical nature, number, and position on the structure and stability of G4 has been investigated in varying concentrations of KCl mimicking the normal and cancer KCl microenvironments. The addition of flanking nucleobases does not alter the G4 topology. However, the presence of merely a single flanking nucleobase destabilizes the telomeric G4. This destabilizing effect is more prominent for thymine than adenine flanking nucleobase, probably due to the formation of the intermolecular G4 topology by thymine. Interestingly, the change in the stability of the telomeric G4 in the presence of thymine flanking nucleobase is sensitive to the concentration of KCl relevant to the normal and cancerous microenvironments, in contrast to adenine. Flanking nucleobases have a greater impact at the 5' end compared to the 3' end, particularly noticeable in KCl concentrations resembling the normal microenvironment rather than the cancerous one. These findings indicate that the effect of the flanking nucleobases on telomeric G4 is different in the KCl salt relevant to normal and cancerous microenvironments. This study may be helpful in attaining molecular-level insight into the role of G4 in telomeric length regulation under normal and cancerous KCl salt conditions.

人类端粒G-四联体(G4)的稳定性与癌症疾病直接相关。人类端粒主要与侧翼核碱基有关,它们会影响 G4 的稳定性。因此,本研究在不同浓度的氯化钾中模拟正常和癌症氯化钾微环境,研究了侧翼核碱基的化学性质、数量和位置对 G4 结构和稳定性的影响。添加侧翼核碱基并不会改变 G4 的拓扑结构。然而,仅仅一个侧翼核碱基的存在就会破坏端粒 G4 的稳定性。与腺嘌呤侧翼核碱基相比,胸腺嘧啶侧翼核碱基的脱稳作用更为明显,这可能是由于胸腺嘧啶形成了分子间的 G4 拓扑结构。有趣的是,胸腺嘧啶侧翼核碱基存在时端粒 G4 稳定性的变化对正常和癌症微环境相关的氯化钾浓度很敏感,而腺嘌呤则不同。与 3' 端相比,侧翼核碱基对 5' 端的影响更大,在氯化钾浓度与正常微环境而非癌症微环境相似时尤其明显。这些发现表明,侧翼核碱基对端粒 G4 的影响在与正常和癌症微环境相关的氯化钾盐中是不同的。这项研究可能有助于从分子水平深入了解G4在正常和癌症KCl盐条件下对端粒长度调控的作用。
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引用次数: 0
Promotion of Fast and Efficient Singlet Fission Process of PDI Dimers by Selenium Substitution. 通过硒置换促进 PDI 二聚体的快速高效单裂变过程
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-07-15 DOI: 10.1021/acs.jpcb.4c01744
Yubo Yang, Wenli Su, Hang Wang, Xiaotian Bao, Xinfeng Liu, Zhishan Bo, Wenkai Zhang

Singlet fission (SF) is a triplet generation mechanism capable of turning a singlet exciton into two triplet excitons. It has the potential to enhance the power conversion efficiency of single-junction solar cells. Perylene diimides (PDIs) are a class of dye molecules with photovoltaic properties and are beginning to receive more and more attention due to their potential for SF. Here, we report a selenium-substituted PDI dimer, Se-PDI-II, and we studied its SF mechanism by using steady-state, transient absorption, and time-resolved photoluminescence spectroscopy. Compared with the unsubstituted dimer PDI-II, we found that the introduction of selenium atoms can suppress excimer emission during the SF process, showing much higher SF efficiency and triplet yield.

单重子裂变(SF)是一种三重子生成机制,能够将一个单重子激子转化为两个三重子激子。它有可能提高单结太阳能电池的功率转换效率。苝二亚胺(PDIs)是一类具有光伏特性的染料分子,由于其具有 SF 的潜力,正开始受到越来越多的关注。在此,我们报告了一种硒取代的 PDI 二聚体 Se-PDI-II,并利用稳态、瞬态吸收和时间分辨光致发光光谱研究了其 SF 机制。与未取代的二聚体 PDI-II 相比,我们发现硒原子的引入可以抑制 SF 过程中的准分子发射,显示出更高的 SF 效率和三重子产率。
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引用次数: 0
Phase-State-Dependent Silica Nanoparticle Uptake of Giant Unilamellar Vesicles. 相态依赖性硅纳米粒子对巨型单拉米小泡的吸收。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-07-12 DOI: 10.1021/acs.jpcb.4c02383
Manuel M Sirch, Andrej Kamenac, Simon V Neidinger, Achim Wixforth, Christoph Westerhausen

We quantify endocytosis-like nanoparticle (NP) uptake of model membranes as a function of temperature and, therefore, phase state. As model membranes, we use giant unilamellar vesicles (GUV) consisting of 1,2-dipentadecanoyl-sn-glycero-3-phosphocholine (15:0 PC). Time-series micrographs of the vesicle shrinkage show uptake rates that are a highly nonlinear function of temperature. A global maximum appears close to the main structural phase transition at T = Tm + 3 K = 37 °C and a minor peak at the pretransition T = Tp = 22 °C. The quality of linear fits to the shrinkage, and thus uptake kinetics, reveals a deviation from the linear trend at the vesicle shrinkage peaks. Taking values for the bending modulus as a function of temperature from literature and Helfrich's model allows us to draw qualitative conclusions on the membrane tension and the adhesion of the NP to the membrane as a function of temperature. These findings provide valuable insights into the dynamic interplay between temperature, membrane phase transitions, and NP uptake, shedding light on the complex behavior of biological membranes.

我们对模型膜的类似内吞作用的纳米颗粒(NP)摄取进行量化,这是温度的函数,因此也是相态的函数。作为模型膜,我们使用了由 1,2-二-十碳酰基-sn-甘油-3-磷酸胆碱(15:0 PC)组成的巨型单拉米尔囊泡 (GUV)。囊泡收缩的时间序列显微照片显示,吸收率是温度的高度非线性函数。在 T = Tm + 3 K = 37 °C 的主要结构相变附近出现了一个总体最大值,而在相变前的 T = Tp = 22 °C 出现了一个小峰值。对收缩以及吸收动力学的线性拟合质量显示,囊泡收缩峰值处偏离了线性趋势。根据文献中的弯曲模量值与温度的函数关系和赫尔弗里希模型,我们可以得出膜张力和 NP 与膜的粘附力与温度的函数关系的定性结论。这些发现对温度、膜相变和 NP 吸收之间的动态相互作用提供了宝贵的见解,揭示了生物膜的复杂行为。
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引用次数: 0
Protonation State of a Bioactive Compound Regulates Its Release from Lamellar Gel-Phase Bilayers. 生物活性化合物的质子化状态可调节其从胶状双分子层的释放
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-07-12 DOI: 10.1021/acs.jpcb.4c02442
Choon-Peng Chng, Shikhar Gupta, Changjin Huang

Lamellar gel networks (LGNs) in personal care or pharmaceutical lotions and creams provide an opaque cream appearance and a creamy texture to these products. Within the LGNs, the lamellar gel (Lβ) phase composed of regularly spaced bilayers of surfactants and long-chain fatty alcohols is predominately responsible for the unique rheological properties of the LGNs. To extend the shelf life of LGN-containing products, bioactive compounds with antimicrobial properties are often incorporated into the formulation. However, how the protonation state of the bioactive compounds regulates their release from the Lβ-phase bilayers is currently unknown. Using molecular dynamics simulations, we found that the protonated (neutral) form of cinnamic acid, a common antimicrobial food additive, has a retention ratio higher than that of its deprotonated (charged) counterpart in the Lβ-phase bilayer. From free energy calculations, we determined that not only is the protonated molecule more stable in the hydrophobic interior of the bilayer but also the formation of hydrogen-bonded dimers significantly enhances its stability within the bilayer. Thus, the protonation state has a profound impact on bioavailability of the compounds. Our results also highlight the importance of considering possible oligomeric states of molecules when performing calculations to estimate the permeability of molecules within various bilayers.

个人护理或药用乳液和膏霜中的层状凝胶网络(LGN)可为这些产品带来不透明的膏霜外观和奶油质感。在 LGN 中,由表面活性剂和长链脂肪醇规则间隔双层组成的层状凝胶(Lβ)相是 LGN 独特流变特性的主要成因。为了延长含 LGN 产品的保质期,通常会在配方中加入具有抗菌特性的生物活性化合物。然而,生物活性化合物的质子化状态如何调节其从 Lβ 相双层膜中的释放目前尚不清楚。通过分子动力学模拟,我们发现肉桂酸(一种常见的抗菌食品添加剂)的质子化(中性)形式在 Lβ 相双层中的保留率高于其去质子化(带电)形式的保留率。通过自由能计算,我们确定质子化分子不仅在双分子层的疏水内部更加稳定,而且氢键二聚体的形成也大大增强了其在双分子层中的稳定性。因此,质子化状态对化合物的生物利用度有着深远的影响。我们的研究结果还强调了在计算估计分子在各种双分子层内的渗透性时考虑分子可能的低聚物状态的重要性。
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引用次数: 0
Fracture of Epoxy Networks Using Atomistic Simulations. 利用原子模拟研究环氧树脂网络的断裂。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-07-11 DOI: 10.1021/acs.jpcb.4c02350
Iakovos Delasoudas, Spyros V Kallivokas, Vassilis Kostopoulos

Predicting fracture properties through all-atomistic simulations poses challenges due to classical force field limitations in breaking covalent bonds and the computational demands of reactive force fields like ReaxFF. In addressing this, we propose a scale-bridging method for forecasting the fracture behavior of highly cross-linked epoxy combining classical force fields, the LAMMPS package REACTER, and for bond breaking a parameter based on experimental distance criterion. In our analysis, we anticipate the macroscopic fracture energy GC of the epoxy network through the application of a continuum fracture mechanics model developed for fibrils. In addition, we extract the value of the stress intensity factor KI. This modeling approach is specifically implemented for a frequently used epoxy system that consists of bisphenol F and DETDA hardener. Notably, our results demonstrate a robust correlation with existing literature and experimental studies. Moreover, our approach boasts a substantial computational time advantage, facilitating calculations that are significantly faster compared to those performed using reactive force fields.

由于经典力场在共价键断裂方面的局限性以及 ReaxFF 等反应力场的计算要求,通过全原子模拟预测断裂特性面临挑战。针对这一问题,我们提出了一种规模桥接方法,结合经典力场、LAMMPS 软件包 REACTER 和基于实验距离准则的断键参数,预测高度交联环氧树脂的断裂行为。在分析中,我们通过应用为纤维开发的连续断裂力学模型,预测环氧网络的宏观断裂能 GC。此外,我们还提取了应力强度因子 KI 的值。这种建模方法特别适用于一种常用的环氧体系,该体系由双酚 F 和 DETDA 硬化剂组成。值得注意的是,我们的结果表明与现有文献和实验研究具有很强的相关性。此外,我们的方法在计算时间上具有很大优势,与使用反应力场进行的计算相比,计算速度明显更快。
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引用次数: 0
60 Years of Betaine 30─From Solvatochromic Discovery to Future Frontiers. 甜菜碱 30 的 60 年--从 Solvatochromic 发现到未来前沿。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-07-11 DOI: 10.1021/acs.jpcb.4c02813
Rathiesh Pandian, Henrik Burda, Ibrahim Alfurayj, Christian Reichardt, Clemens Burda

Betaine-30 (B30) was reported by Karl Dimroth and Christian Reichardt et al. in 1963 as a solvatochromic probe that can be easily synthesized, shows good solubility, and remains stable in various organic solvents and solutions. Its strongly negatively solvatochromic behavior arises from differential solvation between its electronic ground and excited states, making it a valuable tool for assessing solvent polarity using the ET(30) polarity scale, also devised by Dimroth and Reichardt. In addition, advancements in femtosecond laser spectroscopy in the 1990s greatly improved the understanding of B30's relaxation dynamics following photoexcitation. In solvents capable of hydrogen bonding, such as alcohols, intermolecular hydrogen-bond rearrangement contributes to the multiple relaxation components observed. Since the 1990s, the applications of B30 have expanded beyond simple organic solvents to include complex solvent mixtures, such as electrolyte solutions for battery technologies and eutectic solvent mixtures. Given the growing importance of these complex solvent mixtures, B30 is becoming an increasingly valuable tool for studying previously unexplored solvation properties.

甜菜碱-30(B30)是 Karl Dimroth 和 Christian Reichardt 等人于 1963 年报道的一种溶解变色探针,它易于合成,溶解性好,在各种有机溶剂和溶液中保持稳定。其强烈的负溶解变色行为源于其电子基态和激发态之间的溶解度差异,这使其成为使用 ET(30) 极性标度评估溶剂极性的重要工具,该标度也是由 Dimroth 和 Reichardt 设计的。此外,20 世纪 90 年代飞秒激光光谱技术的发展也大大提高了人们对 B30 光激发后弛豫动力学的理解。在具有氢键功能的溶剂(如醇类)中,分子间氢键的重新排列促成了所观察到的多种弛豫成分。自 20 世纪 90 年代以来,B30 的应用已从简单的有机溶剂扩展到复杂的溶剂混合物,如电池技术的电解质溶液和共晶溶剂混合物。鉴于这些复杂混合溶剂的重要性与日俱增,B30 正日益成为研究以前未探索过的溶解特性的重要工具。
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引用次数: 0
The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. 开放力场计划:分子建模的开放软件和开放科学。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-07-11 DOI: 10.1021/acs.jpcb.4c01558
Lily Wang, Pavan Kumar Behara, Matthew W Thompson, Trevor Gokey, Yuanqing Wang, Jeffrey R Wagner, Daniel J Cole, Michael K Gilson, Michael R Shirts, David L Mobley

Force fields are a key component of physics-based molecular modeling, describing the energies and forces in a molecular system as a function of the positions of the atoms and molecules involved. Here, we provide a review and scientific status report on the work of the Open Force Field (OpenFF) Initiative, which focuses on the science, infrastructure and data required to build the next generation of biomolecular force fields. We introduce the OpenFF Initiative and the related OpenFF Consortium, describe its approach to force field development and software, and discuss accomplishments to date as well as future plans. OpenFF releases both software and data under open and permissive licensing agreements to enable rapid application, validation, extension, and modification of its force fields and software tools. We discuss lessons learned to date in this new approach to force field development. We also highlight ways that other force field researchers can get involved, as well as some recent successes of outside researchers taking advantage of OpenFF tools and data.

力场是基于物理学的分子建模的关键组成部分,它将分子系统中的能量和力描述为相关原子和分子位置的函数。在此,我们将对开放力场(Open Force Field,OpenFF)计划的工作进行回顾并提供科学现状报告,该计划的重点是建立下一代生物分子力场所需的科学、基础设施和数据。我们介绍了开放力场计划和相关的开放力场联盟,描述了力场开发和软件的方法,并讨论了迄今取得的成就和未来的计划。OpenFF 根据开放和许可协议发布软件和数据,以便快速应用、验证、扩展和修改力场和软件工具。我们讨论了迄今为止力场开发新方法的经验教训。我们还强调了其他力场研究人员可以参与其中的方法,以及最近外部研究人员利用 OpenFF 工具和数据所取得的一些成功。
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引用次数: 0
Virtual Special Issue on Machine Learning in Physical Chemistry Volume 2 物理化学中的机器学习》虚拟特刊第 2 卷。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-07-11 DOI: 10.1021/acs.jpcb.4c03823
Andrew L. Ferguson*,  and , Jim Pfaendtner*, 
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引用次数: 0
Quantitative Optical Imaging of Oxygen in Brain Vasculature. 脑血管中氧的定量光学成像。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-07-11 DOI: 10.1021/acs.jpcb.4c01277
Emily Rathbone, Dan Fu

The intimate relationship between neuronal activity and cerebral oxygenation underpins fundamental brain functions like cognition, sensation, and motor control. Optical imaging offers a noninvasive approach to assess brain oxygenation and often serves as an indirect proxy for neuronal activity. However, deciphering neurovascular coupling─the intricate interplay between neuronal activity, blood flow, and oxygen delivery─necessitates independent, high spatial resolution, and high temporal resolution measurements of both microvasculature oxygenation and neuronal activation. This Perspective examines the established optical techniques employed for brain oxygen imaging, specifically functional near-infrared spectroscopy, photoacoustic imaging, optical coherence tomography, and two-photon phosphorescent lifetime microscopy, highlighting their fundamental principles, strengths, and limitations. Several other emerging optical techniques are also introduced. Finally, we discuss key technological challenges and future directions for quantitative optical oxygen imaging, paving the way for a deeper understanding of oxygen metabolism in the brain.

神经元活动与脑氧合之间的密切关系是认知、感觉和运动控制等大脑基本功能的基础。光学成像提供了一种评估脑氧合的无创方法,通常可作为神经元活动的间接替代物。然而,解读神经血管耦合--神经元活动、血流和氧输送之间错综复杂的相互作用--需要对微血管氧合和神经元激活进行独立、高空间分辨率和高时间分辨率的测量。本视角审视了用于脑氧成像的成熟光学技术,特别是功能性近红外光谱仪、光声成像、光学相干断层扫描和双光子磷光寿命显微镜,强调了它们的基本原理、优势和局限性。此外,还介绍了其他几种新兴光学技术。最后,我们讨论了定量光学氧成像的关键技术挑战和未来方向,为深入了解大脑中的氧代谢铺平了道路。
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引用次数: 0
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The Journal of Physical Chemistry B
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