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Accuracy and Reproducibility of Lipari-Szabo Order Parameters From Molecular Dynamics. 分子动力学中 Lipari-Szabo 阶参数的准确性和可重复性
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-07 Epub Date: 2024-10-28 DOI: 10.1021/acs.jpcb.4c04895
Thanh T Lai, Charles L Brooks

The Lipari-Szabo generalized order parameter probes the picosecond to nanosecond time scale motions of a protein and is useful for rationalizing a multitude of biological processes such as protein recognition and ligand binding. Although these fast motions are an important and intrinsic property of proteins, it remains unclear what simulation conditions are most suitable to reproduce methyl symmetry axis side chain order parameter data (Saxis2) from molecular dynamics simulations. In this study, we show that, while Saxis2 tends to converge within tens of nanoseconds, it is essential to run 10 to 20 replicas starting from configurations close to the experimental structure to obtain the best agreement with experimental Saxis2 values. Additionally, in a comparison of force fields, AMBER ff14SB outperforms CHARMM36m in accurately capturing these fast time scale motions, and we suggest that the origin of this performance gap is likely attributed to differences in side chain torsional parametrization and not due to differences in the global protein conformations sampled by the force fields. This study provides insight into obtaining accurate and reproducible Saxis2 values from molecular simulations and underscores the necessity of using replica simulations to compute equilibrium properties.

Lipari-Szabo 广义阶次参数可探测蛋白质的皮秒到纳秒时间尺度运动,有助于合理解释蛋白质识别和配体结合等多种生物过程。尽管这些快速运动是蛋白质的重要固有特性,但目前仍不清楚什么样的模拟条件最适合从分子动力学模拟中再现甲基对称轴侧链阶次参数数据(Saxis2)。本研究表明,虽然 Saxis2 往往会在几十纳秒内收敛,但必须从接近实验结构的构型开始运行 10 到 20 次副本,才能获得与实验 Saxis2 值的最佳一致性。此外,在力场比较中,AMBER ff14SB 在准确捕捉这些快速时间尺度运动方面优于 CHARMM36m,我们认为造成这种性能差距的原因可能是侧链扭转参数化的差异,而不是力场采样的全局蛋白质构象的差异。这项研究为从分子模拟中获得准确且可重复的 Saxis2 值提供了深入见解,并强调了使用复制模拟来计算平衡特性的必要性。
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引用次数: 0
Hydrophilic Chain Length for Octylphenol Polyoxyethylene Ether Adsorption at the n-Hexadecane-Water Interface: Theoretical and Experimental Study. 正十六烷-水界面吸附辛基苯酚聚氧乙烯醚的亲水链长:理论与实验研究。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-07 Epub Date: 2024-10-24 DOI: 10.1021/acs.jpcb.4c05462
Zhinan Liu, Guicai Zhang, Rongkai Yuan, Xiang Wang

With the advancement of technologies for developing tight and shale reservoirs, nonionic surfactants have garnered significant attention due to their remarkable properties. The structure of these surfactants plays a crucial role in determining the characteristics of the oil-water interface, particularly influencing emulsification behavior and crude oil recovery. This study investigates the effect of varying the number of hydrophilic polar groups (n = 10, 20, 30, 50) in octylphenol polyoxyethylene ether (OP-n) on its adsorption behavior at the n-hexadecane-water interface using molecular dynamics simulation. The impact of these variations on interfacial properties was further analyzed through measurements of interfacial tension and observations of emulsion droplet morphology. The study results indicate that variations in the number of hydrophilic polar groups significantly affect interfacial properties. Increasing the number of hydrophilic polar groups led to a notable increase in the thickness of the n-hexadecane or water phase, as well as the thickness of the water or oil layer and the surfactant layer. Moreover, when the number of hydrophilic polar groups reached 20, the OP-n molecules exhibited a more curled conformation at the interface, enhancing their ability to encapsulate water and resulting in a decrease in the diffusion coefficient of the molecules in each phase. Additionally, interfacial tension was found to be positively correlated with the number of hydrophilic polar groups and remained unchanged beyond a certain emulsion diameter. This study provides a theoretical basis and reference data for optimizing surfactant structures to improve crude oil recovery.

随着致密油藏和页岩油藏开发技术的进步,非离子表面活性剂因其卓越的性能而备受关注。这些表面活性剂的结构在决定油水界面特性方面起着至关重要的作用,尤其影响乳化行为和原油采收率。本研究利用分子动力学模拟研究了改变辛基酚聚氧乙烯醚(OP-n)中亲水极性基团的数量(n = 10、20、30、50)对其在正十六烷-水界面吸附行为的影响。通过测量界面张力和观察乳液液滴形态,进一步分析了这些变化对界面特性的影响。研究结果表明,亲水极性基团数量的变化会显著影响界面特性。增加亲水极性基团的数量会明显增加正十六烷或水相的厚度,以及水层或油层和表面活性剂层的厚度。此外,当亲水极性基团的数量达到 20 个时,OP-n 分子在界面上会呈现出更多的卷曲构象,从而增强了它们封装水的能力,并导致各相中分子的扩散系数降低。此外,研究还发现界面张力与亲水极性基团的数量呈正相关,并且在超过一定乳液直径后保持不变。这项研究为优化表面活性剂结构以提高原油采收率提供了理论依据和参考数据。
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引用次数: 0
Temperature Dependence of Hydrotropy. 水热的温度依赖性
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-07 Epub Date: 2024-10-28 DOI: 10.1021/acs.jpcb.4c04619
Seishi Shimizu, Nobuyuki Matubayasi

The solubility of hydrophobic solutes increases dramatically with the temperature when hydrotropes are added to water. In this paper, the mechanism of this well-known observation will be explained via statistical thermodynamics through (i) enhanced enthalpy-hydrotrope number correlation locally (around the solute) that promotes the temperature dependence and (ii) hydrotrope self-association in the bulk solution that suppresses the temperature dependence. The contribution from (i), demonstrated to be dominant for urea as a hydrotrope, signifies the weakening of interaction energies around the solute (local) than in the bulk that accompanies incoming hydrotrope molecules. Thus, studying hydrotropic solubilization along the temperature and hydrotrope concentration provides complementary information on the local-bulk difference: the local accumulation of hydrotropes around the solute, driven by the enhanced local hydrotrope self-association, is also accompanied by the overall local weakening of energetic interactions, reflecting the fluctuational nature of hydrotrope association and the mediating role of water molecules.

在水中加入氢托品后,疏水性溶质的溶解度会随着温度的升高而急剧增加。本文将通过统计热力学解释这一众所周知的现象的机理,即(i)局部(溶质周围)焓-亲水基数相关性增强,从而促进了温度依赖性;(ii)在大溶液中亲水基团的自结合抑制了温度依赖性。事实证明,(i) 的贡献在作为水媒的尿素中占主导地位,这表明溶质周围(局部)的相互作用能量比溶质中的相互作用能量弱,这与进入的水媒分子有关。因此,沿温度和水胶粒子浓度研究水胶增溶可提供关于局部-整体差异的互补信息:溶质周围水胶粒子的局部积累是由增强的局部水胶粒子自结合驱动的,同时也伴随着能量相互作用的整体局部减弱,这反映了水胶粒子结合的波动性质和水分子的中介作用。
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引用次数: 0
Evaluating the Accuracy of the COMSOL-Based Finite-Element Method for Simulating Plasmon-Modified Fluorescence. 评估基于 COMSOL 的有限元方法在模拟等离子体改性荧光方面的准确性。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-07 Epub Date: 2024-10-23 DOI: 10.1021/acs.jpcb.4c04008
Fernando A Del Castillo, Nyssa T Emerson, Haw Yang

Accurately modeling plasmon-modified fluorescence is important for understanding and guiding the design of experimental nanostructures that reliably enhance fluorescence. They are of particular interest due to their potential to allow localized "hot spots" of high fluorescence enhancement in a reproducible manner. Given the increasingly prevalent use of the COMSOL Multiphysics software package for simulating these phenomena, we investigate its accuracy using an analytically tractable model consisting of a gold nanosphere interacting with either a plane wave or a radiating point dipole. COMSOL simulation results were compared with a formally exact analytical theory. It was found that simulation parameters commonly used for plane-wave scattering do not necessarily produce accurate results for the nanoparticle-plasmon-coupled dipole emission case. Instead, user-input adaptive meshing parameters were found to be helpful in achieving quantitative agreements between COMSOL and analytical theory results for plasmon-modified fluorescence. Our studies suggest convergence to analytically calculated values when a minimum of two additional user-input mesh elements separate the point-dipole position and the nanoparticle surface. This practical insight is expected to aid in the application of COMSOL simulations to planning and interpreting fluorescence modification experiments.

对等离子体修饰荧光进行精确建模,对于理解和指导设计能可靠增强荧光的实验纳米结构非常重要。质子修饰荧光具有以可重现的方式实现局部高荧光增强 "热点 "的潜力,因此特别引人关注。鉴于 COMSOL Multiphysics 软件包越来越普遍地用于模拟这些现象,我们使用一个由金纳米球与平面波或辐射点偶极子相互作用组成的可分析模型来研究它的准确性。我们将 COMSOL 仿真结果与正式的精确分析理论进行了比较。结果发现,常用于平面波散射的仿真参数并不一定能为纳米粒子-质子耦合偶极子发射情况产生精确的结果。相反,我们发现用户输入的自适应网格参数有助于实现 COMSOL 与分析理论结果之间的定量一致。我们的研究表明,当点偶极子位置和纳米粒子表面之间至少有两个额外的用户输入网格元素时,就会收敛到分析计算值。这一实际见解有望帮助人们将 COMSOL 仿真应用于规划和解释荧光修饰实验。
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引用次数: 0
Binding Selectivity Analysis from Alchemical Receptor Hopping and Swapping Free Energy Calculations. 从炼金受体跳跃和交换自由能计算分析结合选择性。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-07 Epub Date: 2024-10-29 DOI: 10.1021/acs.jpcb.4c05732
Solmaz Azimi, Emilio Gallicchio

We present receptor hopping and receptor swapping free energy estimation protocols based on the Alchemical Transfer Method (ATM) to model the binding selectivity of a set of ligands to two arbitrary receptors. The receptor hopping protocol, where a ligand is alchemically transferred from one receptor to another in one simulation, directly yields the ligand's binding selectivity free energy (BSFE) for the two receptors, which is the difference between the two individual binding free energies. In the receptor swapping protocol, the first ligand of a pair is transferred from one receptor to another while the second ligand is simultaneously transferred in the opposite direction. The receptor swapping free energy yields the differences in binding selectivity free energies of a set of ligands, which, when combined using a generalized DiffNet algorithm, yield the binding selectivity free energies of the ligands. We test these algorithms on host-guest systems and show that they yield results that agree with experimental data and are consistent with differences in absolute and relative binding free energies obtained by conventional methods. Preliminary applications to the selectivity analysis of molecular fragments binding to the trypsin and thrombin serine protease confirm the potential of the receptor swapping technology in structure-based drug discovery. The novel methodologies presented in this work are a first step toward streamlined and computationally efficient protocols for ligand selectivity optimization between mutants and homologous proteins.

我们提出了基于炼金术转移法(ATM)的受体跳跃和受体交换自由能估算协议,以模拟一组配体与两个任意受体的结合选择性。在受体跳跃协议中,配体在一次模拟中从一个受体炼金转移到另一个受体,直接得出配体对两个受体的结合选择性自由能(BSFE),即两个单独的结合自由能之差。在受体交换协议中,一对配体中的第一配体从一个受体转移到另一个受体,而第二配体同时向相反方向转移。受体交换自由能得出一组配体的结合选择性自由能的差异,使用广义 DiffNet 算法将这些差异结合起来,就得出了配体的结合选择性自由能。我们在主客体系统上测试了这些算法,结果表明它们得出的结果与实验数据一致,并且与传统方法得出的绝对和相对结合自由能的差异一致。初步应用于分子片段与胰蛋白酶和凝血酶丝氨酸蛋白酶结合的选择性分析,证实了受体交换技术在基于结构的药物发现中的潜力。这项研究提出的新方法是简化配体选择性优化方案的第一步,计算效率高,适用于突变体和同源蛋白之间的配体选择性优化。
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引用次数: 0
Coarse-Grained MD Simulations of the Capillary Interaction between a Sphere and a Binary Fluid with Truncated Lennard-Jones Potentials. 利用截断伦纳德-琼斯势能对球体与二元流体之间的毛细相互作用进行粗粒度 MD 模拟。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-07 Epub Date: 2024-10-28 DOI: 10.1021/acs.jpcb.4c03759
Falk Wüstemann, Paul Zech, Robert Magerle

In atomic force microscopy experiments on fluid samples, a capillary bridge forms between the tip and the fluid, causing an attractive capillary force. Here, we present a computational model of the capillary interaction between a solid sphere and a coarse-grained Lennard-Jones fluid containing 10% antifreeze particles with an enlarged van der Waals radius. The capillary force acting on the sphere is obtained from the displacement of the sphere in a trap potential as the sphere is incrementally approached and then retracted from the fluid. This yields force-distance data similar to that obtained in atomic force microscopy experiments. We use this methodology to study the influence of the cutoff radius of the truncated Lennard-Jones potentials on the capillary force and its temperature dependence. The latter is found to scale with the critical temperature of the system. With the presented approach, the tip-sample interaction can be studied for a wide range of complex fluids, particle shapes, and force-probing schemes.

在对流体样品进行原子力显微镜实验时,针尖与流体之间会形成毛细管桥,从而产生吸引力。在此,我们提出了固体球体与含有 10%范德华半径增大的防冻剂颗粒的粗粒伦纳德-琼斯流体之间毛细作用的计算模型。作用在球体上的毛细力是根据球体逐渐靠近流体并从流体中缩回时,球体在捕获势中的位移计算得出的。这样得到的力距数据与原子力显微镜实验中得到的数据相似。我们使用这种方法来研究截断伦纳德-琼斯电位的截止半径对毛细力的影响及其温度依赖性。我们发现后者与系统的临界温度成正比。利用所提出的方法,可以研究各种复杂流体、颗粒形状和测力方案的尖端-样品相互作用。
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引用次数: 0
Force Fields for Deep Eutectic Mixtures: Application to Structure, Thermodynamics and 2D-Infrared Spectroscopy. 深共晶混合物的力场:结构、热力学和二维红外光谱学的应用。
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-07 Epub Date: 2024-10-24 DOI: 10.1021/acs.jpcb.4c05480
Kai Töpfer, Eric Boittier, Mike Devereux, Andrea Pasti, Peter Hamm, Markus Meuwly

Parametrizing energy functions for ionic systems can be challenging. Here, the total energy function for an eutectic system consisting of water, SCN-, K+ and acetamide is improved vis-a-vis experimentally measured properties. Given the importance of electrostatic interactions, two different types of models are considered: the first (model M0) uses atom-centered multipole whereas the other two (models M1 and M2) are based on fluctuating minimal distributed charges (fMDCM) that respond to geometrical changes of SCN-. The Lennard-Jones parameters of the anion are adjusted to best reproduce experimentally known hydration free energies and densities, which are matched to within a few percent for the final models irrespective of the electrostatic model. Molecular dynamics simulations of the eutectic mixtures with varying water content (between 0 and 100%) yield radial distribution functions and frequency correlation functions for the CN-stretch vibration. Comparison with experiments indicates that models based on fMDCM are considerably more consistent than those using multipoles. Computed viscosities from models M1 and M2 are within 30% of measured values and their change with increasing water content is consistent with experiments. This is not the case for model M0.

离子体系能量函数的参数化是一项挑战。在此,我们根据实验测量的特性改进了由水、SCN-、K+ 和乙酰胺组成的共晶体系的总能量函数。鉴于静电相互作用的重要性,我们考虑了两种不同类型的模型:第一种(模型 M0)使用原子中心多极,而另外两种(模型 M1 和 M2)则基于波动最小分布电荷(fMDCM),对 SCN- 的几何变化做出响应。对阴离子的伦纳德-琼斯参数进行了调整,以最好地再现实验已知的水合自由能和密度。对不同含水量(0 至 100%)的共晶混合物进行分子动力学模拟,得出了 CN 拉伸振动的径向分布函数和频率相关函数。与实验的比较表明,基于 fMDCM 的模型比使用多极子的模型更加一致。模型 M1 和 M2 计算出的粘度在测量值的 30% 以内,而且它们随含水量增加而发生的变化与实验结果一致。而模型 M0 则不然。
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引用次数: 0
Structural Fluctuation in Homodimeric Aminoacyl-tRNA Synthetases Induces Half-of-the-Sites Activity. 同源二聚体氨基酰-tRNA 合成酶的结构波动诱导半位活性
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-07 Epub Date: 2024-10-23 DOI: 10.1021/acs.jpcb.4c05191
Yoshino Okamoto, Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada

Enzymatic activity is regulated by various mechanisms to ensure biologically proper functions. Notable instances of such regulation in homodimeric enzymes include "all-of-the-sites activity" and "half-of-the-sites activity". The difference in these activities lies in whether one or both of the subunits are simultaneously active. Owing to its uniqueness, the mechanism of half-of-the-sites activity has been widely investigated. Consequently, structural asymmetry derived from cooperative motion is considered to induce half-of-the-sites activity. In contrast, recent investigations have suggested that subunit-intrinsic properties or structural fluctuation also induces structural asymmetry. Hence, the mechanism underlying half-of-the-sites activity has not been completely elucidated. Additionally, most previous studies have focused only on half-of-the-sites activity. Therefore, by comparing the structural and dynamical properties of two representative homodimers exhibiting all-of-the-sites and half-of-the-sites activities, respectively, we attempted to elucidate the mechanism of half-of-the-sites activity. Specifically, all-atom molecular dynamics simulations were applied to lysyl-tRNA synthetase and tyrosyl-tRNA synthetase. Our analysis revealed that structural fluctuation is sufficient to induce structural asymmetry in addition to the well-established factor of cooperative motion. Considering that structural fluctuation is a common characteristic of any enzyme, it could be a general factor in half-of-the-sites activity.

酶的活性受到各种机制的调节,以确保发挥适当的生物功能。在同源二聚体酶中,这种调节的显著实例包括 "全位点活性 "和 "半位点活性"。这些活动的区别在于一个亚基或两个亚基是否同时具有活性。由于其独特性,半位点活性的机制已被广泛研究。因此,合作运动产生的结构不对称性被认为是诱导半位活动的原因。相反,最近的研究表明,亚基的内在特性或结构波动也会诱导结构不对称。因此,半位点活动的机制尚未完全阐明。此外,以往的研究大多只关注半位点的活性。因此,我们试图通过比较两种具有代表性的同源二聚体的结构和动力学特性,分别显示出全位点活性和半位点活性,从而阐明半位点活性的机制。具体来说,我们对赖氨酸-tRNA 合成酶和酪氨酸-tRNA 合成酶进行了全原子分子动力学模拟。我们的分析表明,除了公认的合作运动因素外,结构波动足以诱发结构不对称。考虑到结构波动是任何酶的共同特征,它可能是半位点活性的一般因素。
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引用次数: 0
Quantification of the Surface Coverage of Gold Nanoparticles with Mercaptosulfonates Using Isothermal Titration Calorimetry (ITC). 利用等温滴定量热法(ITC)量化巯基磺酸金纳米粒子的表面覆盖率
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-07 Epub Date: 2024-10-29 DOI: 10.1021/acs.jpcb.4c03365
Emilia Tomaszewska, Artur Stępniak, Dominika Wróbel, Katarzyna Bednarczyk, Jan Maly, Małgorzata Krzyżowska, Grzegorz Celichowski, Jarosław Grobelny, Katarzyna Ranoszek-Soliwoda

This manuscript presents a comprehensive study on the quantification of modifier molecules adsorbed on gold nanoparticles (AuNPs) using two complementary techniques Ellman's method (UV-vis spectroscopy) and isothermal titration calorimetry (ITC). In this paper, we compare the feasibility of using the ITC technique and Ellman's method to study the interactions of mercaptosulfonate compounds (sodium mercaptoethanesulfonate, MES, and sodium mercaptoundecanesulfonate, MUS) with the surface of AuNPs of various sizes. The thermodynamic functions of the attachment of mercaptosulfonates to AuNPs were determined, revealing a linear relationship between the number of adsorbed molecules and the surface area of the nanoparticles. The amount of MES and MUS determined by Ellman's method (7 and 11 molecules per square nm, respectively) is more than twice that measured by the ITC technique (3 and 4 molecules per square nm, respectively). The slight differences in the adsorption of MES and MUS on the gold surface are due to differences in the carbon chain length of the ligand molecules. In the case of MES, the formation of the Au-S bond is the dominant stage of the adsorption process, whereas for MUS, the ordering process and self-assembly of molecules on the gold surface are dominant.

本手稿介绍了利用埃尔曼法(紫外可见光谱法)和等温滴定量热法(ITC)这两种互补技术对吸附在金纳米粒子(AuNPs)上的改性剂分子进行定量的综合研究。本文比较了使用 ITC 技术和埃尔曼法研究巯基磺酸盐化合物(巯基乙磺酸钠,MES 和巯基十磺酸钠,MUS)与不同尺寸 AuNPs 表面相互作用的可行性。测定了巯基磺酸盐与 AuNPs 吸附的热力学函数,结果表明吸附分子的数量与纳米粒子的表面积之间存在线性关系。埃尔曼法测定的 MES 和 MUS 的数量(分别为每平方毫米 7 个和 11 个分子)是 ITC 技术(分别为每平方毫米 3 个和 4 个分子)的两倍多。MES 和 MUS 在金表面的吸附量之所以略有不同,是因为配体分子的碳链长度不同。对于 MES,Au-S 键的形成是吸附过程的主要阶段,而对于 MUS,分子在金表面的有序化过程和自组装是主要阶段。
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引用次数: 0
Predicting the Antifungal Activity of Small Organic Compounds on Aspergillus niger Mold using Molecular Dynamics Simulations. 利用分子动力学模拟预测小型有机化合物对黑曲霉的抗真菌活性
IF 2.8 2区 化学 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-11-07 Epub Date: 2024-10-23 DOI: 10.1021/acs.jpcb.4c04209
Souvik Chakraborty, Jia Min Phang, Shikhar Gupta, ChunSong Chua, Mary Moran, Ross Strand, Marco Klähn

Atomistic models of the plasma membrane of the pathogenic mold Aspergillus niger are developed. These models are described with an empirical molecular mechanical (MM) force field in combination with molecular dynamics (MD) simulations. The solvated plasma membrane models are brought into contact with 35 small organic compounds to observe their impact on a variety of membrane properties. All compounds are added at a constant total mass of 1% of the membrane mass. In addition, the ability of these compounds to inhibit the pathogenic cell growth of mold has been measured. Diffusion of compounds into the membrane model is readily observed during MD simulations. Changes in membrane properties found in simulations are not found to correlate with measured antifungal activities of compounds, suggesting that MD simulations of up to 1 μs are not sufficiently long to adequately describe compound-induced membrane disruption. However, properties related to the position and orientation of compounds relative to the membrane surface as well as hydrogen bonds formed between the compounds and the membrane show clear trends that correlate well with measured activities. A combination of these properties enables an activity prediction of compounds in good agreement with measurements. Activity is found predominantly for compounds that can be decomposed into a single continuous hydrophobic and hydrophilic moiety. Such active compounds can be energetically inserted most favorably into the membrane. These insertions destabilize the membrane by disrupting the internal membrane hydrogen bond network and by sliding between neighboring lipids, thereby separating them.

建立了致病霉菌黑曲霉质膜的原子模型。这些模型是用经验分子机械(MM)力场结合分子动力学(MD)模拟来描述的。溶解质膜模型与 35 种小型有机化合物接触,观察它们对各种膜特性的影响。所有化合物的总质量恒定为膜质量的 1%。此外,还测量了这些化合物抑制霉菌致病细胞生长的能力。在 MD 模拟过程中很容易观察到化合物向膜模型中的扩散。模拟中发现的膜特性变化与测得的化合物抗真菌活性并不相关,这表明长达 1 μs 的 MD 模拟时间不足以充分描述化合物引起的膜破坏。不过,与化合物相对于膜表面的位置和方向以及化合物与膜之间形成的氢键有关的特性显示出明显的趋势,与测得的活性有很好的相关性。结合这些特性,可以预测出与测量结果非常一致的化合物活性。发现具有活性的化合物主要是那些可以分解成单一连续的疏水和亲水分子的化合物。这种活性化合物能以最有利的方式插入膜中。这些插入物会破坏膜内部的氢键网络,并在相邻脂质之间滑动,从而使它们分离,从而破坏膜的稳定性。
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引用次数: 0
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