Molecular dynamics simulations on the interactions between nucleic acids and a phospholipid bilayer

Recently,lipid nanoparticles(LNPs)have been extensively investigated as non-viral carriers of nucleic acid vaccines due to their high transport efficiency,safety,and straightforward production and scalability.However,the molecular mechanism underlying the interactions between nucleic acids and phospholipid bilayers within LNPs remains elusive.In this study,we employed the all-atom molecular dynamics simulation to investigate the interactions between single-stranded nucleic acids and a phospholipid bilayer.Our findings revealed that hydrophilic bases,specifically G in single-stranded RNA(ssRNA)and single-stranded DNA(ssDNA),displayed a higher propensity to form hydrogen bonds with phospholipid head groups.Notably,ssRNA exhibited stronger binding energy than ssDNA.Furthermore,divalent ions,particularly Ca2+,facilitated the binding of ssRNA to phospholipids due to their higher binding energy and lower dissociation rate from phospholipids.Overall,our study provides valuable insights into the molecular mechanisms underlying nucleic acidphospholipid interactions,with potential implications for the nucleic acids in biotherapies,particularly in the context of lipid carriers.

Molecular Dynamics Simulations of DOPC Lipid Bilayers: The Effect of Lennard-Jones Parameters of Hydrocarbon Chains

The current Chemistry at Harvard Molecular Mechanics (CHARMM) force field cannot accurately describe the properties of unsaturated phospholipid membranes. In this paper, a series of simulations was performed in which the Lennard- Jones (L-J) parameters of lipid acyl chains of dioleoylphosphatidylcholine (DOPC) were systematically adjusted. The results showed that adjustment of the L-J parameters in lipid acyl chains can significantly improve the current CHARMM force field. It was found that the L-J parameters have different influences on the order parameters of the top half and bottom half of the chain, separated by the cis double bond. The order parameters of the top half and the bottom half of the chain are related to the area/lipid and the length of the chain, respectively.

Molecular dynamics simulations of the effects of sodium dodecyl sulfate on lipid bilayer

Molecular dynamics simulations have been performed on the fully hydrated lipid bilayer with different concentrations of sodium dodecyl sulfate （SDS）. SDS can readily penetrate into the membrane. The insertion of SDS causes a decrease in the bilayer area and increases in the bilayer thickness and lipid tail order, when the fraction of SDS is less than 28%. Through calculating the binding energy, we confirm that the presence of SDS strengthens the interactions among the DPPC lipids, while SDS molecules act as intermedia. Both the strong hydrophilic interactions between sulfate and phosphocholine groups and the hydrophobic interactions between SDS and DPPC hydrocarbon chains contribute to the tight packing and ordered alignment of the lipids. These results are in good agreement with the experimental observations and provide atomic level information that complements the experiments.

Coarse-grained simulations on interactions between spectrins and phase-separated lipid bilayers

Spectrin, the principal protein of the cytoskeleton of erythrocyte, plays a crucial role in the stability and flexibility of the plasma membrane of erythrocyte. In this work, we investigate the interactions between spectrins and phase-separated lipid bilayers using coarse-grained molecular dynamics simulation. We focus on the preference of spectrins with different lipids, the effects of the anionic lipids and the residue mutation on the interactions between spectrins and the lipid bilayers. The results indicate that spectrins prefer to contact with phosphatidylethanolamine(PE) lipids rather than with phosphatidylcholine(PC) lipids, and tend to contact with the liquid-disordered(Ld) domains enriched in unsaturated PE.Additionally, the anionic lipids, which show specific interaction with the positively charged or polar amino acids on the surface of the spectrins, can enhance the attraction between the spectrins and lipid domains. The mutation leads to the decrease of the structural stability of spectrins and increases the curvature of the lipid bilayer. This work provides some theoretical insights into understanding the erythrocyte structure and the mechanism of some blood diseases.

Tail-structure regulated phase behaviors of a lipid bilayer

Lateral heterogeneity of a cell membrane,including the formation of lipid raft-like clusters and the inter-leaflet coupling of specific phase domains,is crucial for cellular functions such as membrane trafficking and transmembrane signaling.However,the wide diversity in lipid species and the consequent complexity in lipid-lipid interplays hinder our understanding of the underlying mechanism.In this work,with coarse-grained molecular dynamics simulations,the effect of lipid tail structures on the phase behavior of a model ternary lipid membrane was systematically explored.A serial of 27 lipid membrane systems consisting of saturated,unsaturated lipids,and cholesterol(Chol)molecules,at a fixed molar ratio of 4:4:2 while varying in lipid structures including tail length,unsaturation degree,and/or position of unsaturated atoms,were constructed.These structural factors were found to exert sophisticated influences on packing states of the constituent molecules,especially Chol,in a bilayer,and modulate the complicated entropy-enthalpy competition of the membrane system accordingly.Specifically,an appropriate difference in effective tail length and distinct feature of the tail ends between the saturated and unsaturated lipid compositions promised an enhanced phase separation of the membrane into the Chol-rich Lo and Chol-poor Ld phase domains,with a full inter-leaflet coupling of each domain.Our results provide insights into the lipid organizations and segregations of the cellular plasma membrane.

Amyloid-β peptide aggregation and the influence of carbon nanoparticles

Soluble peptides or proteins can self-aggregate into insoluble, ordered amyloid fibrils under appropriate conditions. These amyloid aggregates are the hallmarks of several human diseases ranging from neurodegenerative disorders to sys- temic amyloidoses. In this review, we first introduce the common structural features of amyloid fibrils and the amyloid fibrillation kinetics determined from experimental studies. Then, we discuss the structural models of Alzheimer＇s amyloid- β （Aβ） fibrils derived from solid-state nuclear magnetic resonance spectroscopy. On the computational side, molecular dynamics simulations can provide atomic details of structures and the underlying oligomerization mechanisms. We finally summarize recent progress in atomistic simulation studies on the oligomerization of β （including full-length Af and its fragments） and the influence of carbon nanoparticles.

Molecular dynamics study of the infiltration of lipid-wrapping C60 and polyhydroxylated single-walled nanotubes into lipid bilayers

Because of the many potential medical applications of nanoparticles, considerable research has been conducted on the interactions between nanoparticles and biomembranes. We employed coarse- grained molecular dynamics simulations to study the infiltration of lipid-wrapping C60 and polyhy- droxylated single-walled nanotubes. Diffusion coefficients and scaling factors are adopted to quantify the diffusivity of the biomembranes, and the rupture tension is used to measure the lateral strength of the lipid bilayer. According to our simulations, all wrapped nanoparticles, except those wrapped by dipalmitoyl-glycero-phosphoglycerol, can be inserted into the bilayers. Our simulations also re- veal that the bilayers remain in free diffusion after the nanoparticle insertions while their diffusion coefficient can be altered significantly. The polyhydroxylated single-walled nanotubes lead to signif- icant changes to the lateral strength of biomembranes and this effect depends on the quantity of the inserted nanoparticles. The simulations demonstrate the feasibility of using these methods to deliver nanopartieles while some suggestions are given for choosing the appropriate lipids for wrappiug. The results also suggest that the functionalized nanopartieles could be applied in strengthening or weakening the lateral strength of biomembranes for specific purposes.

Cholesterol-induced deformation of the gramicidin A channel inhibiting potassium ion binding and transport

Gramicidin A(gA)is a kind of antibiotic peptide produced by bacillus brevis and it can dimerize across lipid bilayers to form a monovalent cation channel.In this work,we investigate the impact of cholesterol in the lipid bilayer on the binding of potassium ions with the gA channel and the transport of the ions across the channel.The results indicate that cholesterol can significantly influence the conformational stability of the gA channel and cause the channel deformation which inhibits the potassium ion binding with the channel and transport across the channel.The work provides some molecular insights into understanding of influence of lipids on the activity of gA channel in both model membranes and plasma membranes of intact cells.

Modeling biomembranes and red blood cells by coarse-grained particle methods

In this work, the previously developed coarse-grained （CG） particle models for biomembranes and red blood cells （RBCs） are reviewed, and the advantages of the CG particle methods over the continuum and atomistic simulations for modeling biological phenomena are discussed. CG particle models can largely increase the length scale and time scale of atomistic simulations by eliminating the fast degrees of freedom while preserving the mesoscopic structures and properties of the simulated system. Moreover, CG particle models can be used to capture the microstructural alternations in diseased RBCs and simulate the topological changes of biomembranes and RBCs, which are the major challenges to the typical continuum representations of membranes and RBCs. The power and versatility of CG particle methods are demonstrated：through simulating the dynamical processes mvolving significant topological .changes e.g. lipid self-assembly vesicle fusion and membrane budding.

ns脉冲电场诱导细胞脂双层膜电穿孔的仿真分析

为探讨ns脉冲电场诱导细胞器膜产生电穿孔的机理,采用分子动力学软件从原子水平上分析了ns脉冲电场作用下细胞脂双层膜电穿孔形成及其孔径随时间变化的过程,研究了电穿孔形成的机理。结果表明,脂质分子的偶极子在脉冲电场作用下的振动和转动导致脂双层膜出现初始缺损并诱导脂双层膜电穿孔;电穿孔初期的多微孔间存在耦合关系;在4～5 ns内电穿孔形成并达到动态稳定。结果与细胞脂双层膜的粗粒化模型计算吻合较好,为电穿孔技术在生物医学等方面的应用提供了理论指导。

抗菌肽HP(2-20)与POPE脂膜相互作用的分子动力学模拟

作为传统抗生素有力的候选者,抗菌肽是先天免疫体系中的重要组成成分.抗菌肽从起初的接触至随后稳定地吸附到细菌CC的质膜之上,是抗菌肽发挥其抗菌功能的关键初始事件.为揭示这一尚未明了的过程,文中使用分子动力学模拟方法,通过构建抗菌肽HP(2-20)与POPE脂双层的体系,模拟了HP(2-20)与POPE脂膜间的非特异相互作用.结果表明:抗菌肽的N端最先与脂膜接触,随后抗菌肽将维持一种倾斜的姿态,经历一个旋动插入脂膜的过程;同时,抗菌肽将束缚膜上与其邻近的磷脂分子的运动,导致膜的不均匀性,增强脂膜磷脂分子的无序波动,为其它自由的抗菌肽分子更深的插入提供了机会.

碳纳米管表面硅纳米颗粒的结构与热稳定性

利用分子动力学方法研究了碳纳米管表面硅颗粒的结构和热稳定性.发现随着温度的增加,碳纳米管表面硅颗粒结构发生了由笼状结构到帐篷状结构的变化.碳管表面的硅颗粒在熔点附近或更高的温度下,结构变得无序,并沿着碳纳米管轴向方向伸长.此外,通过对比分析碳纳米管表面硅颗粒与自由条件下硅颗粒Lindemann指数的变化,发现碳纳米管表面的硅纳米颗粒熔点要低于自由条件下硅纳米颗粒的熔点.

吸附在Au(100)、Au(110)和Au(111)表面的CTAB双分子层的结构和动力学性质的分子模拟(英文)

金纳米棒的各向异性生长常被认为是由于金表面吸附溴化十六烷基三甲基铵(CTAB)双分子层导致的。利用密度泛函理论(DFT)研究溴离子在(100)、(110)和(111)3种金表面上可能的吸附位点,根据它构建金表面CTAB双分子层模型,再利用分子动力学模拟方法研究这种烷基链互相交错排布的双分子层的结构。此外,动力学性质研究表明外层CTAB有着明显的横向扩散现象,而在法向上则出现上下起伏振动。相比较而言,在(111)表面上的双分子层结构的横向扩散和法向涨落更加显著。用外层单个CTA+脱离双分子层所需要的能量表征金表面CTAB双分子层的稳定性。结果表明(111)表面的CTAB双分子层的稳定性弱于其他两种金表面上的CTAB双分子层。认为这是因为(111)表面上的CTAB双分子层的排布密度相对较低,导致它相对于其他两种表面的双分子层有更高的扩散性和较低的稳定性。这可能是金纳米颗粒倾向于沿(111)表面生长的原因。

Au纳米粒子在超临界CO_2中结构和相互作用

为了可控制备分散性的Au纳米粒子,研究Au纳米粒子在溶剂中的界面结构及相互作用。采用分子动力学模拟方法研究不同温度下氟化的硫醇十二烷钝化的Au纳米粒子在超临界CO_2中的界面结构和相互作用自由能。结果表明:温度升高会略微提升纯排斥的特征。通过自由能的分解,发现Au纳米内核与吸附的有机配体间的相互作用完全决定了自由能的排斥特征。焓熵分析结果表明自由能的排斥特征是由熵贡献引起的。

scCO2溶剂中金纳米颗粒界面性质的分子模拟

基于经典的分子动力学模拟方法,研究了不同的超临界CO2(scCO2)溶剂密度下,金纳米颗粒周围溶剂分子的结构与动力学性质。结果表明,由于金纳米颗粒对scCO2溶剂分子有较大的吸引作用,使scCO2分子紧密地围绕在其表面周围并形成了两个较明显的溶剂层。随着溶剂密度的增加,纳米颗粒在scCO2中的溶剂化程度会减小。通过分析固液界面不同区域内scCO2分子的均方位移及停留时间分布,考察了界面CO2分子的传递性质。研究结果将对金属纳米颗粒在超临界二氧化碳中溶剂化结构和性质提供微观机理。

纳米粒子在具有温度梯度的碳纳米管上运动模式的研究

采用分子动力学(MD)模拟的方法,使用Born-Mayer-Huggins与Lennard-Jones相互作用势函数,研究KI纳米粒子负载在具有一定温度梯度的碳纳米管外壁上的运动特征.模拟结果表明,在纳米粒子由碳管高温端向低温端运动的过程中有两种模式.通过KI纳米粒子在具有温度梯度的碳管上的轨迹分析,说明了这些运动模式与碳纳米管的手性、管径和温度梯度的大小密切相关.通过KI纳米粒子在具有温度梯度的碳管上的受力分析,解释了KI纳米粒子在具有温度梯度的碳管上采取特殊模式运动的原因.本文的工作对于设计纳米尺度的马达有一定的指导意义.

钙离子和镁离子浓度变化对磷脂酰乙醇胺-磷脂酰甘油双分子层膜的影响（英文）

钙离子和镁离子是生物细胞中重要的二价阳离子,对生物膜结构保持和功能行使发挥重要作用。但至今,对两种阳离子在不同浓度下与大肠杆菌内膜相互作用的认识仍存在局限。本文采用动态光散射(DLS)、zeta电势实验、全原子分子动力学模拟(AA-MD),定量研究了不同浓度的钙离子和镁离子对混合磷脂双分子层膜(1-棕榈酰基-2-油酰基-sn-丙三基-3-磷酸乙醇胺(POPE):1-棕榈酰基-2-油酰基-sn-丙三基-3-磷酸甘油(POPG)的摩尔比为3:1)模拟的大肠杆菌内膜的影响。DLS结果表明,在0和1 mmol·L-1钙离子或镁离子溶液中,POPE/POPG脂质体为均匀的单分散体系。当两种离子浓度分别提高到5–100 mmol·L-1范围时,单室脂质体间发生脂分子聚集或脂质体融合事件。Zeta电势数据表明,钙离子或镁离子对电负性的POPE/POPG脂质体均有电荷反转效果。AA-MD模拟计算结果表明,当模拟时间超过100 ns时,各浓度的钙离子稳定地吸附在磷脂双分子层膜上,而镁离子动态地吸附/解吸附于磷脂膜,这些结果与DLS和zeta电势实验基本吻合。同时,通过计算径向分布函数,分析了0、5、100 mmol·L-1浓度溶液中POPE和POPG的磷酸、羰基和羟基基团氧原子的第一配位壳层中的钙离子或镁离子的平均配位数目,结果表明两种离子主要结合在POPE和POPG电负性的磷酸基团上,因此可以解释DLS实验中钙离子或镁离子对POPE/POPG脂质体的电荷反转现象。另外,随着离子浓度的增高,钙离子减小了磷脂双分子层膜的单个磷脂面积,同时使膜的厚度增大,而镁离子对膜的两种参数影响较小。同时,相同浓度条件下两种离子对膜中磷脂分子的取向影响不同。这些模拟结果可在原子水平上解释DLS和zeta电势实验中钙离子和镁离子对POPE/POPG脂质体的不同影响。本文的实验和分子动力学模拟结果可以解释一些与二价阳离子调控相关的生物学过程,例如,膜融合。

分子动力学模拟在药物与膜相互作用研究中的应用

药物与细胞膜的相互作用是决定药物在体内吸收、分布、代谢与排泄的关键因素之一,最终影响临床上的药效与毒副作用.对药物透膜过程的分子动力学模拟可在原子层面上提供药物与膜相互作用的丰富信息,从而指导药物分子的设计与优化以及载药体系如脂质粒的优化.从磷脂双分子层模型、全原子/联合原子模型方法及粗粒化模型方法、膜性质关键参数分析等方面展开介绍,并对系列药物分子与膜的相互作用分子动力学模拟应用实例进行了综述.

分子动力学模拟研究穿膜肽bLFcin6与不同磷脂双层膜的相互作用

穿膜肽是一类由5-30个氨基酸残基组成的有穿膜能力的小分子多肽,可携带各种物质进入细胞内部,发挥各自生物学活性.bLFcin6是一种新的细胞穿透肽,选取含有4-9个残基的bLFcin6为研究对象,用Pymol软件来构建肽的初始结构并下载膜DPPC,POPC,POPG的结构,在优化后搭建肽-膜的初始体系.每个体系模拟了500ns,对肽用GROMOS53a6力场处理,对膜用Berger力场处理,温度设置为323K.在这3个体系中,bLFcin6进入到DPPC的羰基端并与疏水的尾部相互作用;bLFcin6能进入到POPG的亲水头部,不能更深的插入到内部;bLFcin6并不能接触到膜上.分析了在不同氨基酸与膜带电基团之间氢键的形成,发现了带正电的精氨酸在肽-膜之间的相互作用起了一个重要的角色.计算了在不同的氨基酸和膜的质心之间的距离,发现肽的N端首先接触到DPPC和POPG的膜上.此外,不同膜对bLFcin6穿膜能力的影响与脂质分子的结构有关.BLFcin6对不同膜有不同的渗透能力.我们重点强调了精氨酸的重要性,与先前实验和模拟中得到的结果是一致的,这为进一步探究bLFcin6的穿膜机制提供了一定的帮助.

受限在单壁碳纳米管中金纳米粒子相变的分子动力学模拟研究

近年来,负载型金属纳米催化剂的制备及其性能研究一直是催化领域重要的研究课题.通过分子动力学(MD)模拟研究了受限在单壁碳纳米管(SWNT)内金纳米粒子在升温和降温过程中的相变.结果表明,受限金纳米粒子在室温下表现出两种不同类型的圆筒状多层结构.基于MD模拟,我们观察到了一个有趣的现象,即受限金纳米粒子的熔点随粒子增大而降低.对于受限的金纳米粒子来说,每一层的有序-无序的结构转变是受限金纳米粒子熔化的本质结构特征.