模拟构筑二十面体病毒衣壳结构的研究进展

许多病毒具有二十面体对称结构,二十面体病毒衣壳结构的模拟构筑已成为物质结构的研究目标之一.介绍了二十面体病毒衣壳结构的几种模型,对各种模型的特点及应用范围进行了归纳,并对衣壳结构模拟构筑的意义进行了简要介绍.     

人乳头瘤病毒HPV-16衣壳蛋白的结构特征

人乳头瘤病毒HPV-16是引发子宫颈癌的主要元凶.研究HPV-16病毒的结构特点,对于二十面体病毒几何结构的认识、描述和疫苗设计具有重要意义.综述了HPV-16病毒的衣壳结构特征、衣壳蛋白,分析了它们之间的相互作用,并试探性地指出了HPV-16衣壳几何结构的数学问题.     

Al-Fe-Ce非晶合金中的二十面体短程序

采用X射线衍射(XRD)和高分辨透射电镜(HRTEM)对Al-Fe-Ce非晶合金的局域结构进行了研究,分析了二十面体短程序对非晶合金的形成及热稳定性的影响.Al-Fe-Ce非晶合金中的二十面体短程序均匀弥散分布在非晶基体中.Al颗粒被二十面体化学短程序紧紧包围,二十面体化学短程序阻碍了Al颗粒的长大,面心立方铝(fcc-Al)的形核需要二十面体结构的分解及溶于其中的元素的扩散.二十面体结构单元的存在和均匀分布有利于增强非晶合金的玻璃形成能力和非晶相的热稳定性.     

Ni3Al合金液态与非晶中的原子团簇

采用常温常压分子动力学模拟技术，模拟了液态Ni3Al中原子团簇在快速凝固条件下的演变过程，模型采用的是TB(tight binding)作用势.用偶分布函数、键对和多面体等结构参数来描述快速凝固条件下团簇种类和数量的变化，并将团簇结构可视化.在2 000 K下，液态Ni3Al中团簇数量较少，且都是由缺陷二十面体构成；在4×1013 K•s－1的冷速下，团簇的数量随温度的降低不断增加，且出现完整二十面体团簇，体系最终形成了由二十面体和缺陷二十面体团簇网络所组成的非晶结构.     

二十面体壳层结构：纪念C60发现10周年

圆顶建筑、病毒衣壳和Ｃ６０分子笼的生成机制和尺寸差别很大，但都属二十面体壳层，遵循同一几何规律。圆顶建筑和病毒衣壳由近似一等的三角面构成，有１２个五键加３＾５顶，１０（Ｔ－１）个六键连３＾６顶，其中三角面数Ｔ＝ｈ＾２＋ｈｋ＋ｋ＾２是二十面体的一个三角面中的小三角面数，ｈ，ｋ是六角坐标系中３＾５顶的坐标。另一方面，全碳分子笼Ｃｎ（包括其原型Ｃ６０），由１２个五角面与１０（Ｔ－１）个六角面围成，全是三     

二十面体壳层结构——纪念C60发现10周年

圆顶建筑、病毒衣壳和C₆₀分子·笼的生成机制和尺寸差别很大，但都属二十面体壳层，遵循同一几何规律。圆顶建筑和病毒衣壳由近似全等的三角面构成，有12个五键连3⁵顶，10（T-1)个六键连3⁶顶，其中三角面数T=h²+hk十k²是二十面体的一个三角中的小三角面数，h,k是六角坐标系中3⁵顶的坐标。另一方面，全碳分子笼C_n(包括其原型C₆₀)由12个五角面与10(T-1)个六角面围成，全是三键连顶(h,k是一个五角面中心的坐标)。显然，这两类二十面体壳层是对偶的，也就是它们的面、顶有互换关系。本文讨论这些二十面体壳层的几何特征及富勒烯的多样性，强调不同学科间的联系和科学研究的继承与发展的关系。     

钯团簇形成和增长机理的Monte Carlo研究

利用Monte Carlo（MC）方法和Lennard-Jones加Axilord-Teller （LJ＋AT）势能函数,研究了气相中钯团簇的形成过程和增长机理.发现具有二十面体结构的Pd13团簇可以在气相中自发形成,较大的团簇通过在Pd13二十面体结构的表面添加原子组成四面体的方式形成.通过分析团簇结构和能量之间的关系,发现除了Pd13和Pd55以外,Pd19和Pd39团簇也具有五次对称性,都是比较稳定的结构.     

关于B12二十面体结构单元成键情况的探讨

单质硼有多种复杂的晶体结构.对于α-菱形单质硼的结构,有关的教科书大多是作如下描述的:“……其基本的结构单元为正二十面体的对称几何构型.每个面近似为一个等边三角形,20个面相交成12个角顶.每个角顶为一个硼原子所占据,每个硼原子与邻近的5个硼原子等距离.如图1,每个二十面体通过处在腰部的6个硼原子以三中心     

钙钛矿型CaSiO_3解压缩和重压缩过程的分子动力学模拟

用分子动力学模拟方法 (MD)研究了 3 0 0K时钙钛矿型CaSiO3 ,从高压到负压的解压缩过程 .MD模拟获得的P V关系与实验数据相近 ,与已报道的MD模拟数据基本一致 ,所得体积模量也在实验数据分布范围内 .减压缩和重压缩的MD模拟数据与实验结果相似 .钙钛矿型CaSiO3 解压缩成非晶态时 ,存在两个结构破坏阶段 :破坏硅氧八面体和破坏钙氧二十面体 .当钙氧二十面体被破坏后 ,重压缩不能得到钙钛矿型结构 .只要钙氧二十面体未被破坏 ,重压缩可恢复钙钛矿型结构 .本研究得到的结果尚未见相关报道 .由MD模拟数据计算了CaSiO3 系统的红外光谱 ,分析这些数据可知钙钛矿型CaSiO3 解压缩非晶化是一个二阶软模相变 .研究表明钙钛矿型CaSiO3 结构存在一个等容的亚稳极限 ,其解压缩非晶化是一个受动力学控制的亚稳状态 .     

钙钛矿型CaSiO_3解压缩和重压缩过程的分子动力学模拟

用分子动力学模拟方法（MD）研究了300 K时钙钛矿型CaSiO_3，从高压到负压 的解压缩过程。MD模拟获得的P-V关系与实验数据相近，与已报道的MD模拟数据基 本一致，所得体积模量也在实验数据分布范围内。减压缩和重压缩的MD模拟数据与 实验结果相似。钙钛矿型CaSiO_3解压缩成非晶态时，存在两个结构破坏阶段：破 坏硅氧八面体和破坏钙氧二十面体。当钙氧二十面体被破坏后，重压缩不能得到钙 钛矿型结构。只要钙氧二十面体未被破坏，重压缩可恢复钙钛矿型结构。本研究得 到的结果尚未见相关报道。由MD模拟数据计算了CaSiO_3系统的红外光谱，分析这 些数据可知钙钛矿型CaSiO_3解压缩非晶化是一个二阶软模相变。研究表明钙钛矿 型CaSiO_3结构存在一个等容的亚稳极限，其解压缩非晶化是一个受动力学控制的 亚稳状态。     

Correlation of chemical reactivity of Nudaurelia capensis omega virus with a pH-induced conformational change

Nudaurelia capensis omega virus, which undergoes one of the largest known structural changes of icosahedral viruses in response to its environment, exhibits chemical reactivity which depends on its conformational state.     

Sulfonatocalixarenes: molecular capsule and 'Russian doll' arrays to structures mimicking viral geometry

p-Sulfonatocalix[4,5,6,8]arenes are versatile building blocks, able to assemble into 'molecular capsule' arrays based on two calixarenes, as well as a variety of other structural motifs, with the extended structures dominated by the formation of bilayers. For p-sulfonatocalix[4]arene, assembly into nanometre scale spheroids (of either icosahedral or cuboctahedral geometries) as well as nanotubules (all of which take on structural features akin to those of viruses) is possible, depending on the guest molecules and lanthanides present in solution.     

Biotechnological Frontiers of DNA Nanomaterials Continue to Expand: Bacterial Infection using Virus-Inspired Capsids

The elegant geometry of viruses has inspired bio-engineers to synthetically explore the self-assembly of polyhedral capsids employed to protect new cargo or change an enzymatic microenvironment. Recently, Yang and co-workers used DNA nanotechnology to revisit the icosahedral capsid structure of the phiX174 bacteriophage and reloaded the original viral genome as cargo into their fully synthetic architecture. Surprisingly, when using a favorable combination of structural rigidity and dynamic multivalent cargo entrapment, the synthetic particles were able to infect non-competent bacterial cells and produce the original phiX174 bacteriophage. This work presents an exciting new direction of DNA nanotech for bio-engineering applications which involve bacterial interactions.     

Melting and freezing characteristics and structural properties of supported and unsupported gold nanoclusters

Molecular dynamics simulations in conjunction with MEAM potential models have been used to study the melting and freezing behavior and structural properties of both supported and unsupported Au nanoclusters within a size range of 2 to 5 nm. In contrast to results from previous simulations regarding the melting of free Au nanoclusters, we observed a structural transformation from the initial FCC configuration to an icosahedral structure at elevated temperatures followed by a transition to a quasimolten state in the vicinity of the melting point. During the freezing of Au liquid clusters, the quasimolten state reappeared in the vicinity of the freezing point, playing the role of a transitional region between the liquid and solid phases. In essence, the melting and freezing processes involved the same structural changes which may suggest that the formation of icosahedral structures at high temperatures is intrinsic to the thermodynamics of the clusters, rather than reflecting a kinetic phenomenon. When Au nanoclusters were deposited on a silica surface, they transformed into icosahedral structures at high temperatures, slightly deformed due to stress arising from the Au-silica interface. Unlike free Au nanoclusters, an icosahedral solid-liquid coexistence state was found in the vicinity of the melting point, where the cluster consisted of coexisting solid and liquid fractions but retained an icosahedral shape at all times. These results demonstrated that the structural stability in the structures of small Au nanoclusters can be enhanced through interaction with the substrate. Supported Au nanoclusters demonstrated a structural transformation from decahedral to icosahedral motifs during Au island growth, in contrast to the predictions of the minimum-energy growth sequence: icosahedral structures appear first at very small cluster sizes, followed by decahedral structures, and finally FCC structures recovered at very large cluster sizes. The simulations also showed that island shapes are strongly influenced by the substrate, more specifically, the structural characteristic of a Au island is not only a function of size, but also depends on the contact area with the surface, which is controlled by the wetting of the cluster to the substrate.     

Methods of virus formation

Viruses occur in a great variety of shapes and sizes, but for all their diversity in appearance they possess certain characteristics in common: all viruses contain a single nucleic acid molecule – deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) – surrounded by a protective protein coat. Among other things, the protein coat enables the genetic information stored in the nucleic acid to enter a host cell in a usable state, where it can initiate the reproduction of identical virus particles. After penetration of the cell the foreign genetic material of the virus particle first induces the synthesis of macromolecules not normally present in the cell: the viral nucleic acid undergoes replication and very many copies are produced, the protein of the virus coat is synthesized, and then these components are assembled to form a new generation of infectious virus particles. Most viruses also exhibit certain common structural features: their protein coat is built up from subunits arranged in helical or icosahedral fashion around the genetic material.     

MS2 and Qβ bacteriophages reveal the contribution of surface hydrophobicity on the mobility of non‐enveloped icosahedral viruses in SDS‐based capillary zone electrophoresis

SDS is commonly employed as BGE additive in CZE analysis of non‐enveloped icosahedral viruses. But the way by which SDS interacts with the surface of such viruses remains to date poorly known, making complicate to understand their behavior during a run. In this article, two related bacteriophages, MS2 and Qβ, are used as model to investigate the migration mechanism of non‐enveloped icosahedral viruses in SDS‐based CZE. Both phages are characterized by similar size and surface charge but significantly different surface hydrophobicity (Qβ > MS2, where ‘>’ means ‘more hydrophobic than’). By comparing their electrophoretic mobility in the presence or not of SDS on both sides of the CMC, we show that surface hydrophobicity of phages is a key factor influencing their mobility and that SDS‐virus association is driven by hydrophobic interactions at the surface of virions. The CZE analyses of heated MS2 particles, which over‐express hydrophobic domains at their surface, confirm this finding. The correlations between the present results and others from the literature suggest that the proposed mechanism might not be exclusive to the bacteriophages examined here.     

Self‐Assembled Cage‐Like Protein Structures

Proteins and protein‐based assemblies represent the most structurally and functionally diverse molecules found in nature. Protein cages, viruses and bacterial microcompartments are highly organized structures that are composed primarily of protein building blocks and play important roles in molecular ion storage, nucleic acid packaging and catalysis. The outer and inner surface of protein cages can be modified, either chemically or genetically, and the internal cavity can be used to template, store and arrange molecular cargo within a defined space. Owing to their structural, morphological, chemical and thermal diversity, protein cages have been investigated extensively for applications in nanotechnology, nanomedicine and materials science. Here we provide a concise overview of the most common icosahedral viral and nonviral assemblies, their role in nature, and why they are highly attractive scaffolds for the encapsulation of functional materials.     

Structural transitions and melting of copper clusters

Molecular dynamics is used to study the melting and structural transitions of small copper clusters. The melting temperature is found to be proportional to the average coordination number. Small icosahedral clusters melt at slightly higher temperatures than the cubic structures. Small cuboctahedral clusters are not stable but transform via a nondiffusive transition to icosahedral structure.