Surface roughness directed self-assembly of patchy particles into colloidal micelles (original) (raw)
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Influence of Fluctuating Membranes on Self-Assembly of Patchy Colloids
Physical Review Letters, 2012
A coarse-grained computational model is used to investigate the effect of a fluid membrane on patchy-particle assembly into biologically-relevant structures motivated by viral cores and clathrin. For cores, we demonstrate a non-monotonic dependence of the promotion of assembly on membrane stiffness. If the membrane is significantly deformable, cores are enveloped in buds, although this effect is suppressed for very flexible membranes. In the less deformable regime, we observe no marked enhancement for cores, even for strong adhesion to the surface. For clarthrin-like particles, we again observe the formation of buds, whose morphology depends on membrane-flexibility. In self-assembly, the interactions between a collection of components guide them to spontaneously form an ordered structure [1]. Biological self-organization happens within cells, from which all living organisms are composed. Cells are all bounded by a membrane, as are many sub-cellular structures. Thus many self-assembly processes are membrane-influenced. Membranes themselves are also self-assembled, primarily as a lipid bilayer [2]. We focus, however, on structures assembled only from proteinaeous sub-units, particularly viruses and clathrin. The genome of a virus is contained in a core or capsid, a typically mono-disperse shell, assembled from individual protein complexes. Often the shells are approximately spherical, with many having icosahedral symmetry [3]. Viruses are divided into enveloped and nonenveloped types, depending on whether the core is surrounded by a membrane. The envelope in the former group is acquired through budding [4]. For both enveloped [5-10] and nonenveloped [11-13] viruses there is abundant evidence of membrane influence on core assembly. Clathrin, on the other hand, is intrinsically linked to membranes: its main function is the formation of coated vesicles for intra-cellular protein transport [14]. Its three-legged shape allows a collection of individual units to form structures that range from extended hexagonal sheets to closed cages, which always include 12 pentagonal, in addition to different numbers of hexagonal, faces [15]. Assembly is nucleated on cellular membranes by adaptors, protein complexes which bind the lattice to the membrane. Hexagonal sheets on membranes are observed [16] and coated vesicles form through budding [14]. Experimentally, the reversible disassembly and reassembly of viral capsids in solution may be triggered by raising and lowering the pH [17], allowing in vitro experiments of bulk assembly, which is observed, for example, by light scattering [18] or electron microscopy [19]. Similar experiments with clathrin [20] observed bulk assembly into cage structures, finding them to be much more homogeneous when adaptor proteins are present. Much theoretical work on biological bulk self-assembly has used patchy-particle models. Patchy-particles have discrete, attractive interaction sites on their surface and are very versatile in terms of the range of structures that may be assembled [21]. The main focus has been on the assembly of mono-disperse viral capsids [22-26], with simulations reproducing key characteristics such as a lag time, hysteresis and partial capsid formation at high concentrations. Simulations also give more detailed, experimentally inaccessible information about assembly dynamics. A similar coarse-grained simulation approach was also applied
ACS Chemical Biology, 2013
Controlling the geometry of self-assembly will enable a greater diversity of nanoparticles than now available. Viral capsid proteins, one starting point for investigating self-assembly, have evolved to form regular particles. The polyomavirus SV40 assembles from pentameric subunits and can encapsidate anionic cargos. On short ssRNA (≤814 nt), SV40 pentamers form 22-nmdiameter capsids. On RNA too long to fit a T=1 particle, pentamers forms strings of 22-nm particles and heterogeneous particles of 29 to 40 nm diameter. However, on dsDNA SV40 forms 50 nm particles composed of 72 pentamers. A 7.2-Å resolution cryo-EM image reconstruction of 22-nm particles shows that they are built of twelve pentamers arranged with T=1 icosahedral symmetry. At threefold vertices, pentamers each contribute to a three-helix triangle. This geometry of interaction is not seen in crystal structures of T=7 viruses and provides a structural basis for the smaller capsids. We propose that the heterogeneous particles are actually mosaics formed by combining different geometries of interaction from T=1 capsids and virions. Assembly can be trapped in novel conformations because SV40 interpentamer contacts are relatively strong. The implication is that by virtue of their large catalog of interactions, SV40 pentamers have the ability to self-assemble on and conform to a broad range of shapes.
Computer simulation studies of self-assembling macromolecules
Current Opinion in Structural Biology, 2012
Coarse-grained (CG) molecular models are now widely used to understand the structure and functionality of macromolecular self-assembling systems. In the last few years, significant efforts have been devoted to construct quantitative CG models based on data from molecular dynamics (MD) simulations with more detailed all-atom (AA) intermolecular force fields as well as experimental thermodynamic data. We review some of the recent progress pertaining to the MD simulation of selfassembling macromolecular systems, using as illustrations the application of CG models to probe surfactant and lipid selfassembly including liposome and dendrimersome formation as well as the interaction of biomembranes with nanoparticles.
An engineered virus as a scaffold for three-dimensional self-assembly on the nanoscale
Small (Weinheim an der Bergstrasse, Germany), 2005
Significant challenges exist in assembling and interconnecting the building blocks of a nanoscale device and being able to electronically address or measure responses at the molecular level. Self-assembly is one of the few practical strategies for making ensembles of nanostructures and will therefore be an essential part of nanotechnology. In order to generate complex structures through self-assembly, it is essential to develop methods by which different components in solution can come together in an ordered fashion. One approach to achieve ordered self-assembly on the nanoscale is to use biomolecules such as DNA as scaffolds for directed assembly because of the specificity and versatility they provide. Although several groups have demonstrated the usefulness of this approach, building ordered three-dimensional (3D) structures with DNA is difficult, because of the 1D nature of the scaffold. Using viruses as nanoscale scaffolds for devices offers the promise of exquisite control
Nano Letters, 2007
Alphaviruses are animal viruses holding great promise for biomedical applications as drug delivery vectors, functional imaging probes, and nanoparticle delivery vesicles because of their efficient in vitro self-assembly properties. However, due to their complex structure, with a protein capsid encapsulating the genome and an outer membrane composed of lipids and glycoproteins, the in-vitro self-assembly of viruslike particles, which have the functional virus coat but carry an artificial cargo, can be challenging. Fabrication of such alphavirus-like particles is likely to require a two-step process: first, the assembly of a capsid structure around an artificial core, second the addition of the membrane layer. Here we report progress made on the first step: the efficient self-assembly of the alphavirus capsid around a functionalized nanoparticle core.
Generalized Structural Polymorphism in Self-Assembled Viral Particles
Nano Letters, 2008
The protein shells, called capsids, of nearly all spherical viruses adopt icosahedral symmetry; however, self-assembly of such empty structures often occurs with multiple mis-assembly steps resulting in the formation of aberrant structures. Using simple models that represent the coat proteins pre-assembled in the two different predetermined species that are common motifs of viral capsids (i.e., pentameric and hexameric capsomers), we perform molecular dynamics simulations of the spontaneous self-assembly of viral capsids of different sizes containing 1, 3, 4 to 19 proteins in their icosahedral repeating unit (T=1, 3, 4 to 19, respectively). We observe, in addition to icosahedral capsids, a variety of non-icosahedral yet highly ordered and enclosed capsules. Such structural polymorphism is demonstrated to be an inherent property of the coat proteins, independent of the capsid complexity and the elementary kinetic mechanisms. Moreover, there exist two distinctive classes of polymorphic structures: aberrant capsules that are larger than their respective icosahedral capsids, in T=1-7 systems; and capsules that are smaller than their respective icosahedral capsids when T=7-19. Different kinetic mechanisms responsible for self-assembly of those classes of aberrant structures are deciphered, providing insights into the control of the self-assembly of icosahedral capsids.
Journal of the American Chemical Society, 2016
Understanding the fundamental principles underlying supramolecular self-assembly may facilitate many developments, from novel antivirals to self-organized nanodevices. Icosahedral virus particles constitute paradigms to study self-assembly using a combination of theory and experiment. Unfortunately, assembly pathways of the structurally simplest virus capsids, those more accessible to detailed theoretical studies, have been difficult to study experimentally. We have enabled the in vitro self-assembly under close to physiological conditions of one of the simplest virus particles known, the minute virus of mice (MVM) capsid, and experimentally analyzed its pathways of assembly and disassembly. A combination of electron microscopy and high-resolution atomic force microscopy was used to structurally characterize and quantify a succession of transient assembly and disassembly intermediates. The results provided an experiment-based model for the reversible self-assembly pathway of a most simple (T=1) icosahedral protein shell. During assembly, trimeric capsid building blocks are sequentially added to the growing capsid, with pentamers of building blocks and incomplete capsids missing one building block as conspicuous intermediates. This study provided experimental verification of many features of self-assembly of a simple T=1 capsid predicted by molecular dynamics simulations. It also demonstrated atomic force microscopy imaging and automated analysis, in combination with electron microscopy, as a powerful single-particle approach to characterize at high resolution and quantify transient intermediates during supramolecular selfassembly/disassembly reactions. Finally, the efficient in vitro self-assembly achieved for the oncotropic, cell nucleus-targeted MVM capsid may facilitate its development as a drugencapsidating nanoparticle for anti-cancer targeted drug delivery.
Chemical mimicry of viral capsid self-assembly
Proceedings of the National Academy of Sciences, 2007
Stable structures of icosahedral symmetry can serve numerous functional roles, including chemical microencapsulation and delivery of drugs and biomolecules, epitope presentation to allow for an efficient immunization process, synthesis of nanoparticles of uniform size, observation of encapsulated reactive intermediates, formation of structural elements for supramolecular constructs, and molecular computing. By examining physical models of spherical virus assembly we have arrived at a general synthetic strategy for producing chemical capsids at size scales between fullerenes and spherical viruses. Such capsids can be formed by self-assembly from a class of molecules developed from a symmetric pentagonal core. By designing chemical complementarity into the five interface edges of the molecule, we can produce self-assembling stable structures of icosahedral symmetry. We considered three different binding mechanisms: hydrogen bonding, metal binding, and formation of disulfide bonds. The...
Real-time assembly of an artificial virus elucidated at the single-particle level
2019
While the structure of a variety of viruses has been resolved at atomistic detail, their assembly pathways remain largely elusive. Key unresolved issues in assembly are the nature of the critical nucleus starting particle growth, the subsequent self-assembly reaction and the manner in which the viral genome is compacted. These issues are difficult to address in bulk approaches and are effectively only accessible by tracking the dynamics of assembly of individual particles in real time, as we show here. With a combination of single-molecule techniques we study the assembly into rod-shaped virus-like particles (VLPs) of artificial capsid polypeptides, de-novo designed previously. Using fluorescence optical tweezers we establish that oligomers that have pre-assembled in solution bind to our DNA template. If the oligomer is smaller than a pentamer, it performs one-dimensional diffusion along the DNA, but pentamers and larger oligomers are essentially immobile and nucleate VLP growth. Ne...