Related papers: Modeling capsid self-assembly: Design and analysis
We develop coarse-grained models that describe the dynamic encapsidation of functionalized nanoparticles by viral capsid proteins. We find that some forms of cooperative interactions between protein subunits and nanoparticles can…
Understanding protein self-assembly is important for many biological and industrial processes. Proteins can self-assemble into crystals, filaments, gels, and other amorphous aggregates. The final forms include virus capsids and condensed…
Molecular dynamics simulation is used to model the self-assembly of polyhedral shells containing 180 trapezoidal particles that correspond to the T=3 virus capsid. Three kinds of particle, differing only slightly in shape, are used to…
Single-stranded (ss) RNA viruses self-assemble spontaneously in solutions that contain the viral RNA genome molecules and the viral capsid proteins. The self-assembly of empty capsids can be understood on the basis of free energy…
We study the self-assembly behaviour of patchy particles with `protein-like' interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the…
We use computer simulations to investigate self-assembly in a system of model chaperonin proteins, and in an Ising lattice gas. We discuss the mechanisms responsible for rapid and efficient assembly in these systems, and we use measurements…
Motivated by recent experimental findings in chemical synthesis of colloidal particles, we draw an analogy between self-assembly processes occurring in biological systems (e.g. protein folding) and a new exciting possibility in the field of…
A vital constituent of a virus is its protein shell, called the viral capsid, that encapsulates and hence provides protection for the viral genome. Assembly models are developed for viral capsids built from protein building blocks that can…
The coat proteins of many viruses spontaneously form icosahedral capsids around nucleic acids or other polymers. Elucidating the role of the packaged polymer in capsid formation could promote biomedical efforts to block viral replication…
We present a generic computational framework for the simulation of viral capsid assembly which is quantitative and specific. Starting from PDB files containing atomic coordinates, the algorithm builds a coarse grained description of protein…
Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…
Molecular simulations of the self-assembly of cone-shaped particles with specific, attractive interactions are performed. Upon cooling from random initial conditions, we find that the cones self assemble into clusters and that clusters…
Understanding how virus capsids assemble around their nucleic acid (NA) genomes could promote efforts to block viral propagation or to reengineer capsids for gene therapy applications. We develop a coarse-grained model of capsid proteins…
We extend our previously developed general approach (1) to study a phenomenological model in which the simulated packing of hard, attractive spheres on a prolate spheroid surface with convexity constraints produces structures identical to…
Cyanobacteria sequester photosynthetic enzymes into microcompartments which facilitate the conversion of carbon dioxide into sugars. Geometric similarities between these structures and self-assembling viral capsids have inspired models that…
We simulate the assembly dynamics of icosahedral capsids from subunits that interconvert between different conformations (or quasi-equivalent states). The simulations identify mechanisms by which subunits form empty capsids with only one…
We apply Landau theory of crystallization to explain and to classify the capsid structures of small viruses with spherical topology and icosahedral symmetry. We develop an explicit method which predicts the positions of centers of mass for…
Simple RNA viruses self-assemble spontaneously and encapsulate their genome into a shell called the capsid. This process is mainly driven by the attractive electrostatic interaction between the positive charges on capsid proteins and the…
We propose a description for the quasi-equilibrium self-assembly of small, single-stranded (ss) RNA viruses whose capsid proteins (CPs) have flexible, positively charged, disordered tails that associate with the negatively charged RNA…
Curved structures in soft matter and biological systems commonly emerge as a result of self-assembly processes where building blocks aggregate in a controlled manner, giving rise to specific system structure and properties. Learning how to…