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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…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
The formation of quasi-spherical cages from protein building blocks is a remarkable self-assembly process in many natural systems, where a small number of elementary building blocks are assembled to build a highly symmetric icosahedral…
Understanding the pathways by which viral capsid proteins assemble around their genomes could identify key intermediates as potential drug targets. In this work we use computer simulations to characterize assembly over a wide range of…
Understanding how highly symmetric, robust, monodisperse protein cages self-assemble can have major applications in various areas of bio-nanotechnology, such as drug delivery, biomedical imaging and gene therapy. We develop a model to…
Understanding the design of the universe of protein structures may provide insights into protein evolution. We study the architecture of the protein domain universe, which has been found to poses peculiar scale-free properties (Dokholyan et…
Self-assembly at submicroscopic scales is an important but little understood phenomenon. A prominent example is virus capsid growth, whose underlying behavior can be modeled using simple particles that assemble into polyhedral shells.…
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 conjecture that certain patterns (scars), theoretically and numerically predicted to be formed by electrons arranged on a sphere to minimize the repulsive Coulomb potential (the Thomson problem) and experimentally found in spherical…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
A fundamental challenge in protein design is the trade-off between generating structural diversity while preserving motif biological function. Current state-of-the-art methods, such as partial diffusion in RFdiffusion, often fail to resolve…
From the analysis of sizes of approximately 130 small icosahedral viruses we find that there is a typical structural capsid protein, having a mean diameter of 5 nm and a mean thickness of 3 nm, with more than two thirds of the analyzed…
We consider self-assembly of proteins into a virus capsid by the methods of molecular dynamics. The capsid corresponds either to SPMV or CCMV and is studied with and without the RNA molecule inside. The proteins are flexible and described…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
Using X-ray tomography, we experimentally investigate the structural evolution of packings composed of 3D-printed hexapod particles, each formed by three mutually orthogonal spherocylinders, during tap-induced compaction. We identify two…
In many viruses, hundreds of proteins assemble an outer shell (capsid) around the viral nucleic acid to form an infectious virion. How the assembly process selects the viral genome amidst a vast excess of diverse cellular nucleic acids is…
The formation of a viral capsid -- the highly-ordered protein shell that surrounds the genome of a virus -- is the canonical example of self-assembly. The capsids of many positive-sense RNA viruses spontaneously assemble from in vitro…
The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…
We use computer simulations to study a model, first proposed by Wales [1], for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of…