title: Molecular dynamics simulation of reversibly self-assembling shells in solution using trapezoidal particles.
abstract: The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the capsid of a T=1 virus. Growth occurs in the presence of an atomistic solvent and, under suitable conditions, achieves a high yield of complete shells. The simulations provide details of the structure and lifetime of the particle clusters that appear as intermediate states along the growth pathway, and the nature of the transitions between them. In certain respects the growth of size-60 shells from trapezoidal particles resembles the growth of icosahedral shells from triangular particles studied previously, with reversible bonding playing a major role in avoiding incorrect assembly, although the details differ due to particle shape and bond organization. The strong preference for maximal bonding exhibited by the triangular particle clusters is also apparent for trapezoidal particles, but this is now confined to early growth and is less pronounced as shells approach completion along a variety of pathways.
authors.affiliation: Department of Physics, Bar-Ilan University, Ramat-Gan 52900, Israel. rapaport@mail.biu.ac.il
authors.forename: D C
authors.initials: DC
authors.lastname: Rapaport
mesh_terms: D001665:Binding Sites; D036022:Capsid Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D003198:Computer Simulation; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D036022:Capsid Proteins