Control of Quasi-Equivalence in Virus Capsids

Abstract: Many T=3 plant and insect viruses use a molecular switch in form of order/disorder of a segment of the polypeptide chain to regulate the quasi-equivalent contacts. The structure of a mutant of the T=3 capsid of bacteriophage fr confirms that this virus and other members of the Leviviridae family lack a switch mechanism.The geometric principles underlying the construction of spherical virus capsid do not allow more than 60 protein monomers to from a capsid while maintaining an identical chemical environment. Most virus capsid, however, contain many more protein subunits. Quasi-equivalence explains how the capsid proteins can have slightly different interactions in the virus shell. Quasi-equivalence requires the capsids to be constructed from multiples of 60 subunits, where the T number denotes the multiplicity.The structure of the T=4 Nudaurelia capensis ω Virus shows a molecular switch in form of a C-terminal helix inserted in some contacts between protein dimers. This virus is very similar in structure to the T=3 nodaviruses. In the nodaviruses a five-membered helix bundle, formed by cleaved peptides around the five-fold axes on the inside of the shell, are suggested to aid in membrane translocation of the genomic RNA. In Nudaurelia capensis ω Virus the helix bundle is formed by 10 helices, of which 5 are still covalently attached to the capsid proteins.Bacteriophage HK97 has T=7 quasi-symmetry. A domain that is degraded during maturation and is not present in the structure of the mature virion controls the quasi-equivalence. During maturation covalent bonds are formed between the protein subunits, producing a set of interlocking covalently bound rings, resembling chainmail.Structural studies of complexes between the bacteriophage MS2 and variants of its translational operator are also included in this work. A dimer of the MS2 coat protein binds with sequence specificity to an operator in its genomic RNA, and causes translational repression. Structures of multiple RNA segments with altered sequence at some positions which are required for binding to the capsid protein, has been determined.