Topologically Linked Protein Rings in the Bacteriophage HK97 Capsid

Abstract

The crystal structure of the double-stranded DNA bacteriophage HK97 mature empty capsid was determined at 3.6 angstrom resolution. The 660 angstrom diameter icosahedral particle contains 420 subunits with a new fold. The final capsid maturation step is an autocatalytic reaction that creates 420 isopeptide bonds between proteins. Each subunit is joined to two of its neighbors by ligation of the side-chain lysine 169 to asparagine 356. This generates 12 pentameric and 60 hexameric rings of covalently joined subunits that loop through each other, creating protein chainmail: topologically linked protein catenanes arranged with icosahedral symmetry. Catenanes have not been previously observed in proteins and provide a stabilization mechanism for the very thin HK97 capsid.

Mechanically bonded macromolecules

“…Using this approach (Strategy II), we have achieved 27 (Scheme 2) the synthesis of two main-chain poly(bis [2]catenane)s 4Á8nPF 6 and 5Á8nPF 6 , a main-chain poly([2]catenane) 6Á4nPF 6 , and a pendant poly [2]catenane 7Á4nPF 6 with degrees of polymerisation up to as far as 25.…”

“…In one example, two hydroxymethyl groups were installed on the macrocyclic polyether component of the monomeric [2]catenane, while the CBPQT 4+ component remained unfunctionalised. Reaction of this [2]catenane with bis(4-isocyanatophenyl)methane yielded the pendant poly[2]-catenane 7Á4nPF 6 . Chloride salts of all these polycatenanes (4Á8nCl-7Á4nCl) were analysed in aqueous solution by gel permeation chromatography (GPC).…”

“…These M n values correspond to degrees of polymerisation from 15 up to 25. Compared to Olympiadane 2Á12PF 6 , 4Á8nPF 6 -7Á4nPF 6 have much higher molecular weights, but are polydisperse, i.e., they are mixtures of species with different molecular weights, on account of the nature of the step-growth polymerisation process.…”

“…A series of such dumbbell-shaped molecules (9a-9fÁnPF 6 ), containing n (n = 2, 3, 4, 6, 10, 14, respectively) dialkylammonium centres, were synthesised firstly by reductive amination with derivatives of benzylamine and benzaldehydes, then by protonation of the secondary amines followed by counterion exchange. The clipping reaction of 2,6-dipyridinedicarboxaldehyde and tetraethyleneglycol bis(2-aminophenyl)ether, templated by 9a-9dÁ nPF 6 , gave the thermodynamically stable [3]-, [4]-, [5]-, and [7]rotaxanes (10a-10dÁnPF 6 ) in nearly quantitative yields in MeNO 2 . When n = 10, 4-octyloxypyridinedicarboxaldehyde was used, in a 21-component self-assembly reaction in order to improve the solubility of the product 10eÁnPF 6 .…”

“…Interlocked molecules which contain one or more mechanical bonds have been identified in biomacromolecules, e.g., catenated circular DNA 5 and protein chainmail 6 (Fig. 1a and b), to cite but two examples from mother nature.…”