Structural Biology 2019: NMR Exploration of The Phage Protein Structure Compendium- Andrei T. Alexandrescu, University of Connecticut

Viruses enclose their genomes in protein shells called capsids, assembled from multiple copies of one or more types of coat proteins. (i) Phage P22 has an icosahedral capsid comprised of 420 copies of a coat protein based on the HK97-fold, which additionally contains a genetically inserted domain (I-domain). The NMR structure of the P22 I-domain has a 6-stranded β-barrel fold, flanked by two long disordered loops called the S and D-loops. The dynamic loops form functionally important interactions within and between the coat proteins. We recently extended NMR studies of the P22 I-domain to the distantly related phages CUS-3 and Sf6, to examine the extent to which the structure and disorder of the I-domain is conserved in these three representatives of divergent phage groups. While the 6-stranded -barrel fold is conserved, there are considerable differences in secondary structure at the periphery of the conserved fold and in loop dynamics, that relate to variations in surface morphologies between the phages. (ii) To further understand capsid surface properties we studied the phage L encoded decoration protein (Dec). Dec trimers non-covalently bind both phages L and P22, preferentially at icosahedral quasi-three-fold sites. Dec binding stabilizes the capsids against the internal pressure that results from dsDNA genome packaging. The NMR structure of the Dec monomer has a globular segment comprised of an OB-fold structure, followed by a 40-residue disordered tail that folds into a trimeric -helix spike when Dec binds capsids. (iii) P22 phage capsids do not assemble spontaneously but through a nucleated process governed by scaffolding protein (Scaff). The Scaff amino acid sequence encodes an intrinsically disordered protein (IDP), with a C-terminal helix-turn-helix domain that binds coat protein to nucleate capsid assembly. When Scaff is incorporated into P22 procapsids to form a 23 MDa complex, NMR signals from N-terminal portion of the protein persist, indicating this segment retains its flexibility when bound to procapsids. The unstructured character of the N-terminus is likely important for the dissociation and release of Scaff during the genome packaging step, accompanying phage maturation.

Author(s): Andrei T. Alexandrescu

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