t Antiviral Res. Author manuscript; available in PMC 2016 September 01. Zlotnick et al. Page 4 suggest that capsids are more conformationally restricted than dimers. Structures of T=4 capsid with bound drugs show that the CD dimer in particular can make dramatic structural changes to accommodate a bound small molecule. Though HAP1 and AT130 have different chemistries, they fit in the same pocket at the interdimer contact. Unlike canonical protein-protein interactions, those holding a virus capsid together are based on weak association energy and are therefore, unsurprisingly, non-complementary. HAP1 and AT130 fill a gap between two dimers, increasing the buried hydrophobic surface. In order to adjust to the bulge, the CD dimers shift their assembly domain C-terminal inter-dimer contacts, which allosterically lead to partial unfolding of the intra-dimer four helix bundles. A major role of the HBV capsid is to package nucleic acid and shuttle it to the nucleus. Cryo-EM structures have shown that RNA and the basic CTD line the capsid interior. However, CTDs, which carry a nuclear localization signal, can be transiently exposed on the capsid exterior . As might be expected for authentic RNA-filled cores, where assembly is initiated by a specific P-pgRNA complex that is central to multiple template transfers, it appears that the P protein has a specific location with respect to the capsid, but interior to the RNA layer. Mass spectrometry has led to important insights into HBV structure. Because HBV capsids have been the subject of numerous assembly studies ), it is important to note that capsids from E coli and assembled in vitro under mild conditions lead to complete capsids. However, as predicted by theory, when association energy is relatively strong, incomplete capsids PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19853262 are readily trapped. The capsids and dimers that are able to adopt so many structures are found to be extremely flexible based on protease sensitivity and the hydrogendeuterium exchange rate. Author Manuscript Author Manuscript Author Manuscript Author Manuscript Cp and cccDNA The HBV lifecycle can be revisited from the perspective of core protein, a perspective we will follow through the rest of this review. The root of chronic HBV infection is a genomic episome, covalently closed circular DNA. Recycling mature relaxed circular DNA-filled) cores to the nucleus replenishes cccDNA to maintain infection. However, years of treatment with nucleoside analogs, which prevent formation of new virions, only sporadically results in loss of virus. Thus, cccDNA is persistent throughout the cycle of infectivity. cccDNA is decorated with the usual proteins of euchromatin with the addition of two HBV proteins: X and Cp. The 118414-82-7 interaction of Cp with core protein is poorly understood and this information is just beginning to accumulate. Cp was identified on cccDNA isolated from stably transfected Antiviral Res. Author manuscript; available in PMC 2016 September 01. Zlotnick et al. Page 5 AD38 cells and found to correlate with changes in the number of nucleosomes. 
Indeed, nucleosome spacing, at least on duck HBV cccDNA appears non-random. Chromatin Immuno-Precipitation has shown that Cp is preferentially associated with CpG islands. The presence of Cp on CpG island 2 correlates with increased activity of cccDNA, while methylation of DNA in CpG islands 2 and 3 correlates with decreased cccDNA activity. Of note, small molecules that drive Cp assembly, presumably depleting the concentration of f