Buried surface analysis of HIV-1 reverse transcriptase p66/p51 heterodimer and its interaction with dsDNA template/primer

The p66/p51 human immunodeficiency virus type 1 reverse transcriptase is a heterodimer with identical N‐terminal amino acid sequences. The enzyme contains two polymerization domains and one RNase H domain, which is located at the C‐terminus of the p66 subunit. Both polymerization domains fold into four individual subdomains that are not arranged in a similar fashion, forming an unusually asymmetric dimer. The complexity of the RT p66/p51 heterodimer structure is simplified using solvent‐accessibility surface areas to describe the buried surface area of contact among the different subdomains. In addition, the RT/DNA contacts in the recently published RT/DNA/Fab structure. [Jacobo‐Molina et al., Proc. Natl Acad. Sci. USA 90, 6320–6324 (1993)] are described using the same approach. Finally, the RT/DNA complex is compared with other dimeric DNA‐binding proteins. It was found that the size of the protein and the extent of the dimer interface were not directly related to the extent of contact between the protein and the DNA. Furthermore, RT, the only protein that is not a sequence specific DNA binding protein in this analysis, had the largest surface of interaction with the nucleic acid.