netLibrary - eBook Summary Structure-based Drug Design by ...

Document
Page 101
crystallized under different conditions, forming crystals that are in a different space group with different
crystal-packing interactions, the dimer observed for the ASV core is essentially identical with that of
HIV-1 integrase, although the solvent-excluded surface is smaller (only 740 Å 2). This difference is
largely due to the absence of helix F in the ASV structure.
The core domain dimer of HIV-1 integrase is held together by several hydrophobic and polar
interactions. Hydrophobic interactions dominate the interface between helix E from one monomer and
helices A and B from the other. There is a buried salt bridge between Glu87 of the third β strand and
Lys103 on helix A. There are also some water-mediated polar interactions between these two secondary
structure elements. There are direct hydrogen bonds between residues on helix A and residues on helix E
across the interface including one between Lys185 (the substitution responsible for the improved
solubility and therefore crystallizability) and the main-chain carbonyl on Ala105. In the ASV core,
His198 is in this position, forming a very similar hydrogen bond with the carbonyl oxygen of Ala110.
There are about 10 water molecules buried in the interface, all involved in hydrogen bonds. The part of
the solvent-accessible surface of the monomer which becomes buried upon dimer formation displays a
high degree of shape compatibility with itself: by rotating it 180° around the crystallographic two-fold
axis, the resulting surface will fit the original one without forming large pockets. It is possible that the
core domain of HIV-1 integrase has evolved to optimize this compatibility in order to increase its
stability. It would be interesting to see the effect on protein activity of site-directed mutations aimed at
disrupting this interface and hence the dimer (or possibly the higher order multimers in the context of
the full-length protein).
D. Implications of Crystallographic Dimer for the Chemistry of Catalysis
The nearly spherical nature of the dimer formed by two monomers of the integrase catalytic core places
active sites on respective monomers on opposite sides of the dimer: approximately 35 Å separates the
carboxylate oxygens of Asp64 of each monomer. While we are convinced that the observed dimer is not
an artifact or consequence of crystallization, it would seem difficult to reconcile this distance with the
observation that, during in vivo strand transfer, cuts on the target DNA occur with a separation of five
base pairs, corresponding to 15–20 Å in B-form DNA. How can a single dimer accomplish this? One
possibility is that the cuts do not occur simultaneously. One end of the viral DNA could be joined by a
reaction at one active site, followed by carefully controlled movement of DNA and protein relative to
one another such that the second active site is now positioned five base pairs away from the initial site of
strand transfer. It has been proposed, in a variation on this theme, that the first strand-transfer
http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_101.html [4/5/2004 4:51:57 PM]