C-Terminal Domain of Integrase Binds between the Two Active Sites

Abstract

HIV integrase (HIV-IN), one of three HIV enzymes, is a target for the treatment of AIDS, but the full biological assembly has been difficult to characterize, hampering inhibitor design. The recent crystallographic structures of integrase from prototype foamy virus (PFV-IN) with bound DNA were a breakthrough, revealing how viral DNA organizes two integrase dimers into a tetramer that has the two active sites appropriately spaced for insertion of the viral DNA into host DNA. . Instead, we found two symmetry-related positions for the PFV-IN CTD that indicate formation of a CTD dimer between the two active sites. Our predicted CTD dimer is consistent with crosslinking studies showing interactions of the CTD with viral DNA that appear to be blocked in the PFV-IN structures. The CTD dimer can insert two arginine-rich loops between the two bound vDNA molecules and the host DNA, a region that is unoccupied in the PFV-IN crystallographic structures. The positive potential from these two loops would alleviate the large negative potential created by the close proximity of two viral vDNA ends, helping to bring together the two active sites and assisting host DNA binding. This study demonstrates the ability of computational docking to evaluate complex crystallographic assemblies, identify interactions that are influenced by the crystal environment, and provide plausible alternatives.

Toward Rational Design of High-efficiency Enzyme Cascades

“…Although there were modeling efforts finding a significant proximity channeling effect, most of them were carried out over a short time scale. For example, a coarse-grained Brownian dynamics simulation by Roberts et al considered the first 4 ms, 31 and a Monte Carlo simulation by Chado et al simulated 137 ms. 32 Therefore, these results mainly captured the initial "channeling time" phase; however, this effect was notably not observed by Chado et al at high enzyme densities.…”

The Preserved HTH-Docking Cleft of HIV-1 Integrase Is Functionally Critical

“…The involvement of CTD in IN multimerization (Andrake and Skalka, 1995; Bojja et al, 2013; Jenkins et al, 1996) and stabilization of viral DNA binding (Ballandras-Colas et al, 2016; Maertens et al, 2010; Yin et al, 2016) is well recognized. Recent computational modeling has indeed predicted that CTD forms a dimer that binds between two CCD at the dimer-dimer interface, which should correctly space the two active CCD domains for the corresponding staggered integration of HIV-1 IN (Roberts, 2015), a prediction that has most recently been supported by the RSV and MMTV intasome structures (Ballandras-Colas et al, 2016; Yin et al, 2016). CTD has also been shown to play an important role in the aberrant IN multimerization and aggregation induced by allosteric IN inhibitors (ALLINIs), which bind to a pocket at the dimeric interface of IN CCD domains (Gupta et al, 2014; Shkriabai et al, 2014).…”

Considering both small and large scale motions of vascular endothelial growth factor (VEGF) is crucial for reliably predicting its binding affinities to DNA aptamers

“…61,62 Due to this advantage, DOT2 has been employed for docking for various protein-DNA interactions, such as DNA-DNA repair enzymes, [63][64][65][66] the nucleosome, 67 and viral DNA-integrase. 68,69 DOT2 calculates intermolecular energies as the sum of electrostatic and van der Waals (VDW) energy terms. We used the AMBER library (uhbd.amber84.prot.dna.rlb) 70 as the residue library to assign partial atomic charges for both VEGF 165 and DNA aptamer.…”