Structure, dynamics and hydration of the nogalamycin-d(ATGCAT)(2) complex determined by NMR and molecular dynamics simulations in solution

The structure of the 1:1 nogalamycin:d(ATGCAT)(2) complex has been determin ed in solution from high-resolution NMR data and restrained molecular dynam ics (rMD) simulations using an explicit solvation model. The antibiotic int ercalates at the 5'-TpG step with the nogalose lying along the minor groove towards the centre of the duplex. Many drug DNA nuclear Overhauser enhance ments (NOEs) in the minor groove are indicative of hydrophobic interactions over the TGCA sequence. Steric occlusion prevents a second nogalamycin mol ecule from binding at the symmetry-related 5'-CpA site, leading to the conc lusion that the observed binding orientation in this complex is the preferr ed orientation free of the complication of end-effects (drug molecules occu py terminal intercalation sites in all X-ray structures) or steric interact ions between drug molecules (other NMR structures have two drug molecules b ound in close proximity), as previously suggested. Fluctuations in key stru ctural parameters such as rise, helical twist, slide, shift, buckle and sug ar pucker have been examined from an analysis of the final 500 ps of a 1 ns rMD simulation, and reveal that many sequence-dependent structural feature s previously identified by comparison of different X-ray structures lie wit hin the range of dynamic fluctuations observed in the MD simulations. Water density calculations on MD simulation data reveal a time-averaged pattern of hydration in both the major and minor groove, in good agreement with the extensive hydration observed in two related X-ray structures in which noga lamycin is bound at terminal 5'-TpG sites. However, the pattern of hydratio n determined from the sign and magnitude of NOE and ROE cross-peaks to wate r identified in 2D NOESY and ROESY experiments identifies only a few "bound " water molecules with long residence times. These solvate the charged bicy cloaminoglucose sugar ring, suggesting an important role for water molecule s in mediating drug-DNA electrostatic interactions within the major groove. The high density of water molecules found in the minor groove in X-ray str uctures and MD simulations is found to be associated with only weakly bound solvent in solution. (C) 1999 Academic Press.