Towards simulating fully charged protein-DNA systems in water : Zif268-DNA as a test case

Abstract: In this thesis, we develop a computing strategy to simulate fully charged protein-DNA systems with a general force field (GROMOS87). The ions neutralizing the phosphates (P-ions) are submitted to global symmetry constraints. A model exhibiting ionic-atmosphere effects on mobile P-ions was implemented via very weak restraint forces. The same set of molecular parameters for atom types is used for both the protein and the DNA oligomer. Protein-protein, DNA-DNA, protein-DNA and water-water interactions are the invariant part of the simulation framework. The corrections found necessary to describe solvent-solute interactions are incorporated now as standard.The computing framework was tested with Zif268-DNA complex. Zif268 is a 3-zinc finger domain found in the growth factor-inducible protein zif268 related to the transcription factor gene zif268. The analyses show that the rigged GROMOS87 force field yields a fairly appropriate representation of the fully charged protein-DNA complex in solution. The DNA sequence used 5'-GCGTGGGGCGT-3' represents one possible high-affinity binding site. A second one where thymine (T4) was mutated into a guanine (G4) was tested. The results show protein-DNA recognition sites to behave in a similar manner thereby opening an opportunity to study possible dynamic recognition determinants. One aspect of it was addressed by studying the zinc-fingers alone. In water, the protein shows a trend to adopt an extend finger conformation. To disentangle solvation effects from intrinsic properties, a set of dry MD trajectories were calculated. Result: the accessible configurational space also includes elongated conformations resembling those found from another zinc-finger protein (transcription factor IIIA) experimentally determined in solution; in the complex, Zif hugs the DNA. After soaking the in vacuo configurations, the MD results suggest Zif268 in solution may have an elongated average conformation of the 3-finger polypeptide.This put the functionality - defined as the ability to make the proper protein-DNA complex- on the protein's ability to sustain large conformational changes relating it to its linkers dynamic properties. All the information gathered so far can be used to construct a set of two-finger chimeras as templates in modeling the two zinc-finger negative regulator mediating carbon catabolism repression in Aspergillus Nidulans (CreA).