Aleksandras Gutmanas
Chalmers University of Technology
School of Physics and Engineering Physics
Supervisor: Martin Billeter
Gothenburg University
Department of Biochemistry and Biophysics
December 8, 1998
Homeodomains are highly conserved 60 amino acid polypeptides, participating in the regulation of gene expression. The stucture of the Antennapedia (Antp) homeodomain complexed with its operator DNA was solved by NMR (PDB code--1AHD), and recently by X-ray crystallography.
Homeodomains bind to the major groove of the DNA by a helical fragment designated as recognition helix. Residues 47, 50, 51 and 54 of this recognition helix are thought to be responsible for the specific recognition of DNA. From biochemical studies, it was shown, that the mutation Q50K in the closely related ftz homeodomain reduces the binding affinity, which can, however, be restored by replacing the operator DNA sequence CCATT by GGATT.
In four parallel 200 ps molecular dynamics simulations the different interaction patterns of all combinations of wild type and mutant homeodomain and DNA are explored. Particular attention is given to the role of interfacial water, whose presence has been demonstrated experimentally by NMR and X-ray crystallography.
Water molecules can penetrate the interface from the bulk water as well as leave the interfacial region already within these 200 ps simulations. Besides expected differences in the contact network of residue 50, the conserved Asn51, also contacts different bases in the four runs.
The main result of the simulations agrees with above biochemical studies: the mutant homeodomain preferentially binds to the DNA sequence GGATT, whereas the wild type--to the sequence CCATT.