THE DES(1-6)ANTENNAPEDIA HOMEODOMAIN - COMPARISON OF THE NMR SOLUTIONSTRUCTURE AND THE DNA-BINDING AFFINITY WITH THE INTACT ANTENNAPEDIA HOMEODOMAIN

The nuclear magnetic resonance (NMR) solution structure of an N-termin ally truncated mutant Antennapedia homeodomain, des(1-6)Antp(C39S), ha s been deter mined from 935 nuclear Overhauser effect upper distance c onstraints and 148 dihedral angle constraints by using the programs DI ANA and OPAL. Twenty conformers representing the solution structure of des(1-6)Antp(C39S) have an average root-mean-square distance relative to the mean coordinates of 0.56 Angstrom for the backbone atoms of re sidues 8-59. Comparison with the intact Antp(C39S) homeodomain shows t hat the two proteins have identical molecular architectures. The remov al of the N-terminal residues 1-6, which are flexibly disordered in th e intact homeodomain, causes only strictly localized structure variati ons and does not noticeably affect the adjoining helix I from residues 10-21. The DNA-binding constant of des(1-6)Antp(39S) is approximate t o 10-fold reduced relative to the intact Antp(C39S) homeodomain, which can now be attributed to the absence of the previously reported conta cts of the N-terminal polypeptide segment of the intact Antp(C39S) hom eodomain with the minor groove of the DNA duplex.