Solution Conformation of a Heptadecapeptide Comprising the DNA Binding Helix F of the Cyclic AMP Receptor Protein of Escherichia cd Combined use of ‘H Nuclear Magnetic Resonance and Restrained Molecular Dynamics

A nuclear magnetic resonance study on a heptadecamer (17-mer) peptide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia coli is presented under solution conditions (viz. 40% (v/v) trifluorethanol) where it adopts an ordered helical structure as judged by circular dichroism. Using a combination of two-dimensional nuclear magnetic resonance techniques, complete resonance assignments are obtained in a sequential manner. From the two-dimensional nuclear Overhauser enhancement spectra, a set of 87 approximate distance restraints is derived and used as the basis for threedimensional structure determination with a restrained molecular dynamics algorithm in which the interproton distances are incorporated into the total energy function of the system in the form of an additional effective potential term. The convergence properties of this approach are tested by starting from three different initial structures, namely an a-helix, a b-strand and a 3-10 helix. In all three cases, convergence to an a-helical structure is achieved with a root mean square difference of <3 A for all atoms and <2 A for the backbone atoms.