Differential specific radiation damage in the CuII-bound and PdII-bound forms of an α-helical foldamer: a case study of crystallographic phasing by RIP and SAD

Abstract

The high photon flux at third-generation synchrotron sources can inflict significant primary radiation damage upon macromolecular crystals, even when the crystals are cryocooled. However, specific radiation-induced structural changes can be exploited for de novo phasing by an approach known as radiation damage-induced phasing (RIP). Here, RIP and single-wavelength anomalous dispersion (SAD) phasing were alternatively used to derive experimental phases to 1.2 A resolution for crystals of an alpha-helical 18-residue peptide, MINTS, which was derived from the neurotoxin apamin and the palladium-bound structure of which is now reported. Helix formation is induced by the binding of palladium (or copper) to two histidines spaced four residues apart, while two disulfide bonds tether the N-terminal helix to the C-terminal loop-like part of the peptide. Either RIP or SAD phasing of the palladium-bound and copper-bound forms of MINTS, which crystallized in different space groups, resulted in density maps of superb quality. Surprisingly, RIP phasing of the metal-bound complex structures of MINTS was a consequence of differential radiation damage, resting primarily on the reduction of the disulfide bonds in Pd-MINTS and on depletion of the metal sites in Cu-MINTS. Its miniprotein-like characteristics, versatile metal-binding properties and ease of crystallization suggest MINTS to be a convenient test specimen for methods development in crystallographic phasing based on either synchrotron or in-house X-ray diffraction data.