Direct Phasing of Coiled-Coil Protein Crystals

Abstract

Coiled-coil proteins consisting of multiple copies of helices take part in transmembrane transportation and oligomerization, and are used for drug delivery. Cross-alpha amyloid-like coiled-coil structures, in which tens of short helices align perpendicular to the fibril axis, often resist molecular replacement due to the uncertainty to position each helix. Eight coiled-coil structures already solved and posted in the protein data bank are reconstructed ab initio to demonstrate the direct phasing results. Non-crystallographic symmetry and intermediate-resolution diffraction data are considered for direct phasing. The retrieved phases have a mean phase error around 30∼40°. The calculated density map is ready for model building, and the reconstructed model agrees with the deposited structure. The results indicate that direct phasing is an efficient approach to construct the protein envelope from scratch, build each helix without model bias which is also used to confirm the prediction of AlphaFold and RosettaFold, and solve the whole structure of coiled-coil proteins.