Structural prediction of VPS13C with AlphaFold2
Pietro De Camilli, Shujun Cai
Abstract
This protocol describes the procedure of structural prediction of full-length human VPS13C and its truncation mutant with AlphaFold2 and the procedure to combine each segments into one structure.
Attachments
Steps
Structure prediction
Separate Full-length VPS13C and truncation mutant into three pieces and two pieces, respectively, i.e., a.a. 1-1860, 1201-2340, 1801-3753 for full-length VPS13C and a.a. 1-1762, 1277-3240 for VPS13CΔ1235-1748.
Install AlphaFold 2.0 on the Yale Farnam high performance computer cluster, used for structural prediction of each segment.
Combination of segments
Open UCSF ChimeraX software and import pdb files of segments.
Align the fragments with overlapping regions with “mmaker” command.
Delete the overlapping regions from adjacent fragments with “delete” command.
At the connection point, form a carbon–nitrogen bond with “build join peptide” command to connect two amino acid residues from two fragments.
