Computational protocol: Assembly of the MHC I peptide-loading complex determined by a conserved ionic lock-switch

Similar protocols

Protocol publication

[…] TM-helices were determined from a MAFFT multiple sequence alignment of TAP1 sequences. Helices were built with PyMOL. To assemble 4-TM bundle structures, we used coarse-grained replica-exchange Monte Carlo (MC) simulations with an adapted residue-pair specific short-range Cα-potential. Each TM-helix was allowed to translate and rotate, without consideration of connecting loops. To enhance sampling, 20 replicas between 100 and 300 K were simulated for 106 MC steps, keeping 104 configurations at 100 K for the subsequent stage. Structures were clustered according to DRMS. Full-atom models (including loops) were generated from the cluster centers with MODELLER (v.9.13). Finally, these models were relaxed and rescored using Rosetta (v.3.5) with an implicit membrane potential. 100 models were produced for each cluster and analyzed according to Rosetta score and surface exposure of the experimentally cross-linked residues. MD simulations were performed with GROMACS (v.4.6.5), using the Amber99SB-ILDN force field, POPC lipids, and TIP3P water. NpT ensembles (300 K, 1 bar) were simulated under periodic boundary conditions with PME long-range electrostatics. To generate starting configurations for the MD, pre-oriented proteins were inserted into a pre-equilibrated bilayer (256 lipids), yielding total system sizes of ca. 60,000 atoms. […]

Pipeline specifications

Software tools MAFFT, PyMOL, MODELLER, GROMACS
Application Protein structure analysis