All-atom simulations were run using the ABSINTH abs3.2_opls.prm implicit solvent model and the CAMPARI V2 Monte Carlo simulation ( )73. The combination of ABSINTH and CAMPARI has been used previously to effectively sample the conformational behavior of disordered proteins with good agreement to experiment, notably in the context of highly charged and highly proline-rich IDRs37,74. All simulations were started from randomly generated non-overlapping random-coil conformations, with each replica using a unique starting structure. Monte Carlo simulations evolve the system via a series of moves that perturb backbone and sidechain dihedral angles along with the rigid-body coordinates of both polypeptides and explicit ions. Simulation analysis was performed using SOURSOP 0.1.9 ( ) and MDTraj 1.9.575 ( ). The protein secondary structure was assessed using the DSSP algorithm76.
Unfolder 1.9.5
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