Demo FlexRNA

This example generates logfile demo_FlexRNA.log. The logfile is automatically displayed after completion by the #report directive at the end.

Modules used

Modules Prepare, FlexRNA, and YasaraRefine are used.

Functionality

This example excises dlexible RNA linkers from a model of the RsmE/RsmZ complex, regenerates them by FlexRNA, and refines the model by calling Yasara.

First, the prepare module is used to generate a template containing only the copies of the RsmE protein, the RNA stemloops of RsmZ, and a short piece of an RNA linker that is bound to an RsmE molecule. To this end, structure 2MF1 is downloaded from the PDB and stored in entity RSM0. The six RsmE copies are chains A-F, residues 1-59. They are extracted from the first model {1} of this NMR structure ensemble. The stemloops and linker piece are extracted from chain G of this model. All these parts are merged into entity RSM1. This entity is then saved to file Rsme_Rsmz_rigid_bodies.pbd with pseudo-PDB identifier RSM1.

In order to regenerate the four excised short flexible RNA linkers, FlexRNA is called four times. Each call specifies 75% coverage of the conformation space, generation of one model per template, and a maximum computation time of 0.1 h. In the first call, the input read by addpdb is the rigid-body file generated by the previous Prepare block. The sequence ACAG of the missing nucleotides 16-19 is specified and the 5’-anchor (I)15 and 3’-anchor (G)20 are specified as well. The output PDB file is saved with basis name RsmE_RsmZ_SL1_SL2. This example does not specify distance distribution restraints for the RNA.

In the second call, the addpdb statement refers to the output of the first call. This requires a wildcard filename RsmE_RsmZ_SL1_SL2_*.pdb. The 5’-anchor nucleotide, which would have been (G)35 in the rigid-body file save by Prepare must be referred to as (I)35. This is because the previous FlexRNA module linked chains (I) and (G) and, since the first piece was chain (I), named the resulting chain (I).

The two remaining calls of FlexRNA are analogous to the second call.

Finally, the complete model is refined by a call to YasaraRefine with maximum computatipn time of 1 h.

Outputs

Outputs are the rigid-body template file RsmE_RsmZ_rigid_bodies.pdb and the PDB files of all intermediate models and of the final model.