469397 Computational Screening of Photoactive Cyclic Peptides for Self Assembly and Disassembly
The large potential parameter space for amino acid sequences makes experimental screening cumbersome. We computationally screened cyclic azobenzene-peptide sequences by computing dimer binding free energies for azobenzene-peptide sequences using well-tempered metadynamics . The peptide portion is modeled using the CHARMM 36 force field. Modeling the azobenzene linker required the development of a new force field. We use the CHARMM general force field  to fit parameters for the ground state trans azobenzene linker and the exited state cis azobenzene linker. Separate simulations for the dimer binding free energy with trans and cis azobenzene are performed. Peptide sequences of varying length, side chain size, and side chain hydrophobicity are screened to find dimers that are stable when the azobenzene linker is in the trans configuration, and unstable with the azobenzene linker in the cis configuration.
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