Developing CHARMM Force Field Parameters for the Radical States of Tryptophan and Tyrosine

Amino acid radicals play fundamental roles in many physiological processes ranging from DNA repair and synthesis to respiration and magnetoreception. In particular, tryptophan and tyrosine in their radical states often serve as key intermediates in electron transfer processes. Importantly, the radical states can be long-lived enough to trigger conformational changes in proteins that can be important for biomolecular signaling. Molecular dynamics (MD) simulations provide a perfect means to study the effects of tyrosine and tryptophan oxidation on the conformational dynamics of proteins and to reveal molecular mechanisms of their biological roles. However, a reliable application of MD simulations requires a comprehensive set of molecular mechanics parameters to describe amino acid residues in the radical states. Here, we present a complete set of molecular mechanics parameters for the radical states of tyrosine and tryptophan residues, developed within the framework of the CHARMM force field. Optimized to target a large body of quantum mechanical data, the parameters provide a robust description of the intramolecular energetics, interactions with water, and electrostatic properties of tyrosine and tryptophan in their radical states. The parameters were tested and validated through simulations of model protein systems including the α3W protein, a β-hairpin maquette, and an avian cryptochrome. The simulation results demonstrate the effects of tyrosine and tryptophan oxidation on side-chain dynamics, conformational changes, and general biophysical properties of proteins. We expect that the presented set of force field parameters would be useful for the computational studies of various biological processes that involve oxidation of the tyrosine and tryptophan residues.