q‑Canonical Monte Carlo Sampling for Modeling the Linkage between Charge Regulation and Conformational Equilibria of Peptides

• Published in: The journal of physical chemistry. B 2019-08, Vol.123 (32), p.6952-6967
• Main Authors: Fossat, Martin J, Pappu, Rohit V
• Format: Article
• Language: English
• Subjects: Entropy; Humans; Intrinsically Disordered Proteins - chemistry; Molecular Dynamics Simulation; Monte Carlo Method; Peptide Fragments - chemistry; Protein Conformation; Protein Folding; Thermodynamics
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/acs.jpcb.9b05206

The overall charge content and the patterning of charged residues have a profound impact on the conformational ensembles adopted by intrinsically disordered proteins. These parameters can be altered by charge regulation, which refers to the effects of post-translational modifications, pH-dependent changes to charge, and conformational fluctuations that modify the pK a values of ionizable residues. Although atomistic simulations have played a prominent role in uncovering the major sequence-ensemble relationships of IDPs, most simulations assume fixed charge states for ionizable residues. This may lead to erroneous estimates for conformational equilibria if they are linked to charge regulation. Here, we report the development of a new method we term q-canonical Monte Carlo sampling for modeling the linkage between charge regulation and conformational equilibria. The method, which is designed to be interoperable with the ABSINTH implicit solvation model, operates as follows: For a protein sequence with n ionizable residues, we start with all 2 n charge microstates and use a criterion based on model compound pK a values to prune down to a subset of thermodynamically relevant charge microstates. This subset is then grouped into mesostates, where all microstates that belong to a mesostate have the same net charge. Conformational distributions, drawn from a canonical ensemble, are generated for each of the charge microstates that make up a mesostate using a method we designate as proton walk sampling. This method combines Metropolis Monte Carlo sampling in conformational space with an auxiliary Markov process that enables interconversions between charge microstates along a mesostate. Proton walk sampling helps identify the most likely charge microstate per mesostate. We then use thermodynamic integration aided by the multistate Bennett acceptance ratio method to estimate the free energies for converting between mesostates. These free energies are then combined with the per-microstate weights along each mesostate to estimate standard state free energies and pH-dependent free energies for all thermodynamically relevant charge microstates. The results provide quantitative estimates of the probabilities and preferred conformations associated with every thermodynamically accessible charge microstate. We showcase the application of q-canonical sampling using two model systems. The results establish the soundness of the method and the importance of charge regulation in