pH-dependent response of coiled coils: a coarse-grained molecular simulation study

In a recent work we proposed a coarse-grained methodology for studying the response of peptides when simulated at different values of pH; in this work we extend the methodology to analyse the pH-dependent behaviour of coiled coils. This protein structure presents a remarkable chain stiffness and is formed by two or more long helical peptides that interact like the strands of a rope. Chain length and rigidity are the key aspects needed to extend previous peptide interaction potentials to this particular case; however, the original model, valid for short and medium lengths, is naturally recovered when the length of the chain is reduced. We apply the model and discuss results for two cases: (a) the folding/unfolding transition of a generic coiled coil as a function of pH; (b) behaviour of a specific sequence as a function of acidity conditions. In the latter case results are compared with experimental data from the literature in order to comment about the consistency of our approach.