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Theoretical studies of the dissociation of charged protein complexes in the gas phase Wanasundara, Surajith Nalantha

Abstract

Understanding the dissociation mechanism of multimeric protein complex ions is important for interpreting gas-phase experiments. The aim of this thesis work was to study the dissociation of charged protein complexes. To pursue this, a number of model and molecular dynamics calculations were conducted using the cytochrome c′ dimer. The energetics of differing charge states, partitionings, and configurations were examined in both the low and high charge regimes. It is shown that one must always consider distributions of charge configurations, once protein relaxation effects are taken into account, and that no single configuration dominates. These results also indicate that in the high charge limit, the dissociation is governed by electrostatic repulsion from the net charges. This causes two main trends: i) charges will move so as to approximately maintain constant surface charge density, and ii) the lowest barrier to dissociation is the one that produces fragment ions with equal charges. Free energies are also calculated for the protonated dimer ion as a function of the center of mass distance between the monomers. In addition, the change of intermolecular properties such as intermolecular hydrogen bonds and the smallest separation of intermolecular residues were analyzed. It is found that monomer unfolding competes with complex dissociation, and that the relative importance of these two factors depends upon the charge partitioning in the complex. Symmetric charge partitionings preferentially suppress the dissociation barrier relative to unfolding, and complexes tend to dissociate promptly with little structural change occurring in the monomers. Alternatively, asymmetric charge partitionings preferentially lower the barrier for monomer unfolding relative to the dissociation barrier. In this case, the monomer with the higher charge unfolds before the complex dissociates. For large multimeric proteins, the unfolding and subsequent charging of a single monomer is a favorable process, cooperatively lowering both the unfolding and dissociation barriers at the same time. For the homodimer considered here, this pathway has a large free energy barrier. Overall, the work presented herein demonstrates that molecular dynamics simulation can be useful for understanding the dissociation mechanism of protein complexes.

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