Free Energy Barrier Estimation for the Dissociation of Charged Protein Complexes in the Gas Phase

Abstract

Free energies are calculated for the protonated cytochrome c' dimer ion in the gas phase as a function of the center of mass distance between the monomers. A number of different charge partitionings are examined as well as the behavior of the neutral complex. 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 changes 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 the homodimer considered here, this pathway has a large free energy barrier. The results can be rationalized using schematic two-dimensional free energy surfaces. Additionally, for large multimeric complexes, it is argued that 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.

An Electrostatic Charge Partitioning Model for the Dissociation of Protein Complexes in the Gas Phase

“…Features that have been omitted include the occurrence of unevenly spaced protonation sites, differences in the intrinsic gas phase basicities of individual residues, and thermal excitation effects that might induce some charge asymmetry even in the absence of unfolding. In the future, it will be interesting to extend electrostatic approaches of the type used here to more realistic protein descriptions [44,46,56], possibly even to full-scale molecular dynamics simulations [75]. It is hoped that those future endeavors will further advance the general understanding of gaseous biomolecular ions.…”

“…A conceptual framework has evolved to rationalize the occurrence of asymmetric charge partitioning [3,30,31,33,37,45,46]. This framework is based on the view that electrosprayed multi-protein assemblies initially retain a compact conformation, where excess protons are distributed more or less uniformly on the surface of the complex.…”

“…For example, some theoretical studies predict that chargesymmetric behavior should generally be favored on the basis of kinetic arguments [46,56]. Another aspect that has received little attention is the fact that CID product ions typically display a wide distribution of charge states, despite the use of precursor ions with a precisely defined number of excess protons.…”

“…The last feature is particularly interesting, as it suggests the existence of competing fragmentation pathways. Some previous computational investigations treated charge migration by using manual intervention to move protons among amino acid side chains [44,46,56]. Strategies of that type can make it difficult to adequately account for conformationally driven charge migration.…”

“…We aim to account for product ion abundance distributions in a quantitative way, thereby providing insights into the protein structural changes occurring during collisional activation. This work incorporates ideas put forward in previous studies, particularly Klassen's protein structure model [44], Thachuk's Coulomb repulsion model [46,56], the two-sphere model of Ryce and Wyman [53], and a droplet fission model developed by our group [57].…”