Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons

Abstract

Electrospray ionization mass spectrometry (ESI-MS) has become an indispensable technique for examining noncovalent protein complexes. Collision-induced dissociation (CID) of these multiply protonated gaseous ions usually culminates in ejection of a single subunit with a disproportionately large amount of charge. Experiments suggest that this process involves subunit unfolding prior to separation from the residual complex, as well as H(+) migration onto the unravelling chain. Molecular dynamics (MD) simulations are a promising avenue for gaining detailed insights into these CID events. Unfortunately, typical MD algorithms do not allow for mobile protons. Here we address this limitation by implementing a strategy that combines atomistic force fields (such as OPLS/AA and CHARMM36) with a proton hopping algorithm, focusing on the tetrameric complexes transthyretin and streptavidin. Protons are redistributed over all acidic and basic sites in 20 ps intervals, subject to an energy function that reflects electrostatic interactions and proton affinities. Our simulations predict that nativelike conformers at the onset of collisional heating contain multiple salt bridges. Collisional heating initially causes subtle structural changes that lead to a gradual decline of these zwitterionic patterns. Many of the MD runs show gradual unfolding of a single subunit in conjunction with H(+) migration, culminating in subunit separation from the complex. However, there are also instances where two or more chains start to unfold simultaneously, giving rise to charge competition. The scission point where the "winning" subunit separates from the complex can be attained for different degrees of unfolding, giving rise to product ions in various charge states. The simulated product ion distributions are in close agreement with experimental CID data. Proton enrichment in the departing subunit is driven by charge-charge repulsion, but the combination of salt bridge depletion, charge migration, and proton affinity causes surprising compensation effects among the various energy terms. It appears that this work provides the most detailed account to date of the mechanism whereby noncovalent protein complexes disassemble during CID.

A Molecular Mechanism for Nonphotochemical Quenching in Cyanobacteria

“…Furthermore, a previous publication suggests the N-terminal arm on OCP interferes with the interaction with FRP 49 . Our cross-linking results suggest the N-terminal arm adjoins FRP, reinforcing this view.…”

Collidoscope: An Improved Tool for Computing Collisional Cross-Sections with the Trajectory Method

“…Extending the charge placement algorithms of Williams [46, 47], Grandori [48], and Konermann [49], Collidoscope uses a Metropolis-Hastings-like [50, 51] charge placement algorithm for protonated protein ions based on the ion’s input atomic coordinates, a user-defined charge state, the calculated point-charge electrostatic repulsion energy of a given charge configuration, and the total intrinsic proton affinity of the ion. The N-terminal amine group as well as each residue is considered to be a possible charge site throughout the charge placement computation, with one possible charge per residue.…”

“…At this point, the optimization is considered to have converged, and the charge configuration with the highest PA app among all the iterations is used for CCS calculations. Intrinsic proton affinities used in Collidoscope are identical to those used by Konermann and co-workers [49], and a relative permittivity of 2.5 is used in calculating electrostatic repulsion for all proteins other than GroEL, for which a value of 4 is used. For the proteins investigated here, the main effect of the charge placement algorithm is to spread the charges out among basic sites near the surface of the ion.…”

A Mass‐Spectrometry‐Based Modelling Workflow for Accurate Prediction of IgG Antibody Conformations in the Gas Phase

“…[30] The response of folded proteins entering the gas phase through ESI is most commonly described through the charged residue model (CRM). [36][37][38][39] Whilst others have explored simulating such collapsing structures, [37] these call for computationally complicated methods such as "trajectory stitching" [40] or including mobile proton algorithms, [41,42] which may be impractical for large molecules.H ere,w e have developed an integrative IM-MS-based strategy that enables the prediction of the structure and dynamics of IgG molecules in the gas phase,i ncluding,f or the first time, capturing and simulating the dynamics of human IgG3 (Figure 1a-c). While the behaviour of ag lobular protein transferring into the gas phase of am ass spectrometer can be rationalised under the CRM framework, here we pose the following question:d o these same rules apply to nonglobular and flexible proteins?…”