This project continues our computational investigations into the structural dynamics of gas-phase proteins, aimed at providing a mechanistic understanding of structural changes during native mass spectrometry (MS). Aim 1: Elucidating high-frequency dynamics under collisional activation. Building upon NAISS grant 2024/22-641, we simulate protein complexes across a range of temperatures to model structural transitions induced by collisional activation in ion-mobility MS. Initial simulations revealed an unexpected, high-frequency (GHz-scale) conformational oscillation at specific temperatures. Building on this, we have recently identified other proteins of similar shape which demonstrate similar behavior. We now seek to extend these simulations across multiple proteins, thermal conditions, and charge distributions, to map the mechanistic triggers driving this high-frequency motion for a dedicated follow-up publication. Aim 2: Exploring structural determinants for gas-phase induced structural changes. Working alongside researchers who perform electrospray-ion beam deposition experiments, where native MS is coupled to cryo-EM, we aim to define determinants for which regions of a protein are more susceptible to structural changes when exposed to vacuum. These experiments provide a unique benchmark for this kind of structural changes. We aim to generate gas-phase simulations of proteins and explore different analyses, to see if we can make predictions based on a crystal structure alone. Such insight could provide an efficient route to making structural predictions without first needing to perform computationally demanding MD simulations. The planned first line of action is to use an elastic network approach for predicting compliance properties (Ref 1). Together, these allocations will directly resolve a high-impact manuscript review and expand our understanding of gas-phase biomolecular dynamics. Main supervisor: Erik Marklund, Uppsala University References Scaramozzino et al. (2020), https://doi.org/10.1002/prot.25968