Title:	Simulations of collisional activation and protein assemblies
DNr:	NAISS 2025/23-416
Project Type:	NAISS Small Storage
Principal Investigator:	Louise Persson <louise.persson@kemi.uu.se>
Affiliation:	Uppsala universitet
Duration:	2025-08-01 – 2026-08-01
Classification:	10408
Keywords:

Abstract

Sub-project A) In the proposal NAISS 2025/22-918, I am requesting computing resources for conducting enhanced-sampling molecular dynamics simulations to study the assembly mechanisms of a large protein complex. Part of the storage project I am requesting here is for storing files related to this compute project. Sub-project B) We have used molecular dynamics simulations to study how two protein complexes behave at different temperatures in the gas phase. This can be related to experiments that use collisional activation in tandem with native mass spectrometry. The technique has gained popularity in protein research in the last decade, but data interpretation remains challenging due to poor knowledge of how protein structures change upon activation. Our molecular dynamics simulations give insights into this on the atomistic level. While the heavy computations are essentially finished for this study, I still need to use Tetralith for data analysis, where I have access to certain GROMACS installations. As such, I would like to use part of this storage project for the simulation files.