Illuminating Dynamics: Integrating Computational and Experimental Insights into Photoreceptor Proteins through Molecular Dynamics Simulations

NAISS 2023/5-555


NAISS Medium Compute

Principal Investigator:

Sebastian Westenhoff


Uppsala universitet

Start Date:


End Date:


Primary Classification:

10601: Structural Biology

Secondary Classification:

10602: Biochemistry and Molecular Biology



This is a resubmission of our previous proposal (NAISS 2023/5-488), which has been declined due to lack of experience with AMBER software on NAISS various allocation. To address this we note that we have already successfully used the AMBER software with GPU implementation during a NAISS small allocation on Tetralith (NAISS 2023/22-547). Using the AMBER pmemd.cuda, we ran heavy-atom restrained molecular dynamics simulations, allowing us to elucidate water rearrangements around a chromophore region upon photoactivation (Manuscript in progress). Molecular Dynamics (MD) simulations serve as powerful complements to experimental structural methods, aiding in the elucidation and validation of protein structures and dynamics. This project is dedicated to the detailed analysis of photoreceptor proteins, choses for their pivotal role in capturing the earliest events of photochemical transformation, utilizing cutting-edge time-resolved structural methods. Our group already demonstrates a robust track record in unravelling the complexities of various photochemical processes, as evidenced by publications such as Takala et al. (Nature, 2014) and Claesson et al. (eLife 2020). Building on our prior success, highlighted in the publication by Björling et al. (JCTC, 2015), we aim to further integrate classical MD simulations and enhanced sampling techniques to explore the structural dynamics of photoreceptor proteins. This project adopts an integrated approach, combining computational and experimental methodologies. Cryo-EM and time-resolved x-ray crystallographic scattering have been or will be employed to resolve the structures of diverse photoreceptor proteins, providing a foundation for subsequent MD simulations. Our research, at the intersection of computational and experimental techniques, positions us at the forefront of unravelling the intricate dynamics of photoreceptor proteins and their role in photochemical transformations. The significance of our work extends beyond fundamental scientific inquiry. By deciphering the intricate dynamics of photoreceptor proteins, we pave the way for advancements in biotechnology, drug discovery, and understand the molecular basis of various diseases. This integrated research approach not only contributes to our understanding of fundamental biological processes but also holds the potential to drive innovations with broad applications in both scientific and medical realms.