Multiscale Simulations on Biological Energy Catalysis
Title: Multiscale Simulations on Biological Energy Catalysis
SNIC Project: SNIC 2021/1-40
Project Type: SNIC Large Compute
Principal Investigator: Ville Kaila <>
Affiliation: Stockholms universitet
Duration: 2021-07-01 – 2022-07-01
Classification: 10602 10603 10407


The molecular basis of life is established by a complex membrane-bound protein machinery that efficiently captures and converts chemical and light energy and transduces this into other energy forms. This continued SNIC Large Computing project aims to elucidate molecular principles of proteins that catalyze chemical or light-driven energy transduction in cell respiration and photosynthesis. We tackle these principles by integrating state-of-the-art computational multi-scale simulations that range from classical atomistic and coarse-grained simulations to hybrid quantum/classical (QM/MM) approaches (DFT and correlated ab initio) to obtain a detailed understanding of the structure, energetics, and dynamics of these proteins on a broad range of timescales and spatial resolutions. The molecular simulations are further integrated with and validated by cryo-electron microscopy (cryoEM) and biophysical experiments. The project aims to link the molecular structure and dynamics with the biological function and, based on these, derive a molecular understanding on how enzymes generate electrochemical energy gradients across biological membranes. Our project focusses on 1) mechanisms of long-range proton-electron transport in the complex I superfamily; 2) the functional role of membrane-bound supercomplexes; 3) the functional dynamics of light-driven energy conversion in photosystem II, and 4) energy transduction and catalytic principles of molecular chaperones. This computational consortium involves around 20 researchers (one professor, two staff scientists, five post-doctoral fellows, 8 PhD students, and 2 master students) supported by the ERC, VR, Cancerfonden, and the KAW foundation.