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Functional Proton-Electron Transfer Elements in Biological Energy Conversion

Periodic Reporting for period 3 - bioPCET (Functional Proton-Electron Transfer Elements in Biological Energy Conversion)

Reporting period: 2019-08-01 to 2021-01-31

The ERC project, bioPCET, focuses on understanding molecular principles of how biological systems capture and covert energy. These processes are catalyzed by coupled transfer of protons and electrons (PCET), i.e. two elementary particles, but their fundamental mechanistic principles are still not well understood. The objective of our project is to obtain a molecular-level understanding of how functional elements in proteins power biological energy conversion. This we aim to achieve by studying the catalytic machinery of one of the largest and most intricate enzymes in mitochondria and bacteria, the respiratory complex I. As a main target, we aim to control the functional modules of complex I that we probe by molecular simulation techniques, de novo-protein design, and biophysical studies. The project aims to establish a fundamental understanding of enzyme function that is important for elucidating the molecular basis of life. The information gained can guide the design of novel man-made enzymes for sustainable energy technology, whereas our research on cell respiration is significant for understanding development of disease related to energy metabolism in the cell.
This project is divided in five workpackages and a methodological subproject that focuses on elucidating how different functional modules in complex I establish a 300 Å charge transport process. The initial phase of the project resulted in 11 peer-reviewed publications, one manuscript that is currently in review, and 5 manuscripts that are currently in preparation (see Project Web Page). Many of the publications are published in high-impact journal (JACS, PNAS, Science Adv, Nature Comms) supporting that our project team has secured a high level of research. The work has been presented in multiple leading conferences in the field and communicated in review articles to reach both experts and non-expert audiences. A brief summary of each workpackage (WP) is given below.

In WP1, we have studied functional elements that are used for conversion of chemical energy to redox energy. We have studied how electrons enter the complex I with the redox cofactor NADH, and how this module further bifurcates the electrons into a chain of FeS redox-cofactors. We identified protein residues that are responsible for the catalytic activity and how certain point mutations may enhance the production of reactive oxygen species (ROS), linked to the development of mitochondrial disease. In WP2 and WP3, we have studied functional elements that mediate long-range electron transfer and establish the catalytic core of complex I. We have identified electronic and structural changes linked to the electron transfer process as well as its energetics along the FeS chain. Moreover, we have established the function of key elements that enables complex I to reduce the quinone substrates, and conformational changes linked to this process. In WP4, we have studied elements mediating redox energy for proton pumping, and identified a novel substrate binding-site that may activate the proton pumping activity of the enzyme. In WP5, we have studied how different protein modules establishing the long-range proton-pumping machinery, and how the biological membrane surroundings modulate the biological activity. During the project, we have developed computational simulations methods, linked with protein design and biophysical experiments, that has enabled us to probe the structure and function of the catalytic machinery in complex I on a broad range of time-scales and spatial resolutions.
To probe the connection between protein structure, function, and dynamics, we have developed and applied computational multi-scale methodology that ranges from quantum chemical techniques to large-scale classical approaches that has enabled us to probe the structure, energetics, and dynamics of complex biochemical processes on fs-ms (10-15-10-3 s) timescales for systems comprising up to millions of atoms. Such broad range of methods are normally not applicable for large enzyme complexes. The computational methods have been further combined with protein design and biophysical experiments that have allowed us to validate some of the predicted mechanistic models. During the second half of the project, we aim to further enhance the complementarity between computational-, design-, and biophysical experimental parts.