Ville R. I. Kaila
Technische Universität München (Germany)
Local Project ID:
HPC Platform used:
SuperMUC of LRZ
Respiratory complex I is the largest and most intricate enzyme of the respiratory chain and responsible for converting energy from the reduction of quinone into an electrochemical proton gradient. The aim of the project is to identify key steps in the catalytic process during enzyme turnover, and to understand the mechanism of the long-range electrostatic coupling between sites located up to 200 Å apart. Large-scale Molecular Dynamics simulations of the entire enzyme enabled the exploration of different aspects of its function. These results provide both information on the redox coupling in complex I and how natural enzymes couple distal sites by propagation of electrostatic interactions.
Conversion of foodstuff into energy is essential for all living systems. In eukaryotes, this process takes place in the mitochondria by enzymes of the respiratory chain. Figure 1 shows the largest of those enzymes, complex I or NADH:ubiquinone oxidoreductase, which initiates the cell respiration process in many aerobic organisms. The energy conversion by these respiratory enzymes is achieved by pumping protons across a biological membrane. This creates a potential difference across the membrane, similar as in a battery, that is used in subsequent steps to create new molecules that thermodynamically drive other biological processes.
Since energy is required to move protons across the membrane, the enzymes of the respiratory chain use a series of exergonic chemical reactions and couple them to the proton translocation.
Complex I is the first enzyme of the respiratory chain and it employs the energy from the electron transfer (eT) process from NADH to the quinone (Q) to pump four protons (H+) across the membrane. Membrane-embedded subunits are responsible for the proton translocation (pT) process, but the mechanism is far from being understood. Elucidation of this mechanism is, however, fundamental for understanding the molecular principles that nature uses to convert energy. Moreover, understanding the function of complex I has also important biomedical implications, as many mutations in this enzyme are linked to human mitochondrial disorders. This research project focused on how the movement of electrons from NADH to the Q site leads to formation of quinol (QH2), and how this chemical process triggers proton pumping across the membrane (see Fig. 1).
Results and Methods
With our simulations performed at the HPC Supermuc, we elucidated several unclear mechanistic aspects of complex I that are essential for the understanding key steps involved in activation of the pumping machinery.
Complex I uses quinone (Q) as a substrate, which reacts to quinol (QH2) in a long, ca. 30-40 Å, protein cavity. We identified that the Q molecule can bind in both stacked and hydrogen-bonded binding modes with nearby residues, which in turn modulate the electron transfer rate (2). We also observed that while the first electron transfer step is not coupled to proton transfer, whereas the second electron transfer steps leads to transfer of two protons from nearby residues (Fig. 2).
By modeling the Q molecule in the protein cavity, we found possible molecular reasons why complex I has a preference for long-tailed quinone substrates. These simulations also highlighted important structural regions, which are essential for protein function (3). To this end, our simulations showed that complex I is likely to employ a series of charged amino acids to transmit the “signal” up to 200 Å from the Q reaction site to achieve proton pumping. We observed putative pathways necessary to transfer protons across the membrane, and showed that these form at symmetry-related positions in the membrane domain of complex I (4).
The simulations also allowed us to compare the simple bacterial and highly complex mammalian enzyme motions, and connect them to recently resolved cryo-EM structures. Interestingly, the simulations showed that the motions in the two enzyme "versions" are similar, but not identical, and that the mammalian enzyme is likely to dynamically sample the so-called active and deactive forms of complex I. These findings more generally show how low-frequency motions in enzymes might be linked to the enzyme functions (5).
To elucidate the proton pumping mechanism, we employed long time-scale classical molecular dynamic simulations. The microsecond-timescale simulations were necessary to observe channel opening. The systems, comprising ~1 million atoms, were simulated with NAMD2, a highly parallelized code scaling up to 512 nodes (8192 processors). The entire project used 32 million CPU-hours. A total of ~10 TB of data was generated and stored in the project directories, and was then used for analysis.
References and Links
2. Gamiz-Hernandez AP, Jussupow A, Johansson MP, Kaila VRI (2017) Terminal Electron–Proton Transfer Dynamics in the Quinone Reduction of Respiratory Complex I. J Am Chem Soc 139:16282-16286.
3. Fedor JG, Jones AJY, Di Luca A, Kaila VRI, Hirst J (2017) Correlating kinetic and structural data on ubiquinone binding and reduction by respiratory complex I. Proc Natl Acad Sci 114:12737-12742.
4. Di Luca A, Gamiz-Hernandez AP, Kaila VRI (2017) Symmetry-related Proton Transfer Pathways in Respiratory Complex I. Proc Natl Acad Sci 114:E6314-E6321.
5. Di Luca A, Kaila VRI (2018) Global collective motions in the mammalian and bacterial respiratory complex I. Biochim Biophys Acta - Bioenergetics 1859:326-332.
Ana P. Gamiz-Hernandez, Ville R. I. Kaila (PI), Andrea Di Luca, Shreyas Supekar
Prof. Dr. Ville R. I. Kaila
Department of Chemistry
Technical University of Munich (TUM)
Lichtenbergstr. 4, D-85747 Garching (Germany)
e-mail: ville.kaila [@] ch.tum.de
NOTE: This report was first published in the book "High Performance Computing in Science and Engineering – Garching/Munich 2018".
LRZ project ID: pr48de