LIFE SCIENCES
Regulation of Proton Transfer in Respiratory Complex I
Principal Investigator:
Ville R. I. Kaila
Affiliation:
Department of Chemistry, Technical University of Munich (Germany)
Local Project ID:
pr27xu
HPC Platform used:
SuperMUC and SuperMUC-NG of LRZ
Date published:
Introduction
All organisms need energy to power their essential processes like movement, growth, and reproduction. In all eukaryotes and several bacteria, aerobic respiration forms the main energy production system during which electrons, protons, and oxygen are combined to form water. The energy transduced is converted into an electrochemical proton gradient (or proton motif force, pmf) across a biological membrane that further drives the synthesis of adenosine triphosphate (ATP), the principal energy currency of cells.
The respiratory complex I is the entry point for electrons into many aerobic respiratory chains. Complex I takes up electrons from nicotinamide adenine dinucleotide (NADH) and transfers them to ubiquinone (Q10). The free energy is used to build up a pmf by pumping protons (H+) across a membrane. These processes are separated by large distances of ca. 200 Å (Figure 1), but the coupling principles still remain poorly understood. Single-point mutations in complex I have been linked to several human mitochondrial diseases, that’s why the system is also of great biomedical relevance. In this supercomputing project, we addressed how proton pumping in complex I is activated and regulated, and we designed specific mutations that disturb the function of this complex cellular machinery.
Figure 1: Complex I catalyzes electron transfer from NADH to quinone in its hydrophilic domain (in white) and pumps protons across the antiporter-like subunits of the membrane domain (colored). Nqo13 is an antiporter-like subunit, connected to its neighboring subunits by charged interfaces (blue squares), which can form contacts between the subunits. The proton transfer within the subunit is indicated by an arrow. © TUM
Results and Methods
In this project, we identified several key molecular elements that control proton pumping in complex I. We had previously suggested that charged interfaces between the proton-pumping modules could function as on/off-switches for proton transfer within each subunit. In this project, we calculated free energy profiles for inducing conformational changes in these ion-pairs between closed (“switch off”) and open (“switch on”) states, and how this transition depends on the hydration levels of the protein. We found that the open state is favored at high hydration levels, but kinetically inaccessible in the dry state (Figure 2).
Figure 2: The hydration level within a proton pumping subunit regulates the dynamics of ion-pair opening. In the “open” state (high R), a charged contact is formed with a neighboring subunit, but not in the “closed” state. The ion-pair opening affects in turn the proton transfer reaction barriers (see Figure 3). © TUM
We also probed how the proton transfer reactions are modulated by the proposed ion-pair switching process and the hydration levels. To this end, we used snapshots obtained from our large-scale MD simulations for computing QM/MM free energies for the proton transfer process. Our results suggest that the proton transfer is feasible in the open ion-pair state, but not in the closed ion-pair state (Figure 3).
Figure 3: Hybrid QM/MM calculations, where a chemically reactive region described at the QM (DFT/B3LYP) level is embedded in a classical environment, reveal that proton transfer is thermodynamically and kinetically favored in the open conformation (in blue), but unfavored in the closed state (in red). © TUM
Interestingly, each proton transfer reaction is coupled by the charged interface to the next subunit that, in turn, provides a key step in the signaling propagation across the membrane domain of complex I. To test the coupling principles further, we mutated identified key residues along the proton transfer wires both in silico and in vitro biochemical experiments. Our simulations suggested that the introduced substitutions indeed destabilized the proton transfer reaction, and experimentally lead to a lowered proton pumping and electron transfer activity. In summary, we demonstrated how hydration, conformational switching in conserved ion-pairs, and proton transfer reactions themselves provide key elements in proton pumping of respiratory complex I.
In this project, we used vast resources provided by SuperMUC Phase 2 and later on by SuperMUC-NG to perform the large-scale classical molecular dynamics simulations of respiratory complex I embedded in a lipid membrane/water/ion environment. We employed the NAMD2 molecular dynamics-engine for our simulations with about one million atoms on microsecond timescales. Excellent scaling enabled us to utilize up to 1,536 cores per simulation and to generate about 10 TB of data concentrated in tens of large coordinate trajectories. In subsequent free energy calculations performed using replica exchange umbrella sampling, we performed 20 parallel simulations using up to 11,520 cores. In total, 24 million CPU hours were dedicated to this project.
On-going Research / Outlook
The resources provided by this SuperMUC project were key to generate the data used in deducing the mechanism presented above, and resulted in one JACS-publications [2]. During this project, our simulations migrated from SuperMUC Phase 2 to SuperMUC-NG seamlessly. We are looking forward to broadening our understanding of biological energy conversion in follow-up projects on the SuperMUC-NG infrastructure.
References and Links
[2] Mühlbauer, M. E. , Saura P, Nuber F, Di Luca A, Friedrich T, Kaila VRI (2020) Water-Gated Proton Transfer Dynamics in Respiratory Complex I. J. Am. Chem. Soc. 142, 13718–13728.
Research Team
Ville R. I. Kaila (PI), Andrea Di Luca, Max E. Mühlbauer, Daniel Riepl, Michael Röpke, Patricia Saura.
All: Department of Chemistry, Technical University of Munich (TUM)
Scientific Contact
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
Local project ID: pr27xu
December 2020