| 1. |
- Kim, Hyunho, 1993-, et al.
(författare)
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Quinone Catalysis Modulates Proton Transfer Reactions in the Membrane Domain of Respiratory Complex I
- 2023
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Ingår i: Journal of the American Chemical Society. - 0002-7863 .- 1520-5126. ; 145:31, s. 17075-17086
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Tidskriftsartikel (refereegranskat)abstract
- Complex I is a redox-driven proton pump that drives electron transport chains and powers oxidative phosphorylation across all domains of life. Yet, despite recently resolved structures from multiple organisms, it still remains unclear how the redox reactions in Complex I trigger proton pumping up to 200 Å away from the active site. Here, we show that the proton-coupled electron transfer reactions during quinone reduction drive long-range conformational changes of conserved loops and trans-membrane (TM) helices in the membrane domain of Complex I from Yarrowia lipolytica. We find that the conformational switching triggers a π → α transition in a TM helix (TM3ND6) and establishes a proton pathway between the quinone chamber and the antiporter-like subunits, responsible for proton pumping. Our large-scale (>20 μs) atomistic molecular dynamics (MD) simulations in combination with quantum/classical (QM/MM) free energy calculations show that the helix transition controls the barrier for proton transfer reactions by wetting transitions and electrostatic effects. The conformational switching is enabled by re-arrangements of ion pairs that propagate from the quinone binding site to the membrane domain via an extended network of conserved residues. We find that these redox-driven changes create a conserved coupling network within the Complex I superfamily, with point mutations leading to drastic activity changes and mitochondrial disorders. On a general level, our findings illustrate how catalysis controls large-scale protein conformational changes and enables ion transport across biological membranes.
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| 2. |
- Lebrette, Hugo, 1986-, et al.
(författare)
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Structure of a ribonucleotide reductase R2 protein radical
- 2023
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 382:6666, s. 109-113
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Tidskriftsartikel (refereegranskat)abstract
- Aerobic ribonucleotide reductases (RNRs) initiate synthesis of DNA building blocks by generating a free radical within the R2 subunit; the radical is subsequently shuttled to the catalytic R1 subunit through proton-coupled electron transfer (PCET). We present a high-resolution room temperature structure of the class Ie R2 protein radical captured by x-ray free electron laser serial femtosecond crystallography. The structure reveals conformational reorganization to shield the radical and connect it to the translocation path, with structural changes propagating to the surface where the protein interacts with the catalytic R1 subunit. Restructuring of the hydrogen bond network, including a notably short O-O interaction of 2.41 angstroms, likely tunes and gates the radical during PCET. These structural results help explain radical handling and mobilization in RNR and have general implications for radical transfer in proteins.
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| 3. |
- Pöverlein, Maximilian C., 1997-, et al.
(författare)
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QM/MM Free Energy Calculations of Long-Range Biological Protonation Dynamics by Adaptive and Focused Sampling
- 2024
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Ingår i: Journal of Chemical Theory and Computation. - 1549-9618 .- 1549-9626. ; 20:13, s. 5751-5762
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Tidskriftsartikel (refereegranskat)abstract
- Water-mediated proton transfer reactions are central for catalytic processes in a wide range of biochemical systems, ranging from biological energy conversion to chemical transformations in the metabolism. Yet, the accurate computational treatment of such complex biochemical reactions is highly challenging and requires the application of multiscale methods, in particular hybrid quantum/classical (QM/MM) approaches combined with free energy simulations. Here, we combine the unique exploration power of new advanced sampling methods with density functional theory (DFT)-based QM/MM free energy methods for multiscale simulations of long-range protonation dynamics in biological systems. In this regard, we show that combining multiple walkers/well-tempered metadynamics with an extended system adaptive biasing force method (MWE) provides a powerful approach for exploration of water-mediated proton transfer reactions in complex biochemical systems. We compare and combine the MWE method also with QM/MM umbrella sampling and explore the sampling of the free energy landscape with both geometric (linear combination of proton transfer distances) and physical (center of excess charge) reaction coordinates and show how these affect the convergence of the potential of mean force (PMF) and the activation free energy. We find that the QM/MM-MWE method can efficiently explore both direct and water-mediated proton transfer pathways together with forward and reverse hole transfer mechanisms in the highly complex proton channel of respiratory Complex I, while the QM/MM-US approach shows a systematic convergence of selected long-range proton transfer pathways. In this regard, we show that the PMF along multiple proton transfer pathways is recovered by combining the strengths of both approaches in a QM/MM-MWE/focused US (FUS) scheme and reveals new mechanistic insight into the proton transfer principles of Complex I. Our findings provide a promising basis for the quantitative multiscale simulations of long-range proton transfer reactions in biological systems.
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| 4. |
- Pöverlein, Maximilian, 1997-
(författare)
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Unraveling Biological Energy Catalysis : Multi-Scale Simulations of Respiratory Complex I
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Cellular function is powered by mitochondria through an energy conversion process known as oxidative phosphorylation. Central to this process is respiratory complex I, an enzyme that couples NADH oxidation with ubiquinone reduction and the pumping of protons across the inner mitochondrial membrane. In this thesis, the mechanistic principles of complex I were investigated using multi-scale simulations, including atomistic molecular dynamics simulations and hybrid quantum/classical mechanics (QM/MM) calculations. We found that complex I drives quinone reduction and proton pumping through a network of buried charged residues. These residues couple protonation changes to conformational shifts, electrostatic interactions, and modulations of the hydration dynamics. Additionally, we expanded the applicability of QM/MM to long-range protonation dynamics by developing a novel sampling scheme. This scheme combines advanced sampling methods with a general reaction coordinate to provide a quantitative description of hydration dynamics and conformational changes during proton transfer reactions, which are indispensable for understanding the function of the respiratory enzymes. We further investigated the molecular details of how and why respiratory complexes cluster together to form supercomplexes. Our findings indicate that membrane proteins alter the membrane properties and introduce strain, which could drive the formation of these assemblies. The combined mechanistic findings of this thesis enhance our understanding of respiratory complex I and supercomplexes and their underlying proton transfer reactions, conformational changes, and enzymatic activity.
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| 5. |
- Riepl, Daniel, et al.
(författare)
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Molecular principles of proton-coupled quinone reduction in the membrane-bound superoxide oxidase
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Reactive oxygen species (ROS) are physiologically harmful radicals generated as biproducts of aerobic respiration. To detoxify ROS, most cells employ superoxide scavenging enzymes that disproportionate superoxide (O2•-) to oxygen (O2) and hydrogen peroxide (H2O2). However, the recently discovered membrane-bound superoxide oxidase (SOO) (Nature Chemical Biol 2018) is a minimal 4-helical bundle protein that catalyzes the direct oxidation of O2•- to O2 and drives quinone reduction by mechanistic principles that remain unknown. Here we combine multiscale hybrid quantum/classical (QM/MM) free energy calculations and microsecond molecular dynamics simulations with functional assays and site-directed mutagenesis experiments to probe the energetics and dynamics underlying the charge transfer reactions of the superoxide (O2•-)-driven quinone reduction. We identify a cluster of charged residues at the periplasmic side of the membrane that functions as a O2•- collecting antenna, which shuttles the electrons to the active site for quinone reduction. Based on multidimensional QM/MM string simulations, we suggest that a proton-coupled electron transfer (PCET) reaction from the active site heme b and nearby histidine residues (H87, H158) catalyzes the quinol (QH2) formation, followed by proton uptake from the cytoplasmic side of the membrane. The functional relevance of the identified residues is supported by site-directed mutagenesis and activity assays, with mutations leading to inhibition of the O2•--driven quinone reduction activity. We suggest that the coupled electron and proton transfer reactions build up a proton motive force that support the bacterial energy transduction machinery, with the PCET reactions providing unique design principles of a minimal oxidoreductase.
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| 6. |
- Schubert, Luiz, et al.
(författare)
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Proton Release Reactions in the Inward H+ Pump NsXeR
- 2023
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Ingår i: Journal of Physical Chemistry B. - 1520-6106 .- 1520-5207. ; 127:39, s. 8358-8369
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Tidskriftsartikel (refereegranskat)abstract
- Directional ion transport across biological membranes plays a central role in many cellular processes. Elucidating the molecular determinants for vectorial ion transport is key to understanding the functional mechanism of membrane-bound ion pumps. The extensive investigation of the light-driven proton pump bacteriorhodopsin from Halobacterium salinarum(HsBR) enabled a detailed description of outward proton transport. Although the structure of inward-directed proton pumping rhodopsins is very similar to HsBR, little is known about their protonation pathway, and hence, the molecular reasons for the vectoriality of proton translocation remain unclear. Here, we employ a combined experimental and theoretical approach to tracking protonation steps in the light-driven inward proton pump xenorhodopsin from Nanosalina sp. (NsXeR). Time-resolved infrared spectroscopy reveals the transient deprotonation of D220 concomitantly with deprotonation of the retinal Schiff base. Our molecular dynamics simulations support a proton release pathway from the retinal Schiff base via a hydrogen-bonded water wire leading to D220 that could provide a putative gating point for the proton release and with allosteric interactions to the retinal Schiff base. Our findings support the key role of D220 in mediating proton release to the cytoplasmic side and provide evidence that this residue is not the primary proton acceptor of the proton transiently released by the retinal Schiff base.
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