Biology subjects

Zickermann, V.

Publications and source records attributed to Zickermann, V..

7 recordsLinked to original sources

bioRxiv2026

Coenzyme A is bound to tafazzin - a paradigm change for transacylation

Cardiolipin (CL) is the signature phospholipid of mitochondria. In an obligatory remodeling process, the mitochondrial transacylase tafazzin exchanges its acyl chains to create the highly unsaturated, mature form of CL. Tafazzin dysfunction causes Barth syndrome, a severe multisystem disorder. We determined the structure of tafazzin at a resolution of 2.2 [A] using cryo-electron microscopy (cryo-EM). Until now, the tafazzin reaction has been thought to be independent of coenzyme A (CoA). However, our structure clearly shows an acyl-CoA molecule bound to tafazzin. To decipher how substrates bind to the active site, we combine cryo-EM with structure predictions and molecular dynamics simulations, giving us detailed insights into a transacylation mechanism mediated by CoA. By providing molecular explanations of tafazzin dysfunction caused by pathogenic mutations, we gain a molecular understanding of Barth syndrome.

biochemistry↗

bioRxiv2026

Molecular and Energetic Basis of Histidine Switch Dynamics in Respiratory Complex I

The respiratory complex I in mitochondria and bacteria drives the two-electron reduction of quinone to pump protons across the membrane. The molecular basis of this catalytic reaction remains enigmatic despite significant progress in structural characterization of the complex. A highly conserved histidine residue in the distal antiporter-like subunit of its membrane domain has been shown to undergo conformational changes in molecular simulations and cryo-EM structures. However, the function of histidine switch dynamics, and energetics of its conformational transitions remain unclear. Here, by applying enhanced sampling simulations, we evaluate the energetics of the histidine switch dynamics and demonstrate that it is coupled to the charge state of lysine residues ca. 10 [A] apart, which cause hydrogen bond restructuring and stabilize histidine in specific conformations. Hybrid QM/MM metadynamics simulations show that the histidine participates in gated proton transfer and may function as a proton confurcation device in complex I and related proteins. Importance of workProton pumping by the mitochondrial respiratory chain enzymes needs to be highly directional so that the ATP production occurs as efficiently as possible during high energy demands. With the protons being hard to detect by most methods of structural biology, computer simulation approaches as applied in this work offer critical information on how molecular gates within respiratory complexes can function and help elucidate the challenging questions in the field of mitochondrial bioenergetics.

biophysics↗

bioRxiv2024

Conformational dynamics of a histidine molecular switch in a cation/proton antiporter

Multisubunit Mrp type sodium proton (Na+/H+) antiporters are indispensable for the growth of alkali and salt tolerant bacteria and archaea under challenging conditions. Several subunits of the membrane protein complex are closely related to the membrane bound subunits of mitochondrial respiratory complex I, a key enzyme in aerobic energy metabolism. The molecular mechanism of ion translocation by complex I and Mrp antiporters has remained largely unknown and is the subject of intense debate. Here, we combine the power of site-directed mutagenesis and large-scale atomistic molecular dynamics simulations to elucidate the molecular basis of proton-conducting function of the MrpA subunit of the antiporter. We show that point mutations directly affect the transport activity by perturbing the conformational dynamics of a key histidine residue that acts as a molecular switch. Importantly, we find that charge and protonation state variations drive hydrogen bonding rearrangements and hydration changes, which result in coupled sidechain and backbone level conformational changes of the histidine and neighboring residues. We propose the histidine switch as a unique functional element central to proton transport function in Mrp antiporters and respiratory complex I. Significance statementEnergy conversion in biology is catalyzed by several membrane-bound enzyme complexes that drive transmembrane charge translocation. A key question is how these charges are moved against a membrane gradient in an efficient manner, i.e., what kind of gating and fail-safe mechanisms are employed by the proteins to ensure charge transfer directionality. By studying cation/proton Mrp antiporter, which shares homology with the mitochondrial complex I, we describe a conserved histidine residue acting as a molecular switch crucial for gating transfer of protons. Our work emphasizes the functional significance of conserved and conformationally mobile motifs in proteins. The results will benefit the mechanistic understanding of naturally existing proteins and design of artificial enzymes.

biophysics↗

bioRxiv2023

Role of protonation states in stability of molecular dynamics simulations of high-resolution membrane protein structures

Classical molecular dynamics (MD) simulations provide unmatched spatial and time resolution of protein structure and function. However, accuracy of MD simulations often depends on the quality of force field parameters and the time scale of sampling. Another limitation of conventional MD simulations is that the protonation states of titratable amino acid residues remain fixed during simulations, even though protonation state changes coupled to conformational dynamics are central to protein function. Due to the uncertainty in selecting protonation states, classical MD simulations are sometimes performed with all amino acids modeled in their standard charged states at pH 7. Here we performed and analyzed classical MD simulations on high-resolution cryo-EM structures of two membrane proteins that transfer protons by catalyzing protonation/deprotonation reactions. In simulations performed with amino acids modeled in their standard protonation state the structure diverges far from its starting conformation. In comparison, MD simulations performed with pre-determined protonation states of amino acid residues reproduce the structural conformation, protein hydration, and protein-water and protein-protein interactions of the structure much better. The results suggest it is crucial to perform basic protonation state calculations, especially on structures where protonation changes play an important functional role, prior to launching any MD simulations. Furthermore, the combined approach of protonation state prediction and MD simulations can provide valuable information on the charge states of amino acids in the cryo-EM sample. Even though accurate prediction of protonation states currently remains a challenge, we introduce an approach of combining pKa prediction with cryo-EM density map analysis that helps in improving not only the protonation state predictions, but also the atomic modeling of density data.

biophysics↗

bioRxiv2022

Tunnel dynamics of quinone derivatives and its coupling to protein conformational rearrangements in respiratory complex I

Respiratory complex I in mitochondria and bacteria catalyzes the transfer of electrons from NADH to quinone (Q). The free energy available from the reaction is used to pump protons and to establish a membrane proton electrochemical gradient, which drives ATP synthesis. Even though several high-resolution structures of complex I have been resolved, how Q reduction is linked with proton pumping, remains unknown. Here, microsecond long molecular dynamics (MD) simulations were performed on Yarrowia lipolytica complex I structures where Q molecules have been resolved in the ~30 [A] long Q tunnel. MD simulations of several different redox/protonation states of Q reveal the coupling between the Q dynamics and the restructuring of conserved loops and ion pairs. Oxidized quinone stabilizes towards the N2 FeS cluster, a binding mode not previously described in Yarrowia lipolytica complex I structures. On the other hand, reduced (and protonated) species tend to diffuse towards the Q binding sites closer to the tunnel entrance. Mechanistic and physiological relevance of these results are discussed.

biophysics↗

bioRxiv2022

Ion transfer mechanisms in Mrp-type antiporters from high resolution cryoEM and molecular dynamics simulations

Multiple resistance and pH adaptation (Mrp) cation/proton antiporters are essential for growth of a variety of halophilic and alkaliphilic bacteria under stress conditions. Mrp-type antiporters are closely related to the membrane domain of respiratory complex I. We determined the structure of the Mrp antiporter from Bacillus pseudofirmus by electron cryo-microscopy at 2.2 [A] resolution. The structure resolves more than 99% of the sidechains of the seven membrane subunits MrpA to MrpG plus 360 water molecules, including [~]70 in putative ion translocation pathways. Molecular dynamics simulations based on the high-resolution structure revealed details of the antiport mechanism. We find that switching the position of a histidine residue between three hydrated pathways in the MrpA subunit is critical for proton transfer that drives gated transmembrane sodium translocation. Several lines of evidence indicate that the same histidine-switch mechanism operates in respiratory complex I.

biochemistry↗

bioRxiv2021

High-resolution structure and dynamics of mitochondrial complex I - insights into the proton pumping mechanism

Mitochondrial NADH:ubiquinone oxidoreductase (complex I) is a 1 MDa membrane protein complex with a central role in energy metabolism. Redox-driven proton translocation by complex I contributes substantially to the proton motive force that drives ATP synthase. Several structures of complex I from bacteria and mitochondria have been determined but its catalytic mechanism has remained controversial. We here present the cryo-EM structure of complex I from Yarrowia lipolytica at 2.1 [A] resolution, which reveals the positions of more than 1600 protein-bound water molecules, of which [~]100 are located in putative proton translocation pathways. Another structure of the same complex under steady-state activity conditions at 3.4 [A] resolution indicates conformational transitions that we associate with proton injection into the central hydrophilic axis. By combining high-resolution structural data with site-directed mutagenesis and large-scale molecular dynamics simulations, we define details of the proton translocation pathways, and offer new insights into the redox-coupled proton pumping mechanism of complex I.

biochemistry↗