Computational and Experimental Insights in Redox-Coupled Proton Pumping in Proteins

Editorial

15 September 2021

Editorial: Computational and Experimental Insights in Redox-Coupled Proton Pumping in Proteins

Vivek Sharma

Petra Imhof

and

Petra Hellwig

1,581 views

0 citations

Editors

Vivek Sharma

University of Helsinki

Petra Imhof

University of Erlangen Nuremberg

Petra Hellwig

Université de Strasbourg

Impact

(A,B) Structure of the full membrane domain of complex I and only the Nqo4 subunit of the periplasmic domain from T. thermophilus [PDB ID: 4HEA (Baradaran et al., 2013)] highlighting proton transfer paths. (A) Residues that have been proposed to be important for proton pumping are shown as sticks and labeled as subunit number (one letter amino acid designation-residue number). Quinone is yellow and N2 of each Iron Sulfur cluster is green. Approximate locations of putative proton transfer paths are blue arrows and dashed lines show alternative, proposed paths. (B) Residues that are included in the conservation analysis. Purple sticks: E channel cluster in the center of the protein [Cluster 4 in (Khaniya et al., 2020)]; Sticks colored by atom type: antiporter residues (Baradaran et al., 2013; Di Luca et al., 2017; Haapanen and Sharma, 2017; Gutiérrez-Fernández et al., 2020). (C,D) Conservation analysis shown as Weblogo (Crooks, 2004) representation of multiple sequence alignment of 1,000 complex I sequences (Johnson et al., 2008; Sievers et al., 2011). (C) Residues in the three linear antiporter pathways in Nqo12 (Top), Nqo13 (Middle) and Nqo14 (Bottom) subunits. (D) Residues in the E-channel cluster 4. Residues from Nqo8 (Top), Nqo7 (Middle) and Nqo10 (Bottom).

Review

15 June 2021

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient

Divya Kaur

, 2 more and

M. R. Gunner

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.

6,601 views

37 citations

Original Research

14 June 2021

A Voltammetric Perspective of Multi-Electron and Proton Transfer in Protein Redox Chemistry: Insights From Computational Analysis of Escherichia coli HypD Fourier Transformed Alternating Current Voltammetry

Alister R. Dale-Evans

, 4 more and

Alison Parkin

3,642 views

8 citations

Illustration of inter-helical carboxylate-hydroxyl H-bond motifs. For clarity, only selected backbone groups are shown. Numbers in blue represent H-bond distances in Å. (A) The bacteriorhodopsin proton pump, PDB ID:5ZIM (Hasegawa et al., 2018). (B) The viral ion channel OLPVR1, PDB ID:7AKY (Zabelskii et al., 2021). (C) EAAT1 bound to L-Asp substrate, PDB ID:5LLU (Canul-Tec et al., 2017). (D) The glutamate transporter VGLUT2, PDB ID:64VD (Li et al., 2020). (E) The LacY symporter, PDB ID:2V8N. (F) The HV1 proton channel, PDB ID:5OKK, molecule #7 (Bayrhuber et al., 2019). All molecular graphics were prepared with Visual Molecular Dynamics, VMD (Humphrey et al., 1996).

Perspective

31 May 2021

Proton-Binding Motifs of Membrane-Bound Proteins: From Bacteriorhodopsin to Spike Protein S

Ana-Nicoleta Bondar

2,843 views

7 citations

The dynamics and binding of a newly formed superoxide (model I). O2•− stays bound for a while in the binding pocket near the Qo-site, but eventually escapes into the bulk water. (A) superoxide escapes into the intermembrane space. The red regions indicate the averaged localization of O2 during all 100 simulated unbinding events. Two example trajectories are shown with red and blue colors. (B) a histogram of the number Nb(t) of simulations that still has O2•− bound after a specified simulation time along with a fit of an exponential model, Eq. 6, with a characteristic binding time of τ=4.5 ns.

Original Research

19 May 2021

Modeling the Energy Landscape of Side Reactions in the Cytochrome bc1 Complex

Peter Husen

and

Ilia A. Solov’yov

2,497 views

7 citations

Simplified scheme of two possible reactions of SQo-2Fe2S formation. (A) The semiforward mechanism of UQH2 oxidation by the 2Fe2S cluster at the time when heme bL is unable to accept electron (because of being already reduced) from resulting SQo, leading to the creation of the SQo-2Fe2S state. (B) The semireverse mechanism assumes that the reduced heme bL donates electrons to UQ at the time when the reduced 2Fe2S is close to the Qo site. This leads to the creation of the SQo-2Fe2S state. According to the mechanism shown in A, the redox-active heme bL is not necessary, while the mechanism shown in B requires heme bL for the generation of the SQo-2Fe2S state.

Original Research

07 May 2021

The High-Spin Heme bL Mutant Exposes Dominant Reaction Leading to the Formation of the Semiquinone Spin-Coupled to the [2Fe-2S]+ Cluster at the Qo Site of Rhodobacter capsulatus Cytochrome bc1

Marcin Sarewicz

, 3 more and

Artur Osyczka

2,484 views

5 citations

Catalytic activities of wild type complex I (black) and the D213GH variant (red). (A) Shows the NADH:decyl-Q oxidoreductase activity and (B) the quench of the ACMA fluorescence after reconstitution of the preparations into proteoliposomes. The proton gradient established by the catalytic activity of complex I is dissipated by an addition of carbonyl cyanide 3-chlorophenylhydrazone (CCCP). The insets show the initial activities with a magnified scale.

Original Research

07 May 2021

A Quinol Anion as Catalytic Intermediate Coupling Proton Translocation With Electron Transfer in E. coli Respiratory Complex I

Franziska Nuber

, 4 more and

Thorsten Friedrich

2,682 views

18 citations

ET reaction free energies and outer-sphere reorganization energies of the ET between hemes with O2 (A) and without O2 (B). The gray bars represent values obtained for the five 100ns-long data sets. The green bars are the results of a block average using the data of these five data sets. The red bars correspond to values obtained using the full 300ns-long trajectory. Error bars correspond to twice the uncertainty.

Original Research

04 May 2021

Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations

Xiaojing Wu

, 4 more and

Aurélien de la Lande

4,125 views

7 citations

Review

30 April 2021

Ubiquinone Binding and Reduction by Complex I—Open Questions and Mechanistic Implications

Etienne Galemou Yoga

, 1 more and

Volker Zickermann

NADH: ubiquinone oxidoreductase (complex I) is the first enzyme complex of the respiratory chain. Complex I is a redox-driven proton pump that contributes to the proton motive force that drives ATP synthase. The structure of complex I has been analyzed by x-ray crystallography and electron cryo-microscopy and is now well-described. The ubiquinone (Q) reduction site of complex I is buried in the peripheral arm and a tunnel-like structure is thought to provide access for the hydrophobic substrate from the membrane. Several intermediate binding positions for Q in the tunnel were identified in molecular simulations. Structural data showed the binding of native Q molecules and short chain analogs and inhibitors in the access pathway and in the Q reduction site, respectively. We here review the current knowledge on the interaction of complex I with Q and discuss recent hypothetical models for the coupling mechanism.

7,405 views

22 citations

Original Research

14 April 2021

The Redox-Active Tyrosine Is Essential for Proton Pumping in Cytochrome c Oxidase

Margareta R. A. Blomberg

Cellular respiration involves electron transport via a number of enzyme complexes to the terminal Cytochrome c oxidase (CcO), in which molecular oxygen is reduced to water. The free energy released in the reduction process is used to establish a transmembrane electrochemical gradient, via two processes, both corresponding to charge transport across the membrane in which the enzymes are embedded. First, the reduction chemistry occurring in the active site of CcO is electrogenic, which means that the electrons and protons are delivered from opposite sides of the membrane. Second, the exergonic chemistry is coupled to translocation of protons across the entire membrane, referred to as proton pumping. In the largest subfamily of the CcO enzymes, the A-family, one proton is pumped for every electron needed for the chemistry, making the energy conservation particularly efficient. In the present study, hybrid density functional calculations are performed on a model of the A-family CcOs. The calculations show that the redox-active tyrosine, conserved in all types of CcOs, plays an essential role for the energy conservation. Based on the calculations a reaction mechanism is suggested involving a tyrosyl radical (possibly mixed with tyrosinate character) in all reduction steps. The result is that the free energy released in each reduction step is large enough to allow proton pumping in all reduction steps without prohibitively high barriers when the gradient is present. Furthermore, the unprotonated tyrosine provides a mechanism for coupling the uptake of two protons per electron in every reduction step, i.e. for a secure proton pumping.

3,090 views

20 citations

Schematic representation of the different CcO states distinguishable in our experiment. The four redox-active metal cofactors are figuratively depicted as reduced (green) or oxidized (transparent). The CO probe is shown in its bound states, and the global fit of the potential-dependent CO band intensity is shown as solid gray traces. Dashed vertical lines correspond to the midpoint potentials of the redox transitions. The identified states are labeled according to the nomenclature used in this work. The potential values are given against the Ag/AgCl reference electrode.

Original Research

27 April 2021

Quantification of Local Electric Field Changes at the Active Site of Cytochrome c Oxidase by Fourier Transform Infrared Spectroelectrochemical Titrations

Federico Baserga

, 5 more and

Joachim Heberle

4,152 views

6 citations

Distribution of NrfD-like subunits in Prokaryotes. The diagram indicates the percentage of the species within each phylum containing at least one gene encoding a NrfD-like subunit. The color code is indicated in the figure.

Original Research

13 April 2021

The Ion-Translocating NrfD-Like Subunit of Energy-Transducing Membrane Complexes

Filipa Calisto

and

Manuela M. Pereira

Several energy-transducing microbial enzymes have their peripheral subunits connected to the membrane through an integral membrane protein, that interacts with quinones but does not have redox cofactors, the so-called NrfD-like subunit. The periplasmic nitrite reductase (NrfABCD) was the first complex recognized to have a membrane subunit with these characteristics and consequently provided the family's name: NrfD. Sequence analyses indicate that NrfD homologs are present in many diverse enzymes, such as polysulfide reductase (PsrABC), respiratory alternative complex III (ACIII), dimethyl sulfoxide (DMSO) reductase (DmsABC), tetrathionate reductase (TtrABC), sulfur reductase complex (SreABC), sulfite dehydrogenase (SoeABC), quinone reductase complex (QrcABCD), nine-heme cytochrome complex (NhcABCD), group-2 [NiFe] hydrogenase (Hyd-2), dissimilatory sulfite-reductase complex (DsrMKJOP), arsenate reductase (ArrC) and multiheme cytochrome c sulfite reductase (MccACD). The molecular structure of ACIII subunit C (ActC) and Psr subunit C (PsrC), NrfD-like subunits, revealed the existence of ion-conducting pathways. We performed thorough primary structural analyses and built structural models of the NrfD-like subunits. We observed that all these subunits are constituted by two structural repeats composed of four-helix bundles, possibly harboring ion-conducting pathways and containing a quinone/quinol binding site. NrfD-like subunits may be the ion-pumping module of several enzymes. Our data impact on the discussion of functional implications of the NrfD-like subunit-containing complexes, namely in their ability to transduce energy.

4,166 views

16 citations

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