Cryo-EM structures of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae

The RNF/NQR redox pumps: a versatile system for energy transduction in bacteria and archaea

The Na+ (or H+)-translocating ferredoxin:NAD+ oxidoreductase (also called RNF, rhodobacter nitrogen fixation, complex) catalyzes the oxidation of reduced ferredoxin with NAD+, hereby generating an electrochemical gradient. In the reverse reaction driven by an electrochemical gradient, RNF provides reduced ferredoxin using NADH as electron donor. RNF plays a crucial role in the metabolism of many anaerobes, such as amino acid fermenters, acetogens, or aceticlastic methanogens. The Na+-translocating NADH:quinone oxidoreductase (NQR), which has evolved from an RNF, is found in selected bacterial groups including anaerobic, marine, or pathogenic organisms. Since NQR and RNF are not related to eukaryotic respiratory complex I (NADH:quinone oxidoreductase), members of this oxidoreductase family are promising targets for novel antibiotics. RNF and NQR share a membrane-bound core complex consisting of four subunits, which represent an essential functional module for redox-driven cation transport. Several recent 3D structures of RNF and NQR in different states put forward conformational coupling of electron transfer and Na+ translocation reaction steps. Based on this common principle, putative reaction mechanisms of RNF and NQR redox pumps are compared. KEY POINTS: • Electrogenic ferredoxin:NAD+ oxidoreductases (RNF complexes) are found in bacteria and archaea. • The Na+ -translocating NADH:quinone oxidoreductase (NQR) is evolutionary related to RNF. • The mechanism of energy conversion by RNF/NQR complexes is based on conformational coupling of electron transfer and cation transport reactions.

The Na+-pumping mechanism driven by redox reactions in the NADH-quinone oxidoreductase from Vibrio cholerae relies on dynamic conformational changes

The Na+-pumping NADH-quinone oxidoreductase (Na+-NQR) is a key respiratory enzyme in many marine and pathogenic bacteria that couples electron transfer to Na+-pumping across the membrane. Earlier X-ray and cryo-EM structures of Na+-NQR from Vibrio cholerae suggested that the subunits harboring redox cofactors undergo conformational changes during catalytic turnover. However, these proposed rearrangements have not yet been confirmed. Here, we have identified at least five distinct conformational states of Na+-NQR using: mutants that lack specific cofactors, specific inhibitors or low-sodium conditions. Molecular dynamics simulations based on these structural insights indicate that 2Fe-2S reduction in NqrD/E plays a crucial role in triggering Na+ translocation by driving structural rearrangements in the NqrD/E subunits, which subsequently influence NqrC and NqrF positioning. This study provides the first structural insights into the mechanism of Na+ translocation coupled to electron transfer in Na+-NQR.

A large-scale curated and filterable dataset for cryo-EM foundation model pre-training

Cryo-electron microscopy (cryo-EM) is a transformative imaging technology that enables near-atomic resolution 3D reconstruction of target biomolecule, playing a critical role in structural biology and drug discovery. Cryo-EM faces significant challenges due to its extremely low signal-to-noise ratio (SNR) where the complexity of data processing becomes particularly pronounced. To address this challenge, foundation models have shown great potential in other biological imaging domains. However, their application in cryo-EM has been limited by the lack of large-scale, high-quality datasets. To fill this gap, we introduce CryoCRAB, the first large-scale dataset for cryo-EM foundation models. CryoCRAB includes 746 proteins, comprising 152,385 sets of raw movie frames (116.8 TB in total). To tackle the high-noise nature of cryo-EM data, each movie is split into odd and even frames to generate paired micrographs for denoising tasks. The dataset is stored in HDF5 chunked format, significantly improving random sampling efficiency and training speed. CryoCRAB offers diverse data support for cryo-EM foundation models, enabling advancements in image denoising and general-purpose feature extraction for downstream tasks.

Structural Elucidation of the Mechanism for Inhibitor Resistance in the Na+-Translocating NADH-Ubiquinone Oxidoreductase from Vibrio cholerae

Na+-translocating NADH-ubiquinone oxidoreductase (Na+-NQR) is a unique redox-driven Na+-pump. Since this enzyme is exclusively found in prokaryotes, including the human pathogens Vibrio cholerae and Neisseria gonorrhoeae, it is a promising target for highly selective antibiotics. Korormicin A, a natural product, and a specific and potent inhibitor of V. cholerae Na+-NQR, may become a lead compound for the relevant drug design. We previously showed that the G141A mutation in the NqrB subunit (NqrB-G141A) confers moderate resistance to korormicin A (about 100-fold). However, the efficiency of photoaffinity labeling of the mutant enzyme by a photoreactive korormicin derivative was the same as in the wild-type enzyme. Because of these apparently conflicting results, the molecular mechanism underlying the korormicin A-resistance remains elusive. In the present study, we determined the cryo-EM structure of the V. cholerae NqrB-G141A mutant in the presence of bound korormicin A, and compared it to the corresponding structure from the wild-type enzyme. The toxophoric moiety of korormicin A binds to the mutant enzyme similarly to how it binds to the wild type. However, the added bulk of the alanine-141 excludes the alkyl side chain from the binding cavity, resulting in a decrease in the binding affinity. In fact, isothermal titration calorimetry revealed that the binding affinity of korormicin to the NqrB-G141A mutant is significantly weaker compared to the wild-type. Altogether, we conclude that the inhibitory potency of korormicin A is weaker in the NqrB-G141A mutant due to the decrease in its binding affinity to the altered binding cavity.

The binding modes of quinones in flavoprotein oxidoreductases

Flavoprotein quinone reductases regenerate quinols which serve metabolic and antioxidant roles. These enzymes catalyze the two-electron oxidation of substrates and the subsequent two electron reduction of quinones. Despite the net two electron transfer between substrates, the binding mode of quinones is typically end-on to the flavin, rather than stacked, dictating that the oxidative half reaction cannot proceed via hydride transfer and must instead occur by two successive single electron transfers. Here we present a review of six of the most well-studied flavoprotein quinone reductases to establish a framework for discussing this positional orientation for the quinone oxidant. There are two non-mutually exclusive rationalizations for this binding mode where the flavin isoalloxazine acts as a redox partition. The first is that energetics of the single electron transfer pathway create a kinetic barrier to the reverse reaction, trapping electrons in the quinone pool and countering the high ratio of quinol to quinone present in the membrane. The second is that the end-on binding allows the enzymes to utilize different binding sites for cytosolic and membrane associated substrates, avoiding the need to desorb substrates. These effects may be additive and serve to funnel electrons into the quinone pool as efficiently as possible.

Pinpoint introduction of functional molecular probe into the NqrB subunit of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae

The Na+-translocating NADH-ubiquinone oxidoreductase (Na+-NQR) is a key enzyme in the respiratory chain of numerous pathogenic bacteria, including Vibrio cholerae. The flexible cytoplasmic N-terminal region of the NqrB subunit (Met1-Lys54), which may play an important role in the final UQ reduction at the adjacent NqrA, is the target of specific inhibitors. If we can develop a new method that enables pinpoint introduction of functional probe molecules (such as fluorescent probes) into the N-terminal region, this could lead to new experimental ways of monitoring dynamic structural changes of the region. We previously showed that an electrophilic chemical group, which can be released from korormicin A-templated synthetic ligand, can be predominantly introduced into nucleophilic Lys22 as a "foothold" via ligand-directed (LD) substitution, but the subsequent conjugation of a functional probe molecule to the foothold by Cu+-catalyzed click chemistry required destruction of the enzyme. Accordingly, we now report the nondestructive conjugation of the functional molecule into the N-terminal region via a two-step conjugation technique: first, pinpoint introduction of a foothold tag containing a ring-strained cyclopropene by LD substitution using a new korormicin A-templated ligand (BEK-1) and second, direct conjugation of a fluorescent probe molecule containing tetrazine with the introduced cyclopropene by inverse electron-demand Diels-Alder-type click chemistry. Protein sequence analyses revealed that the fluorescent probe is attached to Lys19, His20, or Lys22 in the region. The extent of conjugation of the fluorescent probe was approximately halved in the presence of different inhibitors, suggesting that the inhibitor binding induces structural changes around the residues.

Molecular principles of redox-coupled sodium pumping of the ancient Rnf machinery

The Rnf complex is the primary respiratory enzyme of several anaerobic prokaryotes that transfers electrons from ferredoxin to NAD+ and pumps ions (Na+ or H+) across a membrane, powering ATP synthesis. Rnf is widespread in primordial organisms and the evolutionary predecessor of the Na+-pumping NADH-quinone oxidoreductase (Nqr). By running in reverse, Rnf uses the electrochemical ion gradient to drive ferredoxin reduction with NADH, providing low potential electrons for nitrogenases and CO2 reductases. Yet, the molecular principles that couple the long-range electron transfer to Na+ translocation remain elusive. Here, we resolve key functional states along the electron transfer pathway in the Na+-pumping Rnf complex from Acetobacterium woodii using redox-controlled cryo-electron microscopy that, in combination with biochemical functional assays and atomistic molecular simulations, provide key insight into the redox-driven Na+ pumping mechanism. We show that the reduction of the unique membrane-embedded [2Fe2S] cluster electrostatically attracts Na+, and in turn, triggers an inward/outward transition with alternating membrane access driving the Na+ pump and the reduction of NAD+. Our study unveils an ancient mechanism for redox-driven ion pumping, and provides key understanding of the fundamental principles governing energy conversion in biological systems.

The Na+-translocating NADH:quinone oxidoreductase (Na+-NQR): Physiological role, structure and function of a redox-driven, molecular machine

Many bacterial processes are powered by the sodium motive force (smf) and in case of pathogens, the smf contributes to virulence. Vibrio cholerae, the causative agent of Cholera disease, possesses a Na+-translocating NADH:quinone oxidoreductase (NQR), a six-subunit membrane protein assembly. The 3D structure of NQR revealed the arrangement of the six subunits NqrABCDEF, the position of all redox cofactors (four flavins, two [2Fe-2S] centers) and the binding sites for the substrates NADH (in NqrF) and ubiquinone (in NqrB). Upon oxidation of NADH, electrons are shuttled twice across the membrane, starting with cytoplasmic FADNqrF and electron transfer to the [2Fe2S] clusterNqrF and from there to an intra-membranous [2Fe-2S] clusterNqrDE, periplasmic FMNNqrC, FMNNqrB and from there to riboflavinNqrB. This riboflavin is located at the cytoplasmic entry site of the sodium channel in NqrB, and it donates electrons to ubiquinone-8 positioned at the cytoplasmic side of NqrB. Targeting the substrate binding sites of NQR is a promising strategy to identify new inhibitors against many bacterial pathogens. Detailed structural information on the binding mode of natural inhibitors and small molecules in the active sites of NQR is now available, paving the way for the development of new antibiotics. The NQR shows different conformations as revealed in recent cryo-EM and crystallographic studies combined with spectroscopic analyses. These conformations represent distinct steps in the catalytic cycle. Considering the structural and functional data available, we propose a mechanism of Na+-NQR based on conformational coupling of electron transfer and Na+ translocation reaction steps.

A New Real-Time Simple Method to Measure the Endogenous Nitrate Reductase Activity (Nar) in Paracoccus denitrificans and Other Denitrifying Bacteria

The transmembrane nitrate reductase (Nar) is the first enzyme in the dissimilatory alternate anaerobic nitrate respiratory chain in denitrifying bacteria. To date, there has been no real-time method to determine its specific activity embedded in its native membrane; here, we describe such a new method, which is useful with the inside-out membranes of Paracoccus denitrificans and other denitrifying bacteria. This new method takes advantage of the native coupling of the endogenous NADH dehydrogenase or Complex I with the reduction of nitrate by Nar through the quinone pool of the inner membranes of P. denitrificans. This is achieved under previously reached anaerobic conditions. Inner controls confirming the specific Nar activity determined by this new method were made by the total inhibition of the Nar enzyme by sodium azide and cyanide, well-known Nar inhibitors. The estimation of the Michaelis-Menten affinity of Nar for NO3- using this so-called Nar-JJ assay gave a Km of 70.4 μM, similar to previously determined values. This new Nar-JJ assay is a suitable, low-cost, and reproducible method to determine in real-time the endogenous Nar activity not only in P. denitrificans, but in other denitrifying bacteria such as Brucella canis, and potentially in other entero-pathogenic bacteria.

Enediyne natural product biosynthesis unified by a diiodotetrayne intermediate

Enediyne natural products are renowned for their potent cytotoxicities but the biosynthesis of their defining 1,5-diyne-3-ene core moiety remains largely enigmatic. Since the discovery of the enediyne polyketide synthase cassette in 2002, genome sequencing has revealed thousands of distinct enediyne biosynthetic gene clusters, each harboring the conserved enediyne polyketide synthase cassette. Here we report that (1) the products of this cassette are an iodoheptaene, a diiodotetrayne and two pentaynes; (2) the diiodotetrayne represents a common biosynthetic intermediate for all known enediynes; and (3) cryptic iodination can be exploited to increase enediyne titers. These findings establish a unified biosynthetic pathway for the enediynes, set the stage to further advance enediyne core biosynthesis and enable fundamental breakthroughs in chemistry, enzymology and translational applications of enediyne natural products.

Versatile roles of protein flavinylation in bacterial extracyotosolic electron transfer

Bacteria perform diverse redox chemistries in the periplasm, cell wall, and extracellular space. Electron transfer for these extracytosolic activities is frequently mediated by proteins with covalently bound flavins, which are attached through post-translational flavinylation by the enzyme ApbE. Despite the significance of protein flavinylation to bacterial physiology, the basis and function of this modification remain unresolved. Here we apply genomic context analyses, computational structural biology, and biochemical studies to address the role of ApbE flavinylation throughout bacterial life. We identify ApbE flavinylation sites within structurally diverse protein domains and show that multi-flavinylated proteins, which may mediate longer distance electron transfer via multiple flavinylation sites, exhibit substantial structural heterogeneity. We identify two novel classes of flavinylation substrates that are related to characterized proteins with non-covalently bound flavins, providing evidence that protein flavinylation can evolve from a non-covalent flavoprotein precursor. We further find a group of structurally related flavinylation-associated cytochromes, including those with the domain of unknown function DUF4405, that presumably mediate electron transfer in the cytoplasmic membrane. DUF4405 homologs are widespread in bacteria and related to ferrosome iron storage organelle proteins that may facilitate iron redox cycling within ferrosomes. These studies reveal a complex basis for flavinylated electron transfer and highlight the discovery power of coupling comparative genomic analyses with high-quality structural models.

IMPORTANCE

This study explores the mechanisms bacteria use to transfer electrons outside the cytosol, a fundamental process involved in energy metabolism and environmental interactions. Central to this process is a phenomenon known as flavinylation, where a flavin molecule-a compound related to vitamin B2-is covalently attached to proteins, to enable electron transfer. We employed advanced genomic analysis and computational modeling to explore how this modification occurs across different bacterial species. Our findings uncover new types of proteins that undergo this modification and highlight the diversity and complexity of bacterial electron transfer mechanisms. This research broadens our understanding of bacterial physiology and informs potential biotechnological applications that rely on microbial electron transfer, including bioenergy production and bioremediation.

Architecture of the RNF1 complex that drives biological nitrogen fixation

Biological nitrogen fixation requires substantial metabolic energy in form of ATP as well as low-potential electrons that must derive from central metabolism. During aerobic growth, the free-living soil diazotroph Azotobacter vinelandii transfers electrons from the key metabolite NADH to the low-potential ferredoxin FdxA that serves as a direct electron donor to the dinitrogenase reductases. This process is mediated by the RNF complex that exploits the proton motive force over the cytoplasmic membrane to lower the midpoint potential of the transferred electron. Here we report the cryogenic electron microscopy structure of the nitrogenase-associated RNF complex of A. vinelandii, a seven-subunit membrane protein assembly that contains four flavin cofactors and six iron-sulfur centers. Its function requires the strict coupling of electron and proton transfer but also involves major conformational changes within the assembly that can be traced with a combination of electron microscopy and modeling.

Matrine attenuating cardiomyocyte apoptosis in doxorubicin-induced cardiotoxicity through improved mitochondrial membrane potential and activation of mitochondrial respiratory chain Complex I pathway

The study aimed to demonstrate that matrine can reduce apoptosis in H9c2 cells induced by the cardiotoxic anticancer drug doxorubicin (DOX).The researchers pretreated H9c2 cells with different concentrations of matrine before exposing them to DOX and cultured them for 24 h. They assessed cell survival rates using cell counting kit-8 and MTT assay. Hoechst 33258 dye kits were used to determine apoptosis, while laser confocal JC-1 method was applied to test the mitochondrial membrane potential (MMP). Complex I activities were detected following the manufacturer's protocol. The results indicated that matrine pretreatment significantly increased the survival rate of H9c2 cells injured by DOX. Additionally, matrine reduced apoptosis in H9c2 cells through the improvement of MMP and activity of Complex I, which were damaged by DOX.

Versatile roles of protein flavinylation in bacterial extracyotosolic electron transfer

Bacteria perform diverse redox chemistries in the periplasm, cell wall, and extracellular space. Electron transfer for these extracytosolic activities is frequently mediated by proteins with covalently bound flavins, which are attached through post-translational flavinylation by the enzyme ApbE. Despite the significance of protein flavinylation to bacterial physiology, the basis and function of this modification remains unresolved. Here we apply genomic context analyses, computational structural biology, and biochemical studies to address the role of ApbE flavinylation throughout bacterial life. We find that ApbE flavinylation sites exhibit substantial structural heterogeneity. We identify two novel classes of flavinylation substrates that are related to characterized proteins with non-covalently bound flavins, providing evidence that protein flavinylation can evolve from a non-covalent flavoprotein precursor. We further find a group of structurally related flavinylation-associated cytochromes, including those with the domain of unknown function DUF4405, that presumably mediate electron transfer in the cytoplasmic membrane. DUF4405 homologs are widespread in bacteria and related to ferrosome iron storage organelle proteins that may facilitate iron redox cycling within ferrosomes. These studies reveal a complex basis for flavinylated electron transfer and highlight the discovery power of coupling comparative genomic analyses with high-quality structural models.

Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions

Pseudomonas aeruginosa is a common cause of urinary tract infections by strains that are often multidrug resistant, representing a major challenge to the world's health care system. This microorganism has a highly adaptable metabolism that allows it to colonize many environments, including the urinary tract. In this work, we have characterized the metabolic strategies used by stationary phase P. aeruginosa cells cultivated in urine-like media to understand the adaptations used by this microorganism to survive and produce disease. Our proteomics results show that cells rely on the Entner-Duodoroff pathway, pentose phosphate pathway, the Krebs cycle/ glyoxylate shunt and the aerobic oxidative phosphorylation to survive in urine-like media and other conditions. A deep characterization of the oxidative phosphorylation showed that the respiratory rate of stationary phase cells is increased 3-4 times compared to cells in the logarithmic phase of growth, indicating that the aerobic metabolism plays critical roles in the stationary phase of cells grown in urine like media. Moreover, the data show that respiratory complex III, succinate dehydrogenase and the NADH dehydrogenase NQR have important functions and could be used as targets to develop new antibiotics against this bacterium.

Functionality of the Na+-translocating NADH:quinone oxidoreductase and quinol:fumarate reductase from Prevotella bryantii inferred from homology modeling

Members of the family Prevotellaceae are Gram-negative, obligate anaerobic bacteria found in animal and human microbiota. In Prevotella bryantii, the Na+-translocating NADH:quinone oxidoreductase (NQR) and quinol:fumarate reductase (QFR) interact using menaquinone as electron carrier, catalyzing NADH:fumarate oxidoreduction. P. bryantii NQR establishes a sodium-motive force, whereas P. bryantii QFR does not contribute to membrane energization. To elucidate the possible mode of function, we present 3D structural models of NQR and QFR from P. bryantii to predict cofactor-binding sites, electron transfer routes and interaction with substrates. Molecular docking reveals the proposed mode of menaquinone binding to the quinone site of subunit NqrB of P. bryantii NQR. A comparison of the 3D model of P. bryantii QFR with experimentally determined structures suggests alternative pathways for transmembrane proton transport in this type of QFR. Our findings are relevant for NADH-dependent succinate formation in anaerobic bacteria which operate both NQR and QFR.

Production of extracellular superoxide radical in microorganisms and its environmental implications: A review

Extracellular superoxide radical (O2•-) is ubiquitous in microbial environments and has significant implications for pollutant transformation. Microbial extracellular O2•- can be produced through multiple pathways, including electron leakage from the respiratory electron transport chain (ETC), NADPH oxidation by the transmembrane NADPH oxidase (NOX), and extracellular reactions. Extracellular O2•- significantly influences the geochemical processes of various substances, including toxic metals and refractory organic pollutants. On one hand, extracellular O2•- can react with variable-valence metals and detoxify certain highly toxic metals, such as As(III), Cr(VI), and Hg(II). On the other hand, extracellular O2•- can directly or indirectly (via Bio-Fenton) degrade many organic pollutants, including a variety of emerging contaminants. In this work, we summarize the production mechanisms of microbial extracellular O2•-, review its roles in the transformation of environmental pollutants, and discuss the potential applications, limiting factors, and future research directions in this field.

Respiratory protein interactions in Dehalobacter sp. strain 8M revealed through genomic and native proteomic analyses

Dehalobacter (Firmicutes) encompass obligate organohalide-respiring bacteria used for bioremediation of groundwater contaminated with halogenated organics. Various aspects of their biochemistry remain unknown, including the identities and interactions of respiratory proteins. Here, we sequenced the genome of Dehalobacter sp. strain 8M and analysed its protein expression. Strain 8M encodes 22 reductive dehalogenase homologous (RdhA) proteins. RdhA D8M_v2_40029 (TmrA) was among the two most abundant proteins during growth with trichloromethane and 1,1,2-trichloroethane. To examine interactions of respiratory proteins, we used blue native gel electrophoresis together with dehalogenation activity tests and mass spectrometry. The highest activities were found in gel slices with the highest abundance of TmrA. Protein distributions across gel lanes provided biochemical evidence that the large and small subunits of the membrane-bound [NiFe] uptake hydrogenase (HupL and HupS) interacted strongly and that HupL/S interacted weakly with RdhA. Moreover, the interaction of RdhB and membrane-bound b-type cytochrome HupC was detected. RdhC proteins, often encoded in rdh operons but without described function, migrated in a protein complex not associated with HupL/S or RdhA. This study provides the first biochemical evidence of respiratory protein interactions in Dehalobacter, discusses implications for the respiratory architecture and advances the molecular comprehension of this unique respiratory chain.

Conformational coupling of redox-driven Na+-translocation in Vibrio cholerae NADH:quinone oxidoreductase

In the respiratory chain, NADH oxidation is coupled to ion translocation across the membrane to build up an electrochemical gradient. In the human pathogen Vibrio cholerae, the sodium-pumping NADH:quinone oxidoreductase (Na+-NQR) generates a sodium gradient by a so far unknown mechanism. Here we show that ion pumping in Na+-NQR is driven by large conformational changes coupling electron transfer to ion translocation. We have determined a series of cryo-EM and X-ray structures of the Na+-NQR that represent snapshots of the catalytic cycle. The six subunits NqrA, B, C, D, E, and F of Na+-NQR harbor a unique set of cofactors that shuttle the electrons from NADH twice across the membrane to quinone. The redox state of a unique intramembranous [2Fe-2S] cluster orchestrates the movements of subunit NqrC, which acts as an electron transfer switch. We propose that this switching movement controls the release of Na+ from a binding site localized in subunit NqrB.

Identifying therapeutic antibacterial peptides against Vibrio cholerae to inhibit the function of Na(+)-translocating NADH-quinone reductase

Vibrio cholerae is the bacteria responsible for cholera, which is a significant threat to many nations. Curing and treating this infection requires identification of the critical protein and development of a drug to inhibit its function. In this context, Na(+)-translocating NADH-quinone reductase was considered a potential therapeutic target. A library of antibacterial peptides with residue lengths of 50 was screened using a docking method, and the five most potent peptides were selected on the basis of a weighted score derived from solvent accessible surface area and docking score. To investigate the stability of the protein-peptide complex, a 100-ns molecular dynamics simulation was performed. These peptides targeted the native dimeric binding interface of Na(+)-transporting NADH-quinone reductase. This study evaluated the binding affinity and conformational stability of these peptides with the protein using different post-simulation metrics. A peptide, CCL28, exhibited steady RMSD characteristics; nonetheless, it modified the docked conformation but stabilized in the new conformation. This peptide also demonstrated the best performance in addressing the protein's native binding interface. It demonstrated a binding free energy of -120 kcal/mol with the protein. Principal component analysis (PCA) revealed that the first PC had the lowest conformational variation and the greatest coverage. Eventually, these peptides were also evaluated using steered molecular dynamics, and it was discovered that CCL28 had a greater maximum force than the other five peptides, at 1139.08 kJ/mol/nm. Targeting the native binding interface, we present a CCL28 peptide with a strong potential to block the biological activity of Vibrio cholerae's Na(+)-translocating NADH-quinone reductase.Communicated by Ramaswamy H. Sarma.

Respiratory complex I in mitochondrial membrane catalyzes oversized ubiquinones

NADH-ubiquinone (UQ) oxidoreductase (complex I) couples electron transfer from NADH to UQ with proton translocation in its membrane part. The UQ reduction step is key to triggering proton translocation. Structural studies have identified a long, narrow, tunnel-like cavity within complex I, through which UQ may access a deep reaction site. To elucidate the physiological relevance of this UQ-accessing tunnel, we previously investigated whether a series of oversized UQs (OS-UQs), whose tail moiety is too large to enter and transit the narrow tunnel, can be catalytically reduced by complex I using the native enzyme in bovine heart submitochondrial particles (SMPs) and the isolated enzyme reconstituted into liposomes. Nevertheless, the physiological relevance remained unclear because some amphiphilic OS-UQs were reduced in SMPs but not in proteoliposomes, and investigation of extremely hydrophobic OS-UQs was not possible in SMPs. To uniformly assess the electron transfer activities of all OS-UQs with the native complex I, here we present a new assay system using SMPs, which were fused with liposomes incorporating OS-UQ and supplemented with a parasitic quinol oxidase to recycle reduced OS-UQ. In this system, all OS-UQs tested were reduced by the native enzyme, and the reduction was coupled with proton translocation. This finding does not support the canonical tunnel model. We propose that the UQ reaction cavity is flexibly open in the native enzyme to allow OS-UQs to access the reaction site, but their access is obstructed in the isolated enzyme as the cavity is altered by detergent-solubilizing from the mitochondrial membrane.