Papers by Armen Mulkidjanian
FEBS Letters, 1999
A stepwise increasing membrane potential was generated in chromatophores of the phototrophic bact... more A stepwise increasing membrane potential was generated in chromatophores of the phototrophic bacterium Rhodobacter capsulatus by illumination with short flashes of light. Proton transfer through ATP-synthase (measured by electrochromic carotenoid bandshift and by pH-indicators) and ATP release (measured by luminescence of luciferin-luciferase) were monitored. The ratio between the amount of protons translocated by F H F I and the ATP yield decreased with the flash number from an apparent value of 13 after the first flash to about 5 when averaged over three flashes. In the absence of ADP, protons slipped through F H F I . The proton transfer through F H F I after the first flash contained two kinetic components, of about 6 ms and 20 ms both under the ATP synthesis conditions and under slip. The slower component of proton transfer was substantially suppressed in the absence of ADP. We attribute our observations to the mechanism of energy storage in the ATPsynthase needed to couple the transfer of four protons with the synthesis of one molecule of ATP. Most probably, the transfer of initial protons of each tetrad creates a strain in the enzyme that slows the translocation of the following protons.
FEBS Letters, 1988
The flash‐induced kinetics of transmembrane electric potential (Δψ) generation with a rise‐time o... more The flash‐induced kinetics of transmembrane electric potential (Δψ) generation with a rise‐time of 0.1–0.2 ms were investigated in Rhodobacter sphaeroides chromatophores by electrometry and by monitoring the electrochromic absorbance changes of carotenoids. An analysis of the results obtained electrometrically shows that this electrogenic phase is observed only after even‐numbered flashes. The sensitivity of this phase to o‐phenanthroline, the flash‐number dependence of its amplitude and the decrease of its rise‐time with decreasing pH indicate that it is due to the dismutation of Q− A and Q− B and to subsequent protonation of a doubly reduced ubiquinone QB molecule. The phase of the carotenoid bandshift with τ∼0.1 ms (the so‐called phase II) was shown to be sensitive to o‐phenanthroline, with its rise‐time decreasing with decreasing pH. It is concluded that a considerable part of phase II of the electrochromic carotenoid changes with τ∼0.1 ms is caused by the electrogenic reaction ...
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2005
F O F 1 -ATP synthase converts two energetic bcurrenciesQ of the cell (ATP and protonmotive force... more F O F 1 -ATP synthase converts two energetic bcurrenciesQ of the cell (ATP and protonmotive force, pmf) by coupling two rotary motors/ generators. Their coupling efficiency is usually very high. Uncoupled proton leakage (slip) has only been observed in chloroplast enzyme at unphysiologically low nucleotide concentration. We investigated the properties of proton slip in chromatophores (sub-bacterial vesicles) from Rhodobacter capsulatus in the singleenzyme-per-vesicle mode. The membrane was energized by excitation with flashing light and the relaxation of the transmembrane voltage and pH difference was photometrically detected. We found that: (1) Proton slip occurred only at low nucleotide concentration (b1 AM) and after pre-illumination over several seconds. (2) Slip induction by pmf was accompanied by the release of c0.25 mol ADP per mole of enzyme. There was no detectable detachment of F 1 from F O . (3) The transmembrane voltage and the pH difference were both efficient in slip induction. Once induced, slip persisted for hours, and was only partially reverted by the addition of ADP or ATP (N1 AM). (4) There was no pmf threshold for the proton transfer through the slipping enzyme; slip could be driven both by voltage and pH difference. (5) The conduction was ohmic and weakly pH-dependent in the range from 5.5 to 9.5. The rate constant of proton transfer under slip conditions was 185 s À1 at pH 8. Proton slip probably presents the free-wheeling of the central rotary shaft, subunit g, in an open structure of the (ah) 3 hexagon with no nucleotides in the catalytic sites.
International Journal of Molecular Sciences
Cellular respiration is associated with at least six distinct but intertwined biological function... more Cellular respiration is associated with at least six distinct but intertwined biological functions. (1) biosynthesis of ATP from ADP and inorganic phosphate, (2) consumption of respiratory substrates, (3) support of membrane transport, (4) conversion of respiratory energy to heat, (5) removal of oxygen to prevent oxidative damage, and (6) generation of reactive oxygen species (ROS) as signaling molecules. Here we focus on function #6, which helps the organism control its mitochondria. The ROS bursts typically occur when the mitochondrial membrane potential (MMP) becomes too high, e.g., due to mitochondrial malfunction, leading to cardiolipin (CL) oxidation. Depending on the intensity of CL damage, specific programs for the elimination of damaged mitochondria (mitophagy), whole cells (apoptosis), or organisms (phenoptosis) can be activated. In particular, we consider those mechanisms that suppress ROS generation by enabling ATP synthesis at low MMP levels. We discuss evidence that th...
Additional file 3: Figure S2. of COGcollator: a web server for analysis of distant relationships between homologous protein families
Schematic presentation of sequence similarity between the subunit FliH of bacterial flagella, sub... more Schematic presentation of sequence similarity between the subunit FliH of bacterial flagella, subunit E of the A/V-type ATPases, subunit b of the N-ATPases and subunits b und δ of the F-type ATP synthases. (PDF 23 kb)
Additional file 1: Tables S1, S2 and S3. of COGcollator: a web server for analysis of distant relationships between homologous protein families
Representative list of 124 genomes sampled from the 711 genomes of the current COG database relea... more Representative list of 124 genomes sampled from the 711 genomes of the current COG database release [2]. Table S2. Representative list of 27 eukaryotic genomes sampled manually. Table S3. Results of the similarity assessment for the homologs of catalytic β-subunit of the bacterial FOF1-type ATP synthase by applying the HHpred algorithm [19]. The top hits for the α- and β-subunits of the F-type ATP synthase of E.coli and the B- and A- subunits of the A-type ATP synthase of Methanosarcina mazei (cf with Table 1) are colored red. (XLSX 29 kb)
Additional file 1: Figure S1. of COGNAT: a web server for comparative analysis of genomic neighborhoods
Phylogenetic tree for the proteins belonging to the COG3002. All 115 proteins from 711 genomes, a... more Phylogenetic tree for the proteins belonging to the COG3002. All 115 proteins from 711 genomes, as available in the COG database, were sampled, with only three truncated sequences being removed. Proteins were aligned with the MUSCLE software [5], conserved blocks' regions containing 384 positions were selected manually. The phylogenetic tree was constructed with the MEGA 7 software [17]. Bootstrap support values calculated from 100 iterations are shown on the branches. A color legend is given below the figure (PDF 143 kb)
International Journal of Biomedicine, 2021
Background: Wsc1 is the best studied of the five mechanosensors of the cell wall integrity (CWI) ... more Background: Wsc1 is the best studied of the five mechanosensors of the cell wall integrity (CWI) signal transduction pathway in Saccharomyces cerevisiae. In genetic and biophysical studies, Wsc1 functions were assessed either in living yeast cells or in crude cell extracts. So far, no attempts to purify the sensor and determine its structure have been reported. Methods: The Wsc1-green fluorescent protein (GFP) fusion was expressed in S. cerevisiae following standard protocols. For solubilization, a 5% (w/v) solution of styrene-maleic acid (SMA) copolymer was added dropwise to the membrane suspension to get a final cell-to-SMA weight ratio of 1:2.5. The suspension was incubated for 30 min at room temperature (RT) and then for 16 hours at 4 °C, followed by centrifugation for 20 min at 134000 g at 4 °C. The supernatant was subsequently purified on affinity resin. Protein samples (3 µL) were placed onto the glow-discharged grid, stained twice, using 1% aquatic uranyl acetate solution fo...
Biochemistry (Moscow), 2015
Cell cytoplasm of archaea, bacteria, and eukaryotes contains substantially more potassium than so... more Cell cytoplasm of archaea, bacteria, and eukaryotes contains substantially more potassium than sodium, and potassium cations are specifically required for many key cellular processes, including protein synthesis. This distinct ionic composition and requirements have been attributed to the emergence of the first cells in potassium-rich habitats. Different, albeit complementary, scenarios have been proposed for the primordial potassium-rich environments based on experimental data and theoretical considerations. Specifically, building on the observation that potassium prevails over sodium in the vapor of inland geothermal systems, we have argued that the first cells could emerge in the pools and puddles at the periphery of primordial anoxic geothermal fields, where the elementary composition of the condensed vapor would resemble the internal milieu of modern cells. Marine and freshwater environments generally contain more sodium than potassium. Therefore, to invade such environments, while maintaining excess of potassium over sodium in the cytoplasm, primordial cells needed means to extrude sodium ions. The foray into new, sodium-rich habitats was the likely driving force behind the evolution of diverse redox-, light-, chemically-, or osmotically-dependent sodium export pumps and the increase of membrane tightness. Here we present a scenario that details how the interplay between several, initially independent sodium pumps might have triggered the evolution of sodium-dependent membrane bioenergetics, followed by the separate emergence of the proton-dependent bioenergetics in archaea and bacteria. We also discuss the development of systems that utilize the sodium/potassium gradient across the cell membranes.
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2014
Photosystem II (PSII) uses light energy to split water into protons, electrons and oxygen. In thi... more Photosystem II (PSII) uses light energy to split water into protons, electrons and oxygen. In this reaction, Nature has solved the difficult chemical problem of efficient four electron oxidation of water to yield oxygen without significant side reactions. In order to use Nature's solution for the design of materials that split water for solar fuel production, it is important to understand the mechanism of the reaction. The X-ray crystal structures of cyanobacterial PSII provide information on the structure of the Mn and Ca ions, the redox-active tyrosine called tyrosine-Z, chloride and the surrounding amino acids that comprise the oxygen-evolving complex (OEC). The structure of the OEC and the water-oxidation chemistry of PSII will be discussed in the light of biophysical and computational studies, inorganic chemistry and X-ray crystallographic information. These insights on the natural photosynthetic system are being applied to develop bioinspired materials for photochemical water oxidation and fuel production.
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2014
small copper protein called sulfocyanin. This complex is enzymatically functional, reducing oxyge... more small copper protein called sulfocyanin. This complex is enzymatically functional, reducing oxygen in the presence of the electron donor ferrous iron, at low pH. A second putative cytochrome ba-Rieske protein complex, reminiscent of archaeal complexes analogous to the bc1 complex, may be involved in regeneration of reducing equivalents by reverse electron flow. A model of energy ferrous iron metabolism of F. acidiphilum is proposed [1]. This study constitutes the first detailed biochemical investigation of iron metabolism in acidophilic Archaea, and confirms that iron respiratory chains are clearly different from an organism to another even among Archaea.
Although the genes that encode membrane proteins make about 30% of the sequenced genomes, the evo... more Although the genes that encode membrane proteins make about 30% of the sequenced genomes, the evolution of membrane proteins and their origins are still poorly understood. Here we address this topic by taking a closer look at those membrane proteins the ancestors of which were present in the Last Universal Common Ancestor, and in particular, the F/V-type rotating ATPases. Reconstruction of their evolutionary history provides hints for understanding not only the origin of membrane proteins, but also of membranes themselves. We argue that the evolution of biological membranes could occur as a process of coevolution of lipid bilayers and membrane proteins, where the increase in the ion-tightness of the membrane bilayer may have been accompanied by a transition from amphiphilic, pore-forming membrane proteins to highly hydrophobic integral membrane complexes.
BMC Evolutionary Biology, 2003
A key event in the origin of life on this planet has been formation of self-replicating RNA-type ... more A key event in the origin of life on this planet has been formation of self-replicating RNA-type molecules, which were complex enough to undergo a Darwinian-type evolution (origin of the "RNA world"). However, so far there has been no explanation of how the first RNA-like biopolymers could originate and survive on the primordial Earth. Results: As condensation of sugar phosphates and nitrogenous bases is thermodynamically unfavorable, these compounds, if ever formed, should have undergone rapid hydrolysis. Thus, formation of oligonucleotide-like structures could have happened only if and when these structures had some selective advantage over simpler compounds. It is well known that nitrogenous bases are powerful quenchers of UV quanta and effectively protect the pentose-phosphate backbones of RNA and DNA from UV cleavage. To check if such a protection could play a role in abiogenic evolution on the primordial Earth (in the absence of the UV-protecting ozone layer), we simulated, by using Monte Carlo approach, the formation of the first oligonucleotides under continuous UV illumination. The simulations confirmed that UV irradiation could have worked as a selective factor leading to a relative enrichment of the system in longer sugar-phosphate polymers carrying nitrogenous bases as UV-protectors. Partial funneling of the UV energy into the condensation reactions could provide a further boost for the oligomerization. These results suggest that accumulation of the first polynucleotides could be explained by their abiogenic selection as the most UV-resistant biopolymers.
LUCA - letzter gemeinsamer Vorfahre allen Lebens
AL-SHAMERY:LEBEN HC O-BK, 2013
Proceedings of the National Academy of Sciences, 1999
The mechanism of proton transfer from the bulk into the membrane protein interior was studied. Th... more The mechanism of proton transfer from the bulk into the membrane protein interior was studied. The light-induced reduction of a bound ubiquinone molecule Q B by the photosynthetic reaction center is accompanied by proton trapping. We used kinetic spectroscopy to measure ( i ) the electron transfer to Q B (at 450 nm), ( ii ) the electrogenic proton delivery from the surface to the Q B site (by electrochromic carotenoid response at 524 nm), and ( iii ) the disappearance of protons from the bulk solution (by pH indicators). The electron transfer to Q B − and the proton-related electrogenesis proceeded with the same time constant of ≈100 μs (at pH 6.2), whereas the alkalinization in the bulk was distinctly delayed (τ ≈ 400 μs). We investigated the latter reaction as a function of the pH indicator concentration, the added pH buffers, and the temperature. The results led us to the following conclusions: ( i ) proton transfer from the surface-located acidic groups into the Q B site followe...
Photosynthetic electrogenic events in native membranes ofChloroflexus aurantiacus. Flash-induced charge displacements within the reaction center-cytochromec 554 complex
Photosynthesis Research, 1994
The thermophilic phototrophChloroflexus aurantiacus possesses a photosynthetic reaction center (R... more The thermophilic phototrophChloroflexus aurantiacus possesses a photosynthetic reaction center (RC) containing a pair of menaquinones as primary (QA) and secondary (QB) electron acceptors and a bacteriochlorophyll dimer (P) as a primary donor. A tetraheme cytochromec 554 with two high(H)- and two low(L)-potential hemes operates as an immediate electron donor for P. The following equilibrium Em,7 values were determined by ESR for the hemes in whole membrane preparations: 280 mV (H1), 150 mV (H2), 95 mV (L1) and 0 mV (L2) (Van Vliet et al. (1991) Eur. J. Biochem. 199: 317-323). Partial electrogenic reactions induced by a laser flash inChl. aurantiacus chromatophores adsorbed to a phospholipid-impregnated collodion film were studied electrometrically at pH 8.3. The photoelectric response included a fast phase of ΔΨ generation (τ < 10 ns, phase A). It was ascribed to the charge separation between P(+) and QA (-) as its amplitude decreased both at high and low Eh values (Em,high=360±10 mV, estimated Em,low∼\s-160 mV) in good agreement with Em values for P/P(+) and QA/QA (-) redox couples. A slower kinetic component appeared upon reduction of the cytochromec 554 hemes (phase C). With H1 reduced before the flash the amplitude of phase C was equal to 15-20% of that of phase A and its rise time was 1.2-1.3 μs: we attribute this phase to the electrogenic electron transfer from H1 to P(+). Pre-reduction of H2 decreased the τ value to about 700-800 ns and increased the amplitude of phase C to 30-35% of that of phase A. Pre-reduction of L1 further accelerated phase C (up to τ of 500 ns) and induced a reverse electrogenic phase with τ of 12 μs and amplitude equal to 10% of phase A. Upon pre-reduction of L2 the rise time of phase C was decreased to about 300 ns and its amplitude decreased by 30%. The acceleration in the onset of phase C is explained by the acceleration of the rate-limiting H1 ⇒ P electrogenic reaction after reduction of the other hemes due to their electrostatic influence; a P-H1-(L1-L2)-H2 alignment of redox centers with an approximately rhombic arrangement of the cytochromec 554 hemes is proposed. The observed reverse phase is ascribed to the post-flash charge redistribution between the hemes. Redox titration of the amplitude of phase C yielded the Em,8.3 values of H1, H2 and L2 hemes: 340±10 mV for H1, 160±20 mV for H2 and -40±40 mV for L2.
Photochemical & Photobiological Sciences, 2007
The cytochrome bc 1 complexes are proton-translocating, dimeric membrane ubiquinol:cytochrome c o... more The cytochrome bc 1 complexes are proton-translocating, dimeric membrane ubiquinol:cytochrome c oxidoreductases that serve as "hubs" in the vast majority of electron transfer chains. After each ubiquinol molecule is oxidized in the catalytic center P at the positively charged membrane side, the two liberated electrons head out, according to the Mitchell's Q-cycle mechanism, to different acceptors. One is taken by the [2Fe-2S] iron-sulfur Rieske protein to be passed further to cytochrome c 1 . The other electron goes across the membrane, via the low-and high-potential hemes of cytochrome b, to another ubiquinone-binding site N at the opposite membrane side. It has been assumed that two ubiquinol molecules have to be oxidized by center P to yield first a semiquinone in center N and then to reduce this semiquinone to ubiquinol. This review is focused on the operation of cytochrome bc 1 complexes in phototrophic purple bacteria. Their membranes provide a unique system where the generation of membrane voltage by light-driven, energy-converting enzymes can be traced via spectral shifts of native carotenoids and correlated with the electron and proton transfer reactions. An "activated Q-cycle" is proposed as a novel mechanism that is consistent with the available experimental data on the electron/proton coupling. Under physiological conditions, the dimeric cytochrome bc 1 complex is suggested to be continually primed by prompt oxidation of membrane ubiquinol via center N yielding a bound semiquinone in this center and a reduced, high-potential heme b in the other monomer of the enzyme. Then the oxidation of each ubiquinol molecule in center P is followed by ubiquinol formation in center N, proton translocation and generation of membrane voltage.
Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 2002
Photosystem II (PSII) oxidizes two water molecules to yield dioxygen plus four protons. Dioxygen ... more Photosystem II (PSII) oxidizes two water molecules to yield dioxygen plus four protons. Dioxygen is released during the last out of four sequential oxidation steps of the catalytic centre (S 0 ⇒ S 1 , S 1 ⇒ S 2 , S 2 ⇒ S 3 , S 3 ⇒ S 4 → S 0 ). The release of the chemically produced protons is blurred by transient, highly variable and electrostatically triggered proton transfer at the periphery (Bohr effect). The extent of the latter transiently amounts to more than one H + /e – under certain conditions and this is understood in terms of electrostatics. By kinetic analyses of electron–proton transfer and electrochromism, we discriminated between Bohr–effect and chemically produced protons and arrived at a distribution of the latter over the oxidation steps of 1 : 0 : 1 : 2. During the oxidation of tyr–161 on subunit D1 (Y Z ), its phenolic proton is not normally released into the bulk. Instead, it is shared with and confined in a hydrogen–bonded cluster. This notion is difficult to r...
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Papers by Armen Mulkidjanian