The mycocidal, membrane-active complex of Cryptococcus humicola is a new type of cellobiose lipid with detergent features

The chemical composition of the mycocidal complex (formerly known as microcin) secreted by Cryptococcus humicola was investigated by chemical, mass spectrometric and nuclear magnetic resonance methods. The results indicate that the mycocidal complex is composed of glycolipids with a highly acetylated (up to five acetyl groups) cellobiose backbone [β-D-Glcp-(1′→4)-β-D-Glcp] linked to the ω-hydroxyl group of α,ω-dihydroxy palmitate [16:0-α,ω-di-OH] with an unsubstituted carboxyl group. The acyl chain forming aglycon can be replaced by [18:0-(α,ω-di-OH)], [18:0-(α,ω-1,ω-tri-OH)], and [18:0-(α,ω-2,ω-tri-OH)]. The complex has a comparatively high surface activity; 0.5 mg/ml of it reduced the surface tension of 0.1 M NaHCO₃ from 71 mN/m to 37 mN/m and interfacial tension against n-hexadecane from 39 mN/m to 10 mN/m. The critical micelle concentration of the complex at pH 4.0, determined by the fluorometric method with N-phenyl-1-naphthylamine as fluorescent probe and by the De Nouy ring method, was 2×10⁻⁵ M (taking the average molecular mass of the complex to be 750); it did not depend on the presence of 100 mM KCl and was an order of magnitude higher at pH 7.0. By fluorescence resonance energy transfer spectroscopy with N-(7-nitro-2,1,3-benzoxadiazol-4-yl)-phosphatidylethanolamine as energy donor and N-(rhodamine B sulfonyl)-phosphatidylethanolamine as energy acceptor the complex was shown to intercalate into the liposomal lipid matrix. Primary lesions caused by the complex in planar lipid bilayers were revealed as short-living current fluctuations of a broad spectrum of amplitudes. The mycocidal effect of the complex is suggested to be associated with its detergent-like properties.     

Energy transfer and molecular switching II. Muscle contraction and enzymatic reactions

In Part I (Barrett, 1981), the concept of chemical parametric excitation was reviewed and applied to the process of nerve action potential excitation and regeneration. In the present paper, the chemical reactions involved in muscle contraction and the enzymatic reaction are examined and shown to be examples of chemical parametric excitation.It is demonstrated that in a model biochemical scheme for an enzymatic reaction, the enzyme is activated from a state, X, to a state, $\text{X}{}^1$, and in this activated state pumps the reaction parametrically. The concept of enzyme is identified with an excited state or state of disequilibrium permitting a release of energy during the dissipation, $\text{X}{}^1\text{→X}$, in the enzymatic reaction, which is powered by the release of energy in the return to the unexcited state X. The demonstration of parametric excitation relations for chemical systems indicates an explanation for the directionality of energy flow and designates an energy pumping role for an enzyme.In muscle contraction, the role of $\text{X}{}^1$ is played by actomyosin and Ca²⁺, and the enzymatic reaction is the hydrolysis of ATP. The release of energy caused by this hydrolysis reaction brings about the conformational changes underlying muscle contraction.     

Picosecond time-resolved energy transfer in Porphyridium cruentum. Part I. In the intact alga

The wavelength-resolved fluorescence emission kinetics of the accessory pigments and chlorophyll a in Porphyridium cruentum have been studied by picosecond laser spectroscopy. Direct excitation of the pigment B-phycoerythrin with a 530 nm, 6 ps pulse produced fluorescence emission from all of the pigments as a result of energy transfer between the pigments to the reaction centre of Photosystem II. The emission from B-phycoerythrin at 576 nm follows a nonexponential decay law with a mean fluorescence lifetime of 70 ps, whereas the fluorescence from R-phycocyanin (640 nm), allophycocyanin (660 nm) and chlorophyll a (685 nm) all appeared to follow an exponential decay law with lifetimes of 90 ps, 118 ps and 175 ps respectively. Upon closure of the Photosystem II reaction centres with 3-(3,4-dichlorophenyl)-1,1-dimethylurea and preillumination the chlorophyll a decay became non-exponential, having a long component with an apparent lifetime of 840 ps. The fluorescence from the latter three pigments all showed finite risetimes to the maximum emission intensity of 12 ps for R-phycocyanin, 24 ps for allophycocyanin and 50 ps for chlorophyll a.A kinetic analysis of these results indicates that energy transfer between the pigments is at least 99% efficient and is governed by an exp $\text{?At}{}^{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}$ transfer function. The apparent exponential behaviour of the fluorescence decay functions of the latter three pigments is shown to be a direct result of the energy transfer kinetics, as are the observed risetimes in the fluorescence emissions.     

Scaling behaviors of weighted food webs as energy transportation networks

Food webs can be regarded as energy transporting networks in which the weight of each edge denotes the energy flux between two species. By investigating 21 empirical weighted food webs as energy flow networks, we found several ubiquitous scaling behaviors. Two random variables A_i and C_i defined for each vertex i, representing the total flux (also called vertex intensity) and total indirect effect or energy store of i, were found to follow power law distributions with the exponents α≈1.32 and β≈1.33, respectively. Another scaling behavior is the power law relationship, , where η≈1.02. This is known as the allometric scaling power law relationship because A_i can be treated as metabolism and C_i as the body mass of the sub-network rooted from the vertex i, according to the algorithm presented in this paper. Finally, a simple relationship among these power law exponents, η=(α−1)/(β−1), was mathematically derived and tested by the empirical food webs.     

Energy transfer pathways in the CAC light-harvesting complex of Rhodomonas salina

Photosynthetic organisms had to evolve diverse mechanisms of light-harvesting to supply photosynthetic apparatus with enough energy. Cryptophytes represent one of the groups of photosynthetic organisms combining external and internal antenna systems. They contain one type of immobile phycobiliprotein located at the lumenal side of the thylakoid membrane, together with membrane-bound chlorophyll a/c antenna (CAC). Here we employ femtosecond transient absorption spectroscopy to study energy transfer pathways in the CAC proteins of cryptophyte Rhodomonas salina. The major CAC carotenoid, alloxanthin, is a cryptophyte-specific carotenoid, and it is the only naturally-occurring carotenoid with two triple bonds in its structure. In order to explore the energy transfer pathways within the CAC complex, three excitation wavelengths (505, 590, and 640 nm) were chosen to excite pigments in the CAC antenna. The excitation of Chl c at either 590 or 640 nm proves efficient energy transfer between Chl c and Chl a. The excitation of alloxanthin at 505 nm shows an active pathway from the S₂ state with efficiency around 50%, feeding both Chl a and Chl c with approximately 1:1 branching ratio, yet, the S₁-route is rather inefficient. The 57 ps energy transfer time to Chl a gives ~25% efficiency of the S₁ channel. The low efficiency of the S₁ route renders the overall carotenoid-Chl energy transfer efficiency low, pointing to the regulatory role of alloxanthin in the CAC antenna.     

The site of inhibition of mitochondrial electron transfer by coenzyme Q analogues.

The effects of 33 quinone derivatives on mitochondrial electron transfer in yeast were examined. Twenty-two of the compounds were also tested for their effects on the growth of yeast cells. Four strong inhibitors of electron transfer were identified: 5-n-undecyl-6-hydroxy-4, 7-dioxobenzothiazole, 7-ω-cyclohexyloctyl-6-hydroxy-5,8-quinolinequinone, 7-n-hexadecyl-mercapto-6-hydroxy-5, 8-quinolinequinone, and 3-n-dodecylmercapto-2-hydroxy-1, 4-naphthoquinone. They inhibit the growth of yeast with ethanol as an energy source, but not when glucose is the energy source. The NADH oxidase activity of isolated mitochondria is 50% inhibited by these quinone derivatives at about 10^?8m, or 0.5 μmol/g mitochondrial protein; 1000-fold higher concentrations do not affect electron transfer from NADH or succinate to coenzyme Q₂. The effects of the inhibitors on cytochrome spectra indicate that they block electron transfer between cytochromes b and c₁. A possible antagonism between these compounds and coenzyme Q at a site between cytochromes b and C₁ is discussed in terms of Mitchell's “protonmotive Q cycle” hypothesis (Mitchell, P. (1976) J. Theor. Biol. 62, 327–367). 6-β-naphthylmercapto-5-chloro-2,3-dimethoxy-1,4-benzoquinone inhibits electron transfer between succinate and coenzyme Q₂ or phenazine methosulfate, suggesting a site in the succinate-coenzyme Q reductase complex with a different quinone specificity from that of the site in the cytochrome bc₁ complex. Seven of the quinone derivatives inhibit growth on both glucose and ethanol media, indicating that their effect is not the result of inhibition of respiration.     

Photosynthetic Acclimation to Temperature in the Desert Shrub, Larrea divaricata: II. Light-harvesting Efficiency and Electron Transport

The response of photosynthetic electron transport and light-harvesting efficiency to high temperatures was studied in the desert shrub Larrea divaricata Cav. Plants were grown at day/night temperatures of 20/15, 32/25, or 45/33 C in rough approximation of natural seasonal temperature variations. The process of acclimation to high temperatures involves an enhancement of the stability of the interactions between the light-harvesting pigments and the photosystem reaction centers. As temperature is increased, the heat-induced dissociation of these complexes results in a decrease in the quantum yield of electron transport at limiting light intensity, followed by a loss of electron transport activity at rate-saturating light intensity. The decreased quantum yield can be attributed to a block of excitation energy transfer from chlorophyll b to chlorophyll a, and changes in the distribution of the excitation energy between photosystems II and I. The block of excitation energy transfer is characterized by a loss of the effectiveness of 480 nm light (absorbed primarily by chlorophyll b) to drive protochemical processes, as well as fluorescence emission by chlorophyll b.     

Ultrafast multi-pulse transient absorption spectroscopy of fucoxanthin chlorophyll a protein from Phaeodactylum tricornutum

We have applied femtosecond transient absorption spectroscopy in pump-probe and pump-dump-probe regimes to study energy transfer between fucoxanthin and Chl a in fucoxanthin-Chl a complex from the pennate diatom Phaeodactylum tricornutum. Experiments were carried out at room temperature and 77?K to reveal temperature dependence of energy transfer. At both temperatures, the ultrafast (<100?fs) energy transfer channel from the fucoxanthin S₂ state is active and is complemented by the second pathway via the combined S₁/ICT state. The S₁/ICT-Chl a pathway has two channels, the fast one characterized by sub-picosecond energy transfer, and slow having time constants of 4.5?ps at room temperature and 6.6?ps at 77?K. The overall energy transfer via the S₁/ICT is faster at 77?K, because the fast component gains amplitude upon lowering the temperature. The pump-dump-probe regime, with the dump pulse centered in the spectral region of ICT stimulated emission at 950?nm and applied at 2?ps after excitation, proved that the S₁ and ICT states of fucoxanthin in FCP are individual, yet coupled entities. Analysis of the pump-dump-probe data suggested that the main energy donor in the slow S₁/ICT-Chl a route is the S₁ part of the S₁/ICT potential surface.     

Excitation and emission wavelength dependence of fluorescence spectra in whole cells of the cyanobacterium Synechocystis sp. PPC6803: Influence on the estimation of Photosystem II maximal quantum efficiency

The fluorescence emission spectrum of Synechocystis sp. PPC6803 cells, at room temperature, displays: i) significant bandshape variations when collected under open (F₀) and closed (F_M) Photosystem II reaction centre conditions; ii) a marked dependence on the excitation wavelength both under F₀ and F_M conditions, due to the enhancement of phycobilisomes (PBS) emission upon their direct excitation. As a consequence: iii) the ratio of the variable and maximal fluorescence (F_V/F_M), that is a commonly employed indicator of the maximal photochemical quantum efficiency of PSII (Φ_{pc, PSII}), displays a significant dependency on both the excitation and the emission (detection) wavelength; iv) the F_V/F_M excitation/emission wavelength dependency is due, primarily, to the overlap of PSII emission with that of supercomplexes showing negligible changes in quantum yield upon trap closure, i.e. PSI and a PBS fraction which is incapable to transfer the excitation energy efficiently to core complexes. v) The contribution to the cellular emission and the relative absorption-cross section of PSII, PSI and uncoupled PBS are extracted using a spectral decomposition strategy. It is concluded that vi) Φ_{pc, PSII} is generally underestimated from the F_V/F_M measurements in this organism and, the degree of the estimation bias, which can exceed 50%, depends on the measurement conditions. Spectral modelling based on the decomposed emission/cross-section profiles were extended to other processes typically monitored from steady-state fluorescence measurements, in the presence of an actinic illumination, in particular non-photochemical quenching. It is suggested that vii) the quenching extent is generally underestimated in analogy to F_V/F_M but that viii) the location of quenching sites can be discriminated based on the combined excitation/emission spectral analysis.     

PSI-SMALP,a Detergent-free Cyanobacterial Photosystem I,Reveals Faster Femtosecond Photochemistry

Cyanobacterial photosystem I (PSI) functions as a light-driven cyt c₆-ferredoxin/oxidoreductase located in the thylakoid membrane. In this work, the energy and charge transfer processes in PSI complexes isolated from Thermosynechococcus elongatus via conventional n-dodecyl-β-D-maltoside solubilization (DM-PSI) and a, to our knowledge, new detergent-free method using styrene-maleic acid copolymers (SMA-PSI) have been investigated by pump-to-probe femtosecond laser spectroscopy. In DM-PSI preparations excited at 740 nm, the excitation remained localized on the long-wavelength chlorophyll forms within 0.1–20 ps and revealed little or no charge separation and oxidation of the special pair, P700. The formation of ion-radical pair P700⁺A1⁻ occurred with a characteristic time of 36 ps, being kinetically controlled by energy transfer from the long-wavelength chlorophyll to P₇₀₀. Quite surprisingly, the detergent-free SMA-PSI complexes upon excitation by these long-wave pulses undergo an ultrafast (<100 fs) charge separation in ∼45% of particles. In the remaining complexes (∼55%), the energy transfer to P₇₀₀ occurred at ∼36 ps, similar to the DM-PSI. Both isolation methods result in a trimeric form of PSI, yet the SMA-PSI complexes display a heterogenous kinetic behavior. The much faster rate of charge separation suggests the existence of an ultrafast pathway for charge separation in the SMA-PSI that may be disrupted during detergent isolation.     

Excitation relaxation dynamics and energy transfer in fucoxanthin–chlorophyll a/c-protein complexes,probed by time-resolved fluorescence

In algae, light-harvesting complexes contain specific chlorophylls (Chls) and keto-carotenoids; Chl a, Chl c, and fucoxanthin (Fx) in diatoms and brown algae; Chl a, Chl c, and peridinin in photosynthetic dinoflagellates; and Chl a, Chl b, and siphonaxanthin in green algae. The Fx–Chl a/c-protein (FCP) complex from the diatom Chaetoceros gracilis contains Chl c₁, Chl c₂, and the keto-carotenoid, Fx, as antenna pigments, in addition to Chl a. In the present study, we investigated energy transfer in the FCP complex associated with photosystem II (FCPII) of C. gracilis. For these investigations, we analyzed time-resolved fluorescence spectra, fluorescence rise and decay curves, and time-resolved fluorescence anisotropy data. Chl a exhibited different energy forms with fluorescence peaks ranging from 677 nm to 688 nm. Fx transferred excitation energy to lower-energy Chl a with a time constant of 300 fs. Chl c transferred excitation energy to Chl a with time constants of 500–600 fs (intra-complex transfer), 600–700 fs (intra-complex transfer), and 4–6 ps (inter-complex transfer). The latter process made a greater contribution to total Chl c-to-Chl a transfer in intact cells of C. gracilis than in the isolated FCPII complexes. The lower-energy Chl a received excitation energy from Fx and transferred the energy to higher-energy Chl a. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: Keys to Produce Clean Energy.     

Energy transfer in purple bacterial photosynthetic units from cells grown in various light intensities

Three photosynthetic membranes, called intra-cytoplasmic membranes (ICMs), from wild-type and the ?pucBA_abce mutant of the purple phototrophic bacterium Rps. palustris were investigated using optical spectroscopy. The ICMs contain identical light-harvesting complex 1–reaction centers (LH1–RC) but have various spectral forms of light-harvesting complex 2 (LH2). Spectroscopic studies involving steady-state absorption, fluorescence, and femtosecond time-resolved absorption at room temperature and at 77 K focused on inter-protein excitation energy transfer. The studies investigated how energy transfer is affected by altered spectral features of the LH2 complexes as those develop under growth at different light conditions. The study shows that LH1 → LH2 excitation energy transfer is strongly affected if the LH2 complex alters its spectroscopic signature. The LH1 → LH2 excitation energy transfer rate modeled with the Förster mechanism and kinetic simulations of transient absorption of the ICMs demonstrated that the transfer rate will be 2–3 times larger for ICMs accumulating LH2 complexes with the classical B800–850 spectral signature (grown in high light) compared to the ICMs from the same strain grown in low light. For the ICMs from the ?pucBA_abce mutant, in which the B850 band of the LH2 complex is blue-shifted and almost degenerate with the B800 band, the LH1 → LH2 excitation energy transfer was not observed nor predicted by calculations.     

The architecture of Rhodobacter sphaeroides chromatophores

The chromatophores of Rhodobacter (Rb.) sphaeroides represent a minimal bio-energetic system, which efficiently converts light energy into usable chemical energy. Despite extensive studies, several issues pertaining to the morphology and molecular architecture of this elemental energy conversion system remain controversial or unknown. To tackle these issues, we combined electron microscope tomography, immuno-electron microscopy and atomic force microscopy. We found that the intracellular Rb. sphaeroides chromatophores form a continuous reticulum rather than existing as discrete vesicles. We also found that the cytochrome bc₁ complex localizes to fragile chromatophore regions, which most likely constitute the tubular structures that interconnect the vesicles in the reticulum. In contrast, the peripheral light-harvesting complex 2 (LH2) is preferentially hexagonally packed within the convex vesicular regions of the membrane network. Based on these observations, we propose that the bc₁ complexes are in the inter-vesicular regions and surrounded by reaction center (RC) core complexes, which in turn are bounded by arrays of peripheral antenna complexes. This arrangement affords rapid cycling of electrons between the core and bc₁ complexes while maintaining efficient excitation energy transfer from LH2 domains to the RCs.     

Caulobacter zeae sp. nov. and Caulobacter radicis sp. nov., novel endophytic bacteria isolated from maize root (Zea mays L.)

Four bacterial strains designated 410^T, 441, 695^T and 736 were isolated from maize root in Beijing, P. R. China. Based on 16S rRNA gene phylogeny, the four strains formed two clusters in the genus Caulobacter. Since strain 441 was a clonal variety of strain 410^T, only three strains were selected for further taxonomic studies. The whole genome average nucleotide identity (ANI) value between strains 410^T and 695^T was 94.65%, and both strains shared less than 92.10% ANI values with their close phylogenetic neighbors Caulobacter vibrioides DSM 9893^T, Caulobacter segnis ATCC 21756^T and Caulobacter flavus CGMCC 1.15093^T. Strains 410^T and 695^T contained Q-10 as the sole ubiquinone and their major fatty acids were C_{16:0, 11-methyl C18:1ω 0}, 11-methyl C_{18: 1}ω7c, summed feature 3 (C_{16:1ω7c and/or C16:1ω 1}ω7c and/or C_{16: 1}ω6c) and summed feature 8 (C_{18:1ω7c and/or C18:1ω 1}ω7c and/or C_{18: 1}ω6c). Their major polar lipids consisted of glycolipids and phosphatidylglycerol, and phenotypic tests differentiated them from their closest phylogenetic neighbors. Based on the results obtained, it is proposed that the three strains represent two novel species, for which the names Caulobacter zeae sp. nov. (type strain 410^T = CGMCC 1.15991 = DSM 104304) and Caulobacter radicis sp. nov. (type strain 695^T = CGMCC 1.16556 = DSM 106792) are proposed.     

Estimating Orientation Factors in the FRET Theory of Fluorescent Proteins: The TagRFP-KFP Pair and Beyond

The orientation factor κ², one of the key parameters defining Förster resonance energy transfer efficiency, is determined by the transition dipole moment orientations of the donor and acceptor species. Using the results of quantum chemical and quantum mechanical/molecular mechanical calculations for the chromophore-containing pockets in selected colored proteins of the green fluorescent protein family, we derived transition dipole moments corresponding to the S_0,min → S₁ excitation for green fluorescent protein, red fluorescent protein (TagRFP), and kindling fluorescent protein, and the S_1,min → S₀ emission for TagRFP. These data allowed us to estimate κ² values for the TagRFP-linker-kindling fluorescent protein tetrameric complex required for constructing novel sensors.     

An assessment to evaluate the validity of different methods for the description of some corrosion inhibitors

New research and development efforts using computational chemistry in studying an assessment of the validity of different quantum chemical methods to describe the molecular and electronic structures of some corrosion inhibitors were introduced. The standard and the highly accurate CCSD method with 6-311++G(d,p), ab initio calculations using the HF/6-31G++(d,p) and MP2 with 6-311G(d,p), 6-31++G(d,p), and 6-311++G(2df,p) methods as well as DFT method at the B3LYP, BP86, B3LYP*, M06L, and M062x/6-31G++(d,p) basis set level were performed on some triazole derivatives and sulfur containing compounds used as corrosion inhibitors. Quantum chemical parameters, such as the energy of the highest occupied molecular orbital energy (E_HOMO), the energy of the lowest unoccupied molecular orbital energy (E_LUMO), energy gap (ΔE), dipole moment (μ), sum of total negative charges (TNC), chemical potential (Pi), electronegativity (χ), hardness (η), softness (σ), local softness (s), Fukui functions (f ⁺,f ^?), electrophilicity (ω), the total energy change (?E_T) and the solvation energy (S.E), were calculated. Furthermore, the accuracy and the applicability of these methods were estimated relative to the highest accuracy and standard CCSD with 6-311++G(d,p) method. Good correlations between the quantum chemical parameters and the corresponding inhibition efficiency (IE%) were found.     

Intramolecular migration of excitation energy in poly-DL-phenylalanine. Study by fluorescence extinction

Electronic energy transfer at the singlet level in poly-DL -phenylalanine was studied by comparing the experimental and theoretical values of the rate constants of fluorescence quenching by CCl₄ and of energy transfer on a fluorescent acceptor (biacetyl). The fitting of the experimental and calculated values leads to a diffusion coefficient of the excitation energy of 3.8 to 4.8 × 10^?5 cm²/s, consistent with 40 residues implied in the migration process.     

Role of fatty acids in cold adaptation of Antarctic psychrophilic Flavobacterium spp.

Cold-loving microorganisms developed numerous adaptation mechanisms allowing them to survive in extremely cold habitats, such as adaptation of the cell membrane. The focus of this study was on the membrane fatty acids of Antarctic Flavobacterium spp., and their adaptation response to cold-stress. Fatty acids and cold-response of Antarctic flavobacteria was also compared to mesophilic and thermophilic members of the genus Flavobacterium. The results showed that the psychrophiles produced more types of major fatty acids than meso- and thermophilic members of this genus, namely C_15:1 iso G, C_15:0 iso, C_15:0 anteiso, C_15:1 ω6c, C_15:0 iso 3OH, C_17:1 ω6c, C_16:0 iso 3OH and C_17:0 iso 3OH, summed features 3 (C_16:1 ω7cand/or C_16:1 ω6c) and 9 (C_16:0 10-methyl and/or C_17:1 iso ω9c). It was shown that the cell membrane of psychrophiles was composed mainly of branched and unsaturated fatty acids. The results also implied that Antarctic flavobacteria mainly used two mechanisms of membrane fluidity alteration in their cold-adaptive response. The first mechanism was based on unsaturation of fatty acids, and the second mechanism on de novo synthesis of branched fatty acids. The alteration of the cell membrane was shown to be similar for all thermotypes of members of the genus Flavobacterium.     

Wavelength-dependent photocycle activity of xanthorhodopsin in the visible region

Xanthorhodopsin (xR) is a dual-chromophore proton-pump photosynthetic protein comprising one retinal Schiff base and one light-harvesting antenna salinixanthin (SX). The excitation wavelength-dependent transient population of the intermediate M demonstrates that the excitation of the retinal at 570 nm leads to the highest photocycle activity and the excitations of SX at 460 and 430 nm reduce the activity to ca. 37% relatively, suggesting an energy transfer pathway from the S₂ state of the SX to the S₁ state of the retinal and a quick internal vibrational relaxation in the S₂ state of SX prior to the energy transfer from SX to retinal.