Oligomeric-State-Dependent Conformational Change of the BLUF Protein TePixD (Tll0078)

The photochemical reaction dynamics of a BLUF (sensors of blue light using FAD) protein, PixD, from a thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (TePixD, Tll0078) were studied by pulsed laser-induced transient grating method. After the formation of an intermediate species with a red-shifted absorption spectrum, two new reaction phases reflecting protein conformational changes were discovered; one reaction phase manifested itself as expansion of partial molar volume with a time constant of 40 μs, whereas the other reaction phase represented a change in the diffusion coefficient D [i.e., the diffusion-sensitive conformational change (DSCC)]. D decreased from 4.9 × 10^− 11 to 4.4 × 10^− 11 m² s^− 1 upon the formation of the first intermediate, and subsequently showed a more pronounced decrease to 3.2 × 10^− 11 m² s^− 1 upon formation of the second intermediate. From a global analysis of signals at various grating wavenumbers, the time constant of D-change was determined to be 4 ms. Although the magnitude and rate constant of the faster volume change were independent of protein concentration, the amplitude of the signal that reflects the later DSCC significantly decreased as the protein concentration decreased. This concentration dependence suggests that two species exist in solution: a reactive species exhibiting the DSCC, and a second species that is nonreactive. The fraction of these species was found to be dependent on the concentration. The difference in reactivity was attributed to the different oligomeric states of TePixD (i.e., pentamer and decamer). The equilibrium of these states in the dark was confirmed by size-exclusion chromatography at various concentrations. These results demonstrated that only the decamer state is responsible for the conformational change. The results may suggest that the oligomeric state is functionally important in the signal transduction of this photosensory protein.     

Determination os sedimentation coefficient distributions for cartilage proteoglycans

Sedimentation coefficient distributions of widely polydisperse proteoglycan preparations were made using a previously developed transport sedimentation methodology. Boundary stability was improved by centrifuging samples in a preformed CsCl density gradient (0.016 g/cm⁴). The results were compared with the distributions obtained with an interferometric analytical centrifugation method. When these two techniques were applied to analyze A1 and A1–D1 proteoglycan preparations, results were in substantial agreement with respect to the mean sedimentation coefficients of the peaks, average S value, sedimentation coefficient distribution, skewness, proportion of monomer and aggregates, and linearity of the plot ln(s) versus C extrapolations to zero concentration. The lower solute concentration compatible with the transport (velocity gradient) method makes this technique particularly suitable for studying the details of proteoglycan distribution of molecular sizes, especially for aggregates.     

Transmembrane cholesterol migration in planar lipid membranes measured with Vibrio cholerae cytolysin as molecular tool

The rate of transbilayer movement (flip-flop) of cholesterol was estimated using planar bilayers with defined initial asymmetry, formed by the opposing monolayers technique. Vibrio cholerae cytolysin (VCC) was utilized as a molecular tool for measuring the cholesterol concentration in the cis leaflet of asymmetric bilayers. To quantify cholesterol flip-flop in planar lipid bilayers, a mathematical model was developed. It considers both the lateral diffusion rate of cholesterol within each monolayer and the flip-flop rate. The difference in initial and steady-state cholesterol contents in bilayer leaflets was used as a start point. Assuming the lateral diffusion coefficient to be of 1 × 10⁻⁸ cm² s⁻¹, the characteristic time of cholesterol flip-flop at 25 ± 2 °C was estimated as <10 s.     

Diffusion of the Reaction Boundary of Rapidly Interacting Macromolecules in Sedimentation Velocity

Sedimentation velocity analytical ultracentrifugation combines relatively high hydrodynamic resolution of macromolecular species with the ability to study macromolecular interactions, which has great potential for studying dynamically assembled multiprotein complexes. Complicated sedimentation boundary shapes appear in multicomponent mixtures when the timescale of the chemical reaction is short relative to the timescale of sedimentation. Although the Lamm partial differential equation rigorously predicts the evolution of concentration profiles for given reaction schemes and parameter sets, this approach is often not directly applicable to data analysis due to experimental and sample imperfections, and/or due to unknown reaction pathways. Recently, we have introduced the effective particle theory, which explains quantitatively and in a simple physical picture the sedimentation boundary patterns arising in the sedimentation of rapidly interacting systems. However, it does not address the diffusional spread of the reaction boundary from the cosedimentation of interacting macromolecules, which also has been of long-standing interest in the theory of sedimentation velocity analytical ultracentrifugation. Here, effective particle theory is exploited to approximate the concentration gradients during the sedimentation process, and to predict the overall, gradient-average diffusion coefficient of the reaction boundary. The analysis of the heterogeneity of the sedimentation and diffusion coefficients across the reaction boundary shows that both are relatively uniform. These results support the application of diffusion-deconvoluting sedimentation coefficient distributions c(s) to the analysis of rapidly interacting systems, and provide a framework for the quantitative interpretation of the diffusional broadening and the apparent molar mass values of the effective sedimenting particle in dynamically associating systems.     

Cyanobacterial cytochrome cM: Probing its role as electron donor for CuA of cytochrome c oxidase

It is well known that efficient functioning of photosynthetic (PET) and respiratory electron transport (RET) in cyanobacteria requires the presence of either cytochrome c₆ (Cytc₆) or plastocyanin (PC). By contrast, the interaction of an additional redox carrier, cytochrome c_M (Cytc_M), with either PET or RET is still under discussion. Here, we focus on the (putative) role of Cytc_M in cyanobacterial respiration. It is demonstrated that genes encoding the main terminal oxidase (cytochrome c oxidase, COX) and cytochrome c_M are found in all 44 totally or partially sequenced cyanobacteria (except one strain). In order to check whether Cytc_M can act as electron donor to COX, we investigated the intermolecular electron transfer kinetics between Cytc_M and the soluble Cu_A domain (i.e. the donor binding and electron entry site) of subunit II of COX. Both proteins from Synechocystis PCC6803 were expressed heterologously in E. coli. The forward and the reverse electron transfer reactions were studied yielding apparent bimolecular rate constants of (2.4 ± 0.1) × 10⁵ M^− 1 s^− 1 and (9.6 ± 0.4) × 10³ M^− 1 s^− 1 (5 mM phosphate buffer, pH 7, 50 mM KCl). A comparative analysis with Cytc₆ and PC demonstrates that Cytc_M functions as electron donor to Cu_A as efficiently as Cytc₆ but more efficient than PC. Furthermore, we demonstrate the association of Cytc_M with the cytoplasmic and thylakoid membrane fractions by immunobloting and discuss the potential role of Cytc_M as electron donor for COX under stress conditions.     

Low temperature solution behaviour of Methylophilus methylotrophus electron transferring flavoprotein: a study by analytical ultracentrifugation

The solution behaviour of electron transferring flavoprotein (ETF) from Methylophilus methylotrophus was investigated at low temperature (4 °C) by analytical ultracentrifugation. The concentration dependence of the apparent weight average molecular weight, M_w,app, established the existence of the protein in heterodimeric state (M = 63,700 Da), but also signified the possible dissociation of the heterodimer at lower concentrations into its constituent subunits (M = 28,900 Da and 33,700 Da, together with FAD and AMP cofactors of collective M = 1120 Da). This similarity in subunit size allows approximate quantification of the dissociation in terms of expressions for a monomer-dimer equilibrium. The dissociative behaviour was confirmed by determination of the point average molecular weight, M_w,app(r), as a function of the ETF concentration, c(r), throughout the sedimentation equilibrium distributions obtained with loading concentrations of 0.4 and 0.7 mg/ml. By means of the recently formulated ``psi' procedure for direct analysis of solute self-association a value of (1.5 ± 0.1) μM has been obtained for the dissociation constant K_d. Sedimentation velocity experiments yielded an estimate of the heterodimer sedimentation coefficient, s⁰ _20,w, of (4.5 ± 0.2) S which for M = 63,700 Da suggests a globular structure. Received: 29 November 1996 / Accepted: 2 December 1996     

Sedimentation coefficients of self-associating species: I. Basic theory

Under the same solution conditions, the apparent weight average sedimentation coefficient, s_wa, and some quantities obtained from it can be combined with the equilibrium constant or constants, K_i, and the monomer concentration, c_I, obtained from sedimentation equilibrium, light scattering or osmotic pressure experiments on the same self-associating solute, so that the individual sedimentation coefficients, s_i, of the self-associating species, and also the hydrodynamic concentration dependence parameter,g or $\text{g}$, can be evaluated. Using two different models for the hydrodynamic concentration parameter, four different methods are presented for the evaluation of the s_i's. Methods for evaluating g or $\text{g}$, once the s_i's are known, are presented. A method for obtaining the number average sedimentation coefficient, s_N, and its application to self-associations is presented. Methods are shown for the evaluation of Z average properties, x_zc, as well as number average properties,x_Nc, of a self-associating solute from its weight average properties, x_wc.     

Single-Molecule Kinetics Reveal Cation-Promoted DNA Duplex Formation Through Ordering of Single-Stranded Helices

In this work, the kinetics of short, fully complementary oligonucleotides are investigated at the single-molecule level. Constructs 6–9 bp in length exhibit single exponential kinetics over 2 orders of magnitude time for both forward (k_on, association) and reverse (k_off, dissociation) processes. Bimolecular rate constants for association are weakly sensitive to the number of basepairs in the duplex, with a 2.5-fold increase between 9 bp (k′_on = 2.1(1) × 10⁶ M⁻¹ s⁻¹) and 6 bp (k′_on = 5.0(1) × 10⁶ M⁻¹ s⁻¹) sequences. In sharp contrast, however, dissociation rate constants prove to be exponentially sensitive to sequence length, varying by nearly 600-fold over the same 9 bp (k_off = 0.024 s⁻¹) to 6 bp (k_off = 14 s⁻¹) range. The 8 bp sequence is explored in more detail, and the NaCl dependence of k_on and k_off is measured. Interestingly, k_onincreases by >40-fold (k_on = 0.10(1) s⁻¹ to 4.0(4) s⁻¹ between [NaCl] = 25 mM and 1 M), whereas in contrast, k_offdecreases by fourfold (0.72(3) s⁻¹ to 0.17(7) s⁻¹) over the same range of conditions. Thus, the equilibrium constant (K_eq) increases by ≈160, largely due to changes in the association rate, k_on. Finally, temperature-dependent measurements reveal that increased [NaCl] reduces the overall exothermicity (ΔΔH° > 0) of duplex formation, albeit by an amount smaller than the reduction in entropic penalty (−TΔΔS° < 0). This reduced entropic cost is attributed to a cation-facilitated preordering of the two single-stranded species, which lowers the association free-energy barrier and in turn accelerates the rate of duplex formation.     

Acrylonitrile Quenching of Trp Phosphorescence in Proteins: A Probe of the Internal Flexibility of the Globular Fold

Quenching of Trp phosphorescence in proteins by diffusion of solutes of various molecular sizes unveils the frequency-amplitude of structural fluctuations. To cover the sizes gap between O₂ and acrylamide, we examined the potential of acrylonitrile to probe conformational flexibility of proteins. The distance dependence of the through-space acrylonitrile quenching rate was determined in a glass at 77 K, with the indole analog 2-(3-indoyl) ethyl phenyl ketone. Intensity and decay kinetics data were fitted to a rate, k(r) = k₀ exp[−(r − r₀)/r_e], with an attenuation length r_e = 0.03 nm and a contact rate k₀ = 3.6 × 10¹⁰ s⁻¹. At ambient temperature, the bimolecular quenching rate constant (kq) was determined for a series of proteins, appositely selected to test the importance of factors such as the degree of Trp burial and structural rigidity. Relative to kq = 1.9 × 10⁹ M⁻¹s⁻¹ for free Trp in water, in proteins kq ranged from 6.5 × 10⁶ M⁻¹s⁻¹ for superficial sites to 1.3 × 10² M⁻¹s⁻¹ for deep cores. The short-range nature of the interaction and the direct correlation between kq and structural flexibility attest that in the microsecond-second timescale of phosphorescence acrylonitrile readily penetrates even compact protein cores and exhibits significant sensitivity to variations in dynamical structure of the globular fold.     

Effects of current speed, shell length and type of sediment on the erosion and transport of juvenile softshell clams (Mya arenaria)

The erosion and transport of juvenile softshell clams (Mya arenaria) was studied in a laboratory flume in relation to free-stream velocity (0, 7, 16, 29 and 35 cm s^− 1), shell length (0-5, 5-10, 10-15, 15-20 mm) and type of sediment (mud, sandy-mud, sand and gravel). Our results showed that these factors interact together on the erosion of clams from the sediment. Juveniles were eroded in great numbers in sand while mud retained them more easily. Bedload transport was initiated at speeds of 16 cm s^− 1. Most of the clams were eroded in sandy sediments at speeds of 29 and 35 cm s^− 1. The smallest individuals were highly vulnerable to erosion compared to the other size classes studied. A results-based model using the logistic regression statistics was proposed. This allowed the estimation of erosion probabilities for a given hydrosedimentary environment. A field validation of the model was then carried out. Field results confirmed the importance of free-stream velocity, shell length and type of sediment on the erosion rate of clams. The differences observed between predicted and field results suggest that the model underestimated the erosion rate in the field. Results are discussed in the context of hydrosedimentary environments found off the eastern coast of Canada.     

The Macroscopic Rate of Nucleic Acid Translocation by Hepatitis C Virus Helicase NS3h Is Dependent on Both Sugar and Base Moieties

The nonstructural protein 3 helicase (NS3h) of hepatitis C virus is a 3′-to-5′ superfamily 2 RNA and DNA helicase that is essential for the replication of hepatitis C virus. We have examined the kinetic mechanism of the translocation of NS3h along single-stranded nucleic acid with bases uridylate (rU), deoxyuridylate (dU), and deoxythymidylate (dT), and have found that the macroscopic rate of translocation is dependent on both the base moiety and the sugar moiety of the nucleic acid, with approximate macroscopic translocation rates of 3 nt s^− 1 (oligo(dT)), 35 nt s^− 1 (oligo(dU)), and 42 nt s^− 1 (oligo(rU)), respectively. We found a strong correlation between the macroscopic translocation rates and the binding affinity of the translocating NS3h protein for the respective substrates such that weaker affinity corresponded to faster translocation. The values of K_0.5 for NS3h translocation at a saturating ATP concentration are as follows: 3.3 ± 0.4 μM nucleotide (poly(dT)), 27 ± 2 μM nucleotide (poly(dU)), and 36 ± 2 μM nucleotide (poly(rU)). Furthermore, results of the isothermal titration of NS3h with these oligonucleotides suggest that differences in TΔS⁰ are the principal source of differences in the affinity of NS3h binding to these substrates. Interestingly, despite the differences in macroscopic translocation rates and binding affinities, the ATP coupling stoichiometries for NS3h translocation were identical for all three substrates (∼ 0.5 ATP molecule consumed per nucleotide translocated). This similar periodicity of ATP consumption implies a similar mechanism for NS3h translocation along RNA and DNA substrates.     

Spontaneous, intervesicular transfer rates of fluorescent, acyl chain-labeled phosphatidylcholine analogs

It was recently shown that the structure of the fluorophore attached to the acyl chain of phosphatidylcholine analogs determines their mechanism of transport across the plasma membrane of yeast cells (Elvington et al., J. Biol Chem. 280:40957, 2005). In order to gain further insight into the physical properties of these fluorescent phosphatidylcholine (PC) analogs, the rate and mechanism of their intervesicular transport was determined. The rate of spontaneous exchange was measured for PC analogs containing either NBD (7-nitrobenz-2-oxa-1,3-diazol-4-yl), Bodipy FL (4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene), Bodipy 530 (4,4-difluoro-5,7-diphenyl-4-bora-3a,4a-diaza-s-indacene), or Bodipy 581 (4,4-difluoro-5-(4-phenyl-1,3-butadienyl)-4-bora-3a,4a-diaza-s-indacene) attached to a five or six carbon acyl chain in the sn-2 position. The rate of transfer between phospholipid vesicles was measured by monitoring the increase in fluorescence as the analogs transferred from donor vesicles containing self-quenching concentrations to unlabeled acceptor vesicles. Kinetic analysis indicated that the transfer of each analog occurred by diffusion through the water phase as opposed to transfer during vesicle collisions. The vesicle-to-monomer dissociation rate constants differed by over four orders of magnitude: NBD-PC (k_dis = 0.115 s^− 1; t_1/2 = 6.03 s); Bodipy FL-PC (k_dis = 5.2 × 10^− 4; t_1/2 = 22.2 min); Bodipy 530-PC (k_dis = 1.52 × 10^− 5; t_1/2 = 12.6 h); and Bodipy 581-PC (k_dis = 5.9 × 10^− 6; t_1/2 = 32.6 h). The large differences in spontaneous rates of transfer through the water measured for these four fluorescent PC analogs reflect their hydrophobicity and may account for their recognition by different mechanisms of transport across the plasma membrane of yeast.     

The effect of flow turbulence on plant growth and several growth regulators in Egeria densa Planchon

The effects of turbulence velocity on Egeria densa Planchon was studied for 12 weeks using mechanically oscillating grid-generated turbulence without mean flow. The root-mean-square of the turbulence velocity fluctuations (u′) ranged from 1.62 ± 0.44 to 2.86 ± 0.8 cm s⁻¹ (high turbulence), 1.36 ± 0.2 to 1.86 ± 0.78 cm s⁻¹ (medium turbulence) and 0.67 ± 0.12 to 0.81 ± 0.16 cm s⁻¹ (low turbulence). The control was subjected to gentle manual mixing once a day. Shoot elongation was significantly reduced with increasing turbulence intensity, and the endogenous indole acetic acid (IAA) concentration was significantly decreased with increasing turbulence intensity and exposure time. The plants exposed to high turbulence showed a 64.6% decrease in endogenous IAA concentration compared to the control, while it was decreased only 26.9% in plants exposed to low turbulence. IAA and cytokinin catabolism was increased, and there was an increase in the hydrogen peroxide concentration of the tissues, which triggered peroxidase activity. The total chlorophyll and chlorophyll a content decreased with the time of exposure. Although the flow turbulence negatively affected plant growth and metabolism, all of the plants survived for the experimental period.     

Direct observation of swimming behaviour in a shallow-water scavenging amphipod Scopelocheirus onagawae in relation to chemoreceptive foraging

Direct observations on foraging behaviour of scavenging lysianassid amphipods have been limited, and no previous study has examined the effect of food odour quantitatively on the behaviour. The present study recorded the swimming behaviour of the amphipod Scopelocheirus onagawae using videographic techniques before and after the introduction of food odour (amino acid solution). S. onagawae showed consistent nocturnal activity swimming at a high speed (16.8 cm s^− 1) with an approximately straight trajectory in various directions before and after the introduction of odour in which the amino acid concentration was below the behavioural threshold concentration for this species (1.0 × 10^− 7 mol l^− 1). High speed multidirectional linear swimming is thought to be advantageous for these amphipods, enabling them to survey across a broad area. After the first encounter with the odour plume above the behavioural threshold concentration, the amphipods slowed down their swimming speed (ca. 9.7 cm s^− 1) with a short time-lag (ca. 0.42 s), and thereafter they frequently turned so that they remained within the odour plume. Once moved out of the odour plume, the amphipods quickly returned to the plume with a shorter response time (ca. 0.1 s) than that in the first detection of the odour plume, suggesting that the sensory adaptation is involved with the tracking of the odour. Our study demonstrated that chemoreception is a major factor causing behavioural change in scavenging amphipods at the edge of the odour plume.     

Promiscuity, stability and cold adaptation of a newly isolated acylaminoacyl peptidase

We report on the characterisation of a member of the acylaminoacyl peptidase family, the first isolated from bacteria. The enzyme was obtained from the psychrophilic bacterium Sporosarcina psychrophila and shows the typical features of cold adaptation (low T_m, optimal temperature of 40 °C, poor thermal stability). It was also tested for substrate specificity, effect of metals, temperature dependence and structure stability and revealed promiscuous catalytic activity on at least two chemically distinct substrates, with k_cat/K_m values for ester hydrolysis and acylamino acids cleavage of 1.7 × 10⁴ s⁻¹ M⁻¹ and 6.2 × 10³ s⁻¹ M⁻¹, respectively. Despite some properties cannot be explained with current models, results report on the relevance of structural and catalytic properties for the successful adaptation to cold temperatures.     

Sedimentation-Diffusion Equilibrium of Monomer-Dimer Mixtures, Studied in the Analytical Ultracentrifuge

By generalizing the fundamental differential equation valid for a single ideal solute, it is usual to define, for a monomer-dimer nonideal mixture, an apparent molecular weight M_w,app = (2RT/[1 - ρV]ω²) (d lnc/dr²); RT has the usual meaning; ρ is the density of the solvent; V is the partial specific volume of the solute, assumed to be the same for the monomer and the dimer; w is the angular velocity of the rotor; c is the solute concentration at the radial position r in the cell. It is shown here that the above equation can be integrated in the case of a monomer-dimer nonideal mixture and that, after integration, we obtain the following relation between c and r: ([1 + 4Kc]^1/2 - 1)/([1 + 4Kc₀]^1/2 - 1]) exp (BM_m[c - c₀]) = exp ([σ_m/2] [r² - r₀²]); σ_m = M_m(1 - ρV)ω²/RT (M_m = molecular weight of the monomer); K is the monomer-dimer equilibrium constant; B is the second virial coefficient, assumed to be the same for the monomer and the dimer. As soon as M_m is known, the above equation permits the calculation of K and B, from the experimental curve c(r). Moreover, the reversibility of the monomer-dimer equilibrium can be tested from this equation: it is necessary and sufficient that the values of K corresponding to different loading concentrations in the cell are identical.     

Determination of protein complex stoichiometry through multisignal sedimentation velocity experiments

Determination of the stoichiometry of macromolecular assemblies is fundamental to an understanding of how they function. Many different biophysical methodologies may be used to determine stoichiometry. In the past, both sedimentation equilibrium and sedimentation velocity analytical ultracentrifugation have been employed to determine component stoichiometries. Recently, a method of globally analyzing multisignal sedimentation velocity data was introduced by Schuck and coworkers. This global analysis removes some of the experimental inconveniences and inaccuracies that could occur in the previously used strategies. This method uses spectral differences between the macromolecular components to decompose the well-known c(s) distribution into component distributions c_k(s); that is, each component k has its own c_k(s) distribution. Integration of these distributions allows the calculation of the populations of each component in cosedimenting complexes, yielding their stoichiometry. In our laboratories, we have used this method extensively to determine the component stoichiometries of several protein-protein complexes involved in cytoskeletal remodeling, sugar metabolism, and host-pathogen interactions. The overall method is described in detail in this work, as are experimental examples and caveats.     

Structure and characterization of amidase from Rhodococcus sp. N-771: Insight into the molecular mechanism of substrate recognition

In this study, we have structurally characterized the amidase of a nitrile-degrading bacterium, Rhodococcus sp. N-771 (RhAmidase). RhAmidase belongs to amidase signature (AS) family, a group of amidase families, and is responsible for the degradation of amides produced from nitriles by nitrile hydratase. Recombinant RhAmidase exists as a dimer of about 107 kDa. RhAmidase can hydrolyze acetamide, propionamide, acrylamide and benzamide with kcat/Km values of 1.14 ± 0.23 mM^− 1s^− 1, 4.54 ± 0.09 mM^− 1s^− 1, 0.087 ± 0.02 mM^− 1s^− 1 and 153.5 ± 7.1 mM^− 1s^− 1, respectively. The crystal structures of RhAmidase and its inactive mutant complex with benzamide (S195A/benzamide) were determined at resolutions of 2.17 Å and 2.32 Å, respectively. RhAmidase has three domains: an N-terminal α-helical domain, a small domain and a large domain. The N-terminal α-helical domain is not found in other AS family enzymes. This domain is involved in the formation of the dimer structure and, together with the small domain, forms a narrow substrate-binding tunnel. The large domain showed high structural similarities to those of other AS family enzymes. The Ser-cis Ser-Lys catalytic triad is located in the large domain. But the substrate-binding pocket of RhAmidase is relatively narrow, due to the presence of the helix α13 in the small domain. The hydrophobic residues from the small domain are involved in recognizing the substrate. The small domain likely participates in substrate recognition and is related to the difference of substrate specificities among the AS family amidases.