Stereoelectronic Properties of N-acetyl-α,β-dehydroamino acid N′-methylamides

Summary α,β-Dehydroamino acids are useful peptide modifiers. However, their stereoelectronic properties still remain insufficiently recognized. Based on FTIR experiments in the range ofv _s(N-H), AI, AII andv _s(C^α=C^β) and ab initio calculations with B3LYP/6–31G*, we studied the solution conformational preferences and the amide electron density perturbation of Ac-ΔXaa-NHMe, where ΔXaa=ΔAla, (E)-ΔAbu, (Z)-ΔAbu, (Z)-ΔLeu, (Z)-ΔPhe and ΔVal. Each of these dehydroamides adopts a C₅ structure, which in Ac-ΔAla-NHMe is fully extended and accompanied by the strong C₅ hydrogen bond. Interaction with bond C^α=C^β lessens the amidic resonance within the flanking amide groups. TheN-terminal C=O bond is noticeably shorter, both amide bonds are longer than the corresponding bonds in the saturated entities and the N-terminal amide system is distorted. Ac-ΔAla-NHMe constitutes an exception. ItsC-terminal amide bond is shorter than the standard one and both amide systems are ideally planar. Ac-(E)-ΔAbu-NHMe shares stereoelectronic features with both Ac-ΔAla-NHMe and (Z)-dehydroamides.     

Theoretical description of hydrogen bonding in oxalic acid dimer and trimer based on the combined extended-transition-state energy decomposition analysis and natural orbitals for chemical valence (ETS-NOCV)

In the present study we have analyzed hydrogen bonding in dimer and trimer of oxalic acid, based on a recently proposed charge and energy decomposition scheme (ETS-NOCV). In the case of a dimer, two conformations, α and β, were considered. The deformation density contributions originating from NOCV’s revealed that the formation of hydrogen bonding is associated with the electronic charge deformation in both the σ—(Δρ_σ) and π-networks (Δρ_π). It was demonstrated that σ-donation is realized by electron transfer from the lone pair of oxygen on one monomer into the empty r_{H - O}^* \rho_{H - O}^* orbital of the second oxalic acid fragment. In addition, a covalent contribution is observed by the density transfer from hydrogen of H-O group in one oxalic acid monomer to the oxygen atom of the second fragment. The resonance assisted component (Δρ_π), is based on the transfer of electron density from the π—orbital localized on the oxygen of OH on one oxalic acid monomer to the oxygen atom of the other fragment. ETS-NOCV allowed to conclude that the σ(O---HO) component is roughly eight times as important as π (RAHB) contribution in terms of energetic estimation. The electrostatic factor (ΔE_elstat) is equally as important as orbital interaction term (ΔE_orb). Finally, comparing β-dimer of oxalic acid with trimer we found practically no difference concerning each of the O---HO bonds, neither qualitative nor quantitative.     

Determination of the residue-specific 15N CSA tensor principal components using multiple alignment media

The individual components of the backbone ¹⁵N CSA tensor, σ₁₁, σ₂₂, σ₃₃, and the orientation of σ₁₁ relative to the NH bond described by the angle β have been determined for uniformly labeled ¹⁵N, ¹³C ubiquitin from partial alignment in phospholipid bicelles, Pf1 phage, and poly(ethylene glycol) by measuring the residue-specific residual dipolar couplings and chemical shift deviations. No strong correlation between any of the CSA tensor components is observed with any single structural feature. However, the experimentally determined tensor components agree with the previously determined average CSA principal components [Cornilescu and Bax (2000) J. Am. Chem. Soc. 122, 10143–10154]. Significant deviations from the averages coincide with residues in β-strand or extended regions, while α-helical residue tensor components cluster close to the average values.Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

Estimation of seasonal changes in translocation rates in leaves of a Japanese larch stand

To estimate the net rate of translocation in leaves of a larch stand, a new approach based on the summation method was proposed and given by a compartment model. The difference between the rate of translocation into and out of leaf biomass, namely, the net translocation rate (ΔT _r /Δt), was usually expressed by the difference between the growth rate of leaf biomass and the surplus production rate provided that the rate of leaf loss due to leaffall and grazing can be considered negligible. The rate, ΔT _r /Δt in a 19-yr-old larch stand, showed characteristic changes; it was positive from early April to late May, but after that it was negative until leaffall in late October. Our results confirmed that for the growth phase of positive ΔT _r /Δt translocation of assimilate stored in non-photosynthetic organs was indispensable for the growth. To quantify this, the ratio of ΔT _r /Δt to growth rate of leaf biomass was proposed.     

Computation of entropy contribution to protein-ligand binding free energy

The entropy contribution ΔS to protein-ligand binding free energy is studied for nine protein-lipid complexes. The entropy effect from the loss of the translational/rotational degrees of freedom (ΔS _tr) is calculated using the ideal gas approach. The change in the vibrational entropy (ΔS _vib) is calculated using the effective quantum oscillator approach with frequencies derived from the coordinate covariance matrix, so the inharmonic effects are taken into account. The change in the entropy of solvation (ΔS _solv) is considered using the binomial cell model (developed by the authors) for the hydrophobic effect. The entropy contribution from loss of conformations that are available for the free ligand (ΔS _conf) is also estimated. It is revealed that the negative in view of binding term ΔS _tr is only partly compensated by increasing of ΔS _vib, so T(ΔS _tr + ΔS _vib + ΔS _conf) < 0 for all complexes under investigation, but taking into account ΔS _solv leads to significantly increased ΔS. For all complexes except biotin-streptavidin, the results are found to be in reasonable agreement with experimental data. Published in Russian in Biokhimiya, 2007, Vol. 72, No. 7, pp. 963–973.     

Mechanosensitive ion channels in chara: influence of water channel inhibitors, HgCl2 and ZnCl2, on generation of receptor potential

Characean internodal cells generate receptor potential (ΔE _m) in response to mechanical stimuli. Upon a long-lasting stimulus, the cells generated ΔE _m at the moment of both compression and decompression, and the amplitude of ΔE _m at the moment of decompression, (ΔE _m)_E, was larger than that at compression. The long-lasting stimulus caused a membrane deformation (ΔD _m) having two components, a rapid one, (ΔD _m)_rapid, at the moment of compression and a slower one, (ΔD _m)_slow, during the long-lasting compression. We assumed that (ΔD _m)_slow might have some causal relation with the larger ΔE _m at (ΔE _m)_E. We treated internodal cells with either HgCl₂ or ZnCl₂, water channel inhibitors, to decrease (ΔD _m)_slow. Both inhibitors attenuated (ΔD _m)_slow during compression. Cells treated with HgCl₂ generated smaller (ΔE _m)_E compared to nontreated cells. On the other hand, cells treated with ZnCl₂ never attenuated (ΔE _m)_E but, rather, amplified it. Thus, the amplitude of (ΔD _m)_slow did not always show tight correlation with the amplitude of (ΔE _m)_E. Furthermore, when a constant deformation was applied to an internodal cell in a medium with higher or lower osmotic value, a cell having higher turgor always showed a larger (ΔE _m)_E. Thus, we concluded that changes in tension at the membrane may be the most important factor to induce activation of mechanosensitive Ca²⁺ channel.     

Microarray and real-time PCR analyses reveal mating type-dependent gene expression in a homothallic fungus

Sordaria macrospora is a homothallic ascomycete which is able to form fertile fruiting bodies without a mating partner. To analyze the molecular basis of homothallism and the role of mating products during fruiting body development, we have deleted the mating type gene Smta-1 encoding a high-mobility group domain (HMG) protein. The ΔSmta-1 deletion strain is morphologically wild type during vegetative growth, but it is unable to produce perithecia or ascospores. To identify genes expressed under control of Smta-1, we performed a cross-species microarray analysis using Neurospora crassa cDNA microarrays hybridized with S. macrospora targets. We identified 107 genes that are more than twofold up- or down-regulated in the mutant. Functional classification revealed that 81 genes have homologues with known or putative functions. Comparison of array data from ΔSmta-1 with those from three phenotypically similar mutants revealed that only a limited set of ten genes is deregulated in all mutants. Remarkably, the ppg2 gene encoding a putative lipopeptide pheromone is 500-fold down-regulated in the ΔSmta-1 mutant while in all other sterile mutants this gene is up-regulated. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Antennal response of codling moth males, Cydia pomonella L. (Lepidoptera: Tortricidae), to the geometric isomers of codlemone and codlemone acetate

Single sensillum recordings from Cydia pomonella male antennae showed three different types of receptor neurons. The most abundant type was most sensitive to the main pheromone compound (E,E)-8,10-dodecadienol, while its response to the geometric isomers E,Z, Z,E and Z,Z was comparable to a tenfold lower dose of (E,E)-8,10-dodecadienol. This neuron type also responded to the four behaviorally antagonistic isomers of (Δ,Δ)-8,10-dodecadienyl acetate, among which it was most sensitive to the E,E isomer. Cross-adaptation studies showed that these compounds were all detected by the same receptor neuron type. Receptor neurons specifically tuned to (E,Z) or (Z,Z)-8,10-dodecadienol were not found, although these two compounds are behaviorally active. A second type of receptor neuron responded to all isomers of (Δ,Δ)-8,10-dodecadienyl acetate and was most sensitive to the E,E isomer. This neuron type did not respond to any of the isomers of (Δ,Δ)-8,10-dodecadienol. A third receptor neuron type was highly sensitive to the plant compound α-farnesene. The finding that the receptor neuron type tuned to the main pheromone compound responded even to strong behavioral antagonists aids the interpretation of ongoing behavioral studies for the development of the mating disruption technique in codling moth. Accepted: 3 March 2000     

Kinetic and thermodynamic analysis of dimerization inhibitors binding to HIV protease monomers by surface plasmon resonance

The analysis of kinetic and thermodynamic parameters of binding of peptide and nonpeptide dimerization inhibitors of HIV protease (HIVp) to the enzyme monomers immobilized on an optical chip has been studied by surface plasmon resonance. The molecular interactions were investigated at different inhibitor concentrations (0–80 μM) and temperatures (15–35°C). Determination of kinetic (k _on, k _off), equilibrium (K _d), and thermodynamic (ΔG, ΔH, and -TΔS) has shown that both inhibitors are characterized by similar interaction parameters and the entropic term (-TΔS) of about −20 kcal/mol is the main driving force for the HIVp complex formation with the inhibitors, while the positive value (14 kcal/mol) of the enthalpic term (ΔH) counteracted the complex formation.     

Probing binding site of bacteriochlorophyll a and carotenoid in the reconstituted LH1 complex from Rhodospirillum rubrum S1 by Stark spectroscopy

Stark spectroscopy is a powerful technique to investigate the electrostatic interactions between pigments as well as between the pigments and the proteins in photosynthetic pigment–protein complexes. In this study, Stark spectroscopy has been used to determine two nonlinear optical parameters (polarizability change Tr(Δα) and static dipole-moment change |Δμ| upon photoexcitation) of isolated and of reconstituted LH1 complexes from the purple photosynthetic bacterium, Rhodospirillum (Rs.) rubrum. The integral LH1 complex was prepared from Rs. rubrum S1, while the reconstituted complex was assembled by addition of purified carotenoid (all-trans-spirilloxanthin) to the monomeric subunit of LH1 from Rs. rubrum S1. The reconstituted LH1 complex has its Q_y absorption maximum at 878 nm. This is shifted to the blue by 3 nm in comparison to the isolated LH1 complex. The energy transfer efficiency from carotenoid to bacteriochlorophyll a (BChl a), which was determined by fluorescence excitation spectroscopy of the reconstituted LH1 complex, is increased to 40%, while the efficiency in the isolated LH1 complex is only 28%. Based on the differences in the values of Tr(Δα) and |Δμ|, between these two preparations, we can calculate the change in the electric field around the BChl a molecules in the two situations to be E _Δ ≈ 3.4 × 10⁵ [V/cm]. This change can explain the 3 nm wavelength shift of the Q_y absorption band in the reconstituted LH1 complex.     

Stereoselective and driving-force-dependent photoinduced electron-transfer reactions of zinc myoglobin with optically active N,N′-dimethylcinchoninium and N,N′-dimethylcinchonidinium ions

In order to understand the detailed mechanism of the stereoselective photoinduced electron-transfer (ET) reactions of zinc-substituted myoglobin (ZnMb) with optically active molecules by flash photolysis, we designed and prepared new optically active agents, such as N,N′-dimethylcinchoninium diiodide ([MCN]I₂) and N,N′-dimethylcinchonidinium diiodide ([MCD]I₂). The photoexcited triplet state of ZnMb, ³(ZnMb)*, was successfully quenched by [MCN]²⁺ and [MCD]²⁺ ions to form the radical pair of ZnMb cation (ZnMb^·+) and reduced [MCN]^·+ and [MCD]^·+, followed by a thermal back ET reaction to the ground state. The rate constants (k _q) for the ET quenching at 25 °C were obtained as k _q(MCN)=(1.9±0.1)×10⁶ M⁻¹ s⁻¹ and k _q(MCD)=(3.0±0.2)×10⁶ M⁻¹ s⁻¹, respectively. The ratio of k _q(MCD)/k _q(MCN)=1.6 indicates that the [MCD]²⁺ preferentially quenches ³(ZnMb)*. The second-order rate constants (k _b) for the thermal back ET reaction from [MCN]^·+ and [MCD]^·+ to ZnMb^·+ at 25 °C were k _b(MCN)=(0.79±0.04)×10⁸ M⁻¹ s⁻¹ and k _b(MCD)=(1.0±0.1)×10⁸ M⁻¹ s⁻¹, respectively, and the selectivity was k _q(MCD)/k _q(MCN)=1.3. Both quenching and thermal back ET reactions are controlled by the ET step. In the quenching reaction, the energy differences of ΔΔH ^≠(MCD–MCN) and ΔΔS ^≠(MCD–MCN) at 25 °C were obtained as −1.1 and 0 kJ mol⁻¹, respectively. On the other hand, ΔΔH ^≠(MCD–MCN)=11±2 kJ mol⁻¹ and TΔΔS ^≠(MCD–MCN)=−10±2 kJ mol⁻¹ were given in the thermal back ET reaction. The highest stereoselectivity of 1.7 for [MCD]^·+ found at low temperature (10 °C) was due to the ΔΔS ^≠ value obtained in the thermal back ET reaction. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Energetics of superhelicity and of B-Z transitions in superhelical DNA

The linking difference, α, imposed upon a superhelically constrained DNA molecule must be partitioned between twisting and bending deformations. Transitions to alternative secondary structures can occur at susceptible sites, altering the local molecular twist by an amount ΔTw _trans. That part of the linking difference not accommodated in this way, the residual linking difference α_res, must be manifested as smooth torsional and flexural deformations of secondary structure. The competition among the alternative ways of accommodating the imposed linking difference α determines a stressed equilibrium state. The superhelical free energy,G(α), is the excess free energy of the equilibrium state at linking difference α above that of the relaxed state under identical conditions. In this paper a method is described by which the free energies associated both to linking,G(α), and to residual linking differences can be determined from data on superhelical conformational transitions. The application of this approach to previously published experimental data on the B-Z transition suggests that the free energy associated with α_res is about 30% larger at substantial superhelicities than it is near the relaxed state. At the onset of transition the functional form ofG(α) is shown to change in a manner dependent upon the length of the Z-susceptible site.     

Chemotactic collapse for the Keller-Segel model

 This work is concerned with the system (S) {u _t =Δu − χ∇ (u∇v) for x∈Ω, t>0Γ v _t =Δv+(u−1) for x∈Ω, t>0 where Γ, χ are positive constants and Ω is a bounded and smooth open set in ℝ². On the boundary ∂Ω, we impose no-flux conditions: (N) ∂u∂n =∂v∂n =0 for x∈∂ Ω, t>0 Problem (S), (N) is a classical model to describe chemotaxis corresponding to a species of concentration u(x, t) which tends to aggregate towards high concentrations of a chemical that the species releases. When completed with suitable initial values at t=0 for u(x, t), v(x, t), the problem under consideration is known to be well posed, locally in time. By means of matched asymptotic expansions techniques, we show here that there exist radial solutions exhibiting chemotactic collapse. By this we mean that u(r, t) →Aδ(y) as t→T for some T<∞, where A is the total concentration of the species. Received 9 March 1995; received in revised form 25 December 1995     

Effect of two intermediate electron donors, NADPH and FADH2, on Spirulina Δ6-desaturase co-expressed with two different immediate electron donors, cytochrome b 5 and ferredoxin, in Escherichia coli

When the gene desD encoding Spirulina Δ⁶-desaturase was heterologously expressed in E. coli, the enzyme was expressed without the ability to function. However, when this enzyme was co-expressed with an immediate electron donor, i.e. the cytochrome b ₅ domain from Mucor rouxii, the results showed the production of GLA (γ-linolenic acid), the product of the reaction catalyzed by Δ⁶-desaturase. The results revealed that in E. coli cells, where cytochrome b ₅ is absent and ferredoxin, a natural electron donor of Δ⁶-desaturase, is present at a very low level, the cytochrome b ₅ domain can complement for the function of ferredoxin in the host cells. In the present study, the Spirulina-ferredoxin gene was cloned and co-expressed with the Δ⁶-desaturase in E. coli. In comparison to the co-expression of cytochrome b ₅ with the Δ⁶-desaturase, the co-expression with ferredoxin did not cause any differences in the GLA level. Moreover, the cultures containing the Δ⁶-desaturase co-expressed with cytochrome b ₅ and ferredoxin were exogenously supplied with the intermediate electron donors, NADPH (nicotinamide adenine dinucleotide phosphate, reduced form) and FADH₂ (flavin adenine dinucleotide, reduced form), respectively. The GLA level in these host cells increased drastically, by approximately 50%, compared to the cells without the intermediate electron donors. The data indicated that besides the level of immediate electron donors, the level of intermediate electron donors is also critical for GLA production. Therefore, if the pools of the immediate and intermediate electron donors in the cells are manipulated, the GLA production in the heterologous host will be affected.     

A mathematical model for the dynamics of large membrane deformations of isolated fibroblasts

In this paper we develop and extend a previous model of cell deformations, initially proposed to describe the dynamical behaviour of round-shaped cells such as keratinocytes or leukocytes, in order to take into account cell pseudopodial dynamics with large amplitude membrane deformations such as those observed in fibroblasts. Beyond the simulation (from a quantitative, parametrized model) of the experimentally observed oscillatory cell deformations, a final goal of this work is to underline that a set of common assumptions regarding intracellular actin dynamics and associated cell membrane local motion allows us to describe a wide variety of cell morphologies and protrusive activity. The model proposed describes cell membrane deformations as a consequence of the endogenous cortical actin dynamics where the driving force for large-amplitude cell protrusion is provided by the coupling between F-actin polymerization and contractility of the cortical actomyosin network. Cell membrane movements then result of two competing forces acting on the membrane, namely an intracellular hydrostatic protrusive force counterbalanced by a retraction force exerted by the actin filaments of the cell cortex. Protrusion and retraction forces are moreover modulated by an additional membrane curvature stress. As a first approximation, we start by considering a heterogeneous but stationary distribution of actin along the cell periphery in order to evaluate the possible morphologies that an individual cell might adopt. Then non-stationary actin distributions are considered. The simulated dynamic behaviour of this cytomechanical model not only reproduces the small amplitude rotating waves of deformations of round-shaped cells such as keratinocytes [as proposed in the original model of Alt and Tranquillo (1995, J. Biol. Syst. 3, 905–916)] but is furthermore in very good agreement with the protrusive activity of cells such as fibroblasts, where large amplitude contracting/retracting pseudopods are more or less periodically extended in opposite directions. In addition, the biophysical and biochemical processes taken into account by the cytomechanical model are characterized by well-defined parameters which (for the majority) can be discussed with regard to experimental data obtained in various experimental situations.     

Low Shear Rheology of Concentrated Tomato Products. Effect of Particle Size and Time

Time-dependent rheological properties of three tomato paste suspensions in the concentration range of 200–1,000 g paste/kg suspension have been investigated by using the vane geometry at shear rates . Creep tests were conducted to analyze the influence of the level of stress on the rheological behavior of the samples before and after homogenization. The experimental results indicate that the suspensions exhibit an elastic behavior at long times and relatively low stresses, which proves that this type of material can be characterized by a yield stress (σ _y). Applying stresses just beyond the yield stress, an initial rheopectic behavior appeared. This increase in viscosity at low deformations was markedly larger after homogenization, and this difference was attributed to changes in the aspect ratio, shape, and orientation of the particles induced by homogenization. These structural changes were also reflected in the transient viscosity when the samples were subjected to larger stresses (σ >> σ _y): before homogenization the suspensions exhibited a steady-state viscosity at large deformations, whereas after homogenization, the transient viscosity continuously decreased. That behavior was attributed to flocculation of the particles. This work was partially presented at the “4th International Symposium on Food Rheology and Structure” in February 19–23, 2006, Zürich, Switzerland.     

Cytochrome f from the Antarctic psychrophile, Chlamydomonas raudensis UWO 241: structure, sequence, and complementation in the mesophile, Chlamydomonas reinhardtii

Although cytochrome f from the Antarctic psychrophile, Chlamydomonas raudensis UWO 241, exhibits a lower apparent molecular mass (34 kD) than that of the mesophile C. reinhardtii (41 kD) based on SDS-PAGE, both proteins are comparable in calculated molecular mass and show 79% identity in amino acid sequence. The difference in apparent molecular mass was maintained after expression of petA from both Chlamydomonas species in either E. coli or a C. reinhardtii ΔpetA mutant and after substitution of a unique third cysteine-292 to phenylalanine in the psychrophilic cytochrome f. Moreover, the heme of the psychrophilic form of cytochrome f was less stable upon heating than that of the mesophile. In contrast to C. raudensis, a C. reinhardtii ΔpetA mutant transformed with petA from C. raudensis exhibited the ability to undergo state transitions and a capacity for intersystem electron transport comparable to that of C. reinhardtii wild type. However, the C. reinhardtii petA transformants accumulated lower levels of cytochrome b ₆ /f complexes and exhibited lower light saturated rates of O₂ evolution than C. reinhardtii wild type. We show that the presence of an altered form of cytochrome f in C. raudensis does not account for its inability to undergo state transitions or its impaired capacity for intersystem electron transport as previously suggested. A combined survey of the apparent molecular mass, thermal stability and amino acid sequences of cytochrome f from a broad range of mesophilic species shows unequivocally that the observed differences in cytochrome f structure are not related to psychrophilly. Thus, caution must be exercised in relating differences in amino acid sequence and thermal stability to adaptation to cold environments. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.