The hydrolysis of primary amide groups in Asn/Gln-containing peptides

Peptides Boc-Ala-Asn/Gln-OH and Boc-Asn/Gln-Ala-OH were saponified with barium hydroxide to corresponding Asp/Glu-containing peptides. Under the conditions of saponification, Boc-Asn-Ala-OH additionally afforded Boc-Asp-OH, isopeptide Boc-Asp(Ala)-OH, and Boc-NHSuc>Ala-OH, with the third being the key intermediate in these transformations. Boc-Asp(OMe)-Ala-OMe underwent similar transformations under treatment with diazomethane or triethylamine. Saponification with barium hydroxide was accompanied by a high epimerization ofN-terminal amino acid residues, whereas the products of the diazomethane treatment of Boc-Asp(OMe)-Ala-OMe had a low degree of epimerization.     

Ramachandran analysis of conserved glycyl residues in homologous proteins of known structure

High conservation of glycyl residues in homologous proteins is fairly frequent. It is commonly understood that glycine tends to be highly conserved either because of its unique Ramachandran angles or to avoid steric clash that would arise with a larger side chain. Using a database of aligned 3D structures of homologous proteins we identified conserved Gly in 288 alignment positions from 85 families. Ninety‐six of these alignment positions correspond to conserved Gly residue with (φ, ψ) values allowed for non‐glycyl residues. Reasons for this observation were investigated by in‐silico mutation of these glycyl residues to Ala. We found in 94% of the cases a short contact exists between the C^β atom of the introduced Ala with the atoms which are often distant in the primary structure. This suggests the lack of space even for a short side chain thereby explaining high conservation of glycyl residues even when they adopt (φ, ψ) values allowed for Ala. In 189 alignment positions, the conserved glycyl residues adopt (φ, ψ) values which are disallowed for Ala. In‐silico mutation of these Gly residues to Ala almost always results in steric hindrance involving C^β atom of Ala as one would expect by comparing Ramachandran maps for Ala and Gly. Rare occurrence of the disallowed glycyl conformations even in ultrahigh resolution protein structures are accompanied by short contacts in the crystal structures and such disallowed conformations are not conserved in the homologues. These observations raise the doubt on the accuracy of such glycyl conformations in proteins.     

Elucidation of the structure of constrained bicyclopeptides in solution by two-dimensional cross-relaxation spectroscopy: Amatoxin analogues

The evaluation of peptide structures in solution is made feasible by the combined use of two-dimensional NMR in the laboratory (NOESY) and rotating frames (ROESY), and by the use of molecular dynamics calculations. The present paper describes how both the NMR method and molecular dynamics calculations were applied to very rigid synthetic bicyclic peptides that are analogues of natural amatoxins. The NMR theory, which allows the estimate of interatomic distances between interacting nuclei, is briefly discussed. The experimental data were compared with those of known solid-state structures. Three amatoxin analogues have been examined. Of these, one is biologically active (S-deoxo γ[R] OH-Ile³-amaninamide) and its structure in the solid state has recently been worked out. The second and third analogues (S-deoxo-Ile³ -Ala⁵-amaninamide and S-deoxo-D -Ile³ -amaninamide, respectively) are inactive and their solid-state structures are unknown. The data presented confirm the authors' previous hypothesis that lack of biological activity of S-deoxo-Ile³-Ala⁵- amaninamide is due to the masking of the tryptophan ring by the methyl group of L -Ala and not to massive conformational changes of the analogue.     

Conformational Characterization of the 1-Aminocyclobutane-1-carboxylic Acid Residue in Model Peptides

A series of N- and C-protected, monodispersed homo-oligopeptides (to the dodecamer level) from the small-ring alicyclic C^α,α-dialkylated glycine 1-aminocyclobutane-1-carboxylic acid (Ac₄c) and two Ala/Ac₄c tripeptides were synthesized by solution methods and fully characterized. The conformational preferences of all the model peptides were determined in deuterochloroform solution by FT-IR absorption and ¹H-NMR. The molecular structures of the amino acid derivatives Z-Ac₄c-OH and Z₂-Ac₄c-OH, the tripeptides Z-(Ac₄c)₃-OtBu, Z-Ac₄c-(L -Ala)₂-OMe and Z-L -Ala-Ac₄c-L -Ala-OMe, and the tetrapeptide Z-(Ac₄c)₄-OtBu were determined in the crystal state by X-ray diffraction. The average geometry of the cyclobutyl moiety of the Ac₄c residue was assessed and the τ(N–C^α–C′) bond angle was found to be significantly expanded from the regular tetrahedral value. The conformational data are strongly in favour of the conclusion that the Ac₄c residue is an effective β-turn and helix former. A comparison with the structural propensities of α-aminoisobutyric acid, the prototype of C^α,α-dialkylated glycines, and the other extensively investigated members of the family of 1-aminocycloalkane-1-carboxylic acids (Ac_nc, with n=3, 5–8) is made and the implications for the use of the Ac₄c residue in conformationally constrained peptide analogues are briefly examined. © 1997 European Peptide Society and John Wiley & Sons, Ltd     

Complex I Controls Mitochondrial and Plasma Membrane Potentials in Nerve Terminals

Reductions in the activities of mitochondrial electron transport chain (ETC) enzymes have been implicated in the pathogenesis of numerous chronic neurodegenerative disorders. Maintenance of the mitochondrial membrane potential (Δψ_m) is a primary function of these enzyme complexes, and is essential for ATP production and neuronal survival. We examined the effects of inhibition of mitochondrial ETC complexes I, II/III, III and IV activities by titrations of respective inhibitors on Δψ_m in synaptosomal mitochondria. Small perturbations in the activity of complex I, brought about by low concentrations of rotenone (1–50 nM), caused depolarisation of Δψ_m. Small decreases in complex I activity caused an immediate and partial Δψ_m depolarisation, whereas inhibition of complex II/III activity by more than 70% with antimycin A was required to affect Δψ_m. A similarly high threshold of inhibition was found when complex III was inhibited with myxothiazol, and inhibition of complex IV by more than 90% with KCN was required. The plasma membrane potential (Δψ_p) had a complex I inhibition threshold of 40% whereas complex III and IV had to be inhibited by more than 90% before changes in Δψ_p were registered. These data indicate that in synaptosomes, both Δψ_m and Δψ_p are more susceptible to reductions in complex I activity than reductions in the other ETC complexes. These findings may be of relevance to the mechanism of neuronal cell death in Parkinson’s disease in particular, where such reductions in complex I activity are present.

     

Conformationally constrained D,L-alternating oligopeptides

The possibility of selectively reducing the number of β-helical structures theoretically possible for a D ,L -alternating peptide by using a N-methyl group as conformational constraint is considered. Some ¹H-nmr data regarding Boc(L -Nle-D -Nle)₃-L -Nle-D -MeNle -L -Nle-D -Nle-L -Nle-OMe (I), its formyl analogue (II), and the pentadecapeptide Boc(D -Leu-L -Leu)₅-D -MeLeu -(L -Leu-D -Leu)₂-OMe (III) are presented. It is shown that these alternating stereocooligopeptides with a N-methyl group in the (n ? 3) (I and II) or (n ? 4) position (III) differ drastically in their behavior from the corresponding nonmethylated compounds. In chloroform, I and II form predominantly ↑↓ β^7.2-helices and III forms almost exclusively ↑↓ β^5.6 or ↑↓ β^7.2-helices. The helices are in every case those having the maximum possible number of interchain H bonds.     

Optimal balancing of xylem efficiency and safety explains plant vulnerability to drought

In vast areas of the world, forests and vegetation are water limited and plant survival depends on the ability to avoid catastrophic hydraulic failure. Therefore, it is remarkable that plants take hydraulic risks by operating at water potentials (ψ) that induce partial failure of the water conduits (xylem). Here we present an eco-evolutionary optimality principle for xylem conduit design that explains this phenomenon based on the hypothesis that conductive efficiency and safety are optimally co-adapted to the environment. The model explains the relationship between the tolerance to negative water potential (ψ₅₀) and the environmentally dependent minimum ψ (ψ_min) across a large number of species, and along the xylem pathway within individuals of two species studied. The wider hydraulic safety margin in gymnosperms compared to angiosperms can be explained as an adaptation to a higher susceptibility to accumulation of embolism. The model provides a novel optimality-based perspective on the relationship between xylem safety and efficiency.     

Seasonal Changes in Water Potential and Turgor Maintenance in Sorghum and Maize under Water Stress

Leaf water (Ψ) and solute (ψ) potential were measured in field sorghum and maize under well irrigated (I) and dryland (NI) conditions throughout a season. Despite decreases in ψ due to slow soil water depletion and to apparent increases in liquid phase plant resistance, midday leaf turgor (ψ_p) in the NI sorghum was maintained at similar levels as in the I treatment throughout the season due to concomitant decreases in ψ_s. Osmotic adjustment was also observed in maize, although ψ_p was significantly lower in the NI treatment as compared to I during the final stages of grain filling. A seasonal shift in the ψ vs. relative water content relation of NI sorghum leaves was observed, more water being retained by the older leaf at any particular ψ. The major factor for turgor maintenance was a net increase in solutes per unit of tissue. The role played by increases in the proportion of tissue volume occupied by cell wall was also evaluated. No stomatal closure due to water stress was found in NI sorghum even though leaf ψ reached —20 bars late in the season. Under similar conditions, stomata closed at —14 to —16 bars in younger plants where water stress was made to develop much faster.     

Statistical torsion angle potential energy functions for protein structure modeling: A bicubic interpolation approach

A set of grid type knowledge‐based energy functions is introduced for ?–χ₁, ψ–χ₁, ?–ψ, and χ₁–χ₂ torsion angle combinations. Boltzmann distribution is assumed for the torsion angle populations from protein X‐ray structures, and the functions are named as statistical torsion angle potential energy functions. The grid points around periodic boundaries are duplicated to force periodicity, and the remedy relieves the derivative discontinuity problem. The devised functions rapidly improve the quality of model structures. The potential bias in the functions and the usefulness of additional secondary structure information are also investigated. The proposed guiding functions are expected to facilitate protein structure modeling, such as protein structure prediction, protein design, and structure refinement. Proteins 2013. Proteins 2013; 81:1156–1165. © 2013 Wiley Periodicals, Inc.     

Physiological markers of stress susceptibility in maize and triticale under different soil compactions and/or soil water contents

Differences between two maize and two triticale genotypes grown in low soil compaction (LSC), moderate soil compaction (MSC) and severe soil compaction (SSC) and with a limited (D) or excess (W) soil water content were observed as a decrease in shoot (S) and root (R) biomass, leaf greening (SPAD) and increase in membrane injury (LI), root and leaf water potential (ψ), photosynthesis (Pn), transpiration (E) and stomata conductance (g_S). Close correlations between ψ_L and ψ_R, and between differences ψ_L and ψ_R (Δψ) were found. Drought or waterlogging with LSC conditions in both maize genotypes resulted in higher WUE than in control plants (LSC C), but under the SSC WUE declined. However, for triticale differences in WUE, between treatments were small and insignificant. In general, changes in markers were greater for genotypes sensitive to the soil compaction (Ankora, CHD-12) than in resistant ones (Tina, CHD-247) and were higher in seedlings grown under SSC conditions.

Abbreviations: ψ_R, ψ_L: root and leaf water potential; C: control; D: drought; E: transpiration rate; FWC: field water capacity; g_S: stomatal conductance; LSC, MSC, SSC: low, moderate and severe soil compaction; P_n: photosynthesis rate; W: waterlogging     

Hydrolysis of primary amide groups in Asn/Gln-containing peptides

Peptides Boc-Ala-Asn/Gln-OH and Boc-Asn/Gln-Ala-OH were saponified with barium hydroxide to corresponding Asp/Glu-containing peptides. Under the conditions of saponification, Boc-Asn-Ala-OH additionally afforded Boc-Asp-OH, isopeptide Boc-Asp(Ala)-OH, and Boc-NHSuc > Ala-OH, with the third being the key intermediate in these transformations. Boc-Asp(OMe)-Ala-OMe underwent similar transformations under treatment with diazomethane or triethylamine. Saponification with barium hydroxide was accompanied by a high epimerization of N-terminal amino acid residues, whereas the products of the diazomethane treatment of Boc-Asp(OMe)-Ala-OMe had a low degree of epimerization.     

Differential scanning calorimetry studies of NaCl effect on the inverse temperature transition of some elastin-based polytetra-, polypenta-, and polynonapeptides

Differential scanning calorimetry studies of the effect of NaCl on protein-based polymer self-assembly has been carried out on six elastin-based synthetic sequential polypeptides- i.e., the polypentapeptide (L -Val¹-L -Pro²-Gly³-L -Val⁴-Gly⁵)_n and its more hydrophobic analogues (L -Leu¹-L -Pro²-Gly³-L -Val⁴-Gly⁵)_n and (L -Val¹-L -Pro²-L -Ala³-L -Val⁴-Gly⁵)_n; the polytetrapeptide (L -Val¹-L -Pro²-Gly³-Gly⁴)_n and its more hydrophobic analogue (L -IIe¹-L -Pro²-Gly³-Gly⁴)_n; and the polynonapeptide (a pentatetra hybrid), (L -Val¹-L -Pro²-Gly³-L -Val⁴-Gly⁵-L -Val⁶-L -Pro⁷-Gly⁸-Gly⁹)_n. Previous physical characterizations of the polypentapeptides have demonstrated the occurrence of an inverse temperature transition since increase in order of the polypentapeptide, as the temperature is raised from below to above that of the transition, has been repeatedly observed using different physical characterizations. In the present experiments, it is observed that the transition temperatures of the polypeptides studied are linearly dependent on NaCl concentration. The molar effectiveness of NaCl in shifting the transition temperature ΔT_m/[N], is about 14°C/[N], with the dependence on peptide hydrophobicity being fairly small. Interestingly, however, the δΔQ/ [N] does depend on the hydrophobicity of a polypeptide.     

Chirality in amino acids beyond the Cα configuration

Based on a CSD search, a meta‐analysis of 1179 structures of 19 natural amino acids H₃NC_αH(R)C′(O)O and their derivatives H₃NC_αH(R)C′(O)O(H/R/M), protonated, esterified, or coordinated at the carboxylic group, shows that the chirality chain with its two steps, established in the preceding paper for alanine, can be extended to natural amino acids. High diastereoselectivities are observed in the induction from the L configuration at C_α to the ?ψ and +ψ conformations, which in turn distort the planar carboxylic group C_αC′(O_cis)O_trans to asymmetric flat tetrahedra, showing that the chirality chain is an integral part of natural amino acids.     

Modelling the Effects of Water Stress and Temperature on Seed Germination of Radish and Cantaloupe

Cantaloupe (Cucumis melo L.) and radish (Raphanus sativus L.) are considered as important vegetables with potential for national and international markets due to their sugars, vitamins and minerals. This study arranged, therefore, to simultaneously investigate the effect of temperature (T) and water potential (ψ) on seed germination (SG) of these plants using two hydrothermal time (HTT) models and to determine cardinal Ts and base water potential (ψ_b(50)) for both species. The results indicated that SG of both species was more affected by ψ than T (p ≤ 0.001). At Ts below an optimum temperature (T_o) the ψ_b(50) was constant (− 0.582 and − 0.760 MPa for radish and cantaloupe, respectively) and then increased linearly by 0.0481 and 0.0446 MPa °C⁻¹ as T increased above T_o (as thermoinhibition) until 0 MPa at the ceiling temperature (T_c), respectively. As the first report, however, we observed that the T at which ψ_b(50) begins to change was the same here (that is, T_d = T_o), when determined by either model for both species. This result suggests that the assumption in Rowse and Finch-Savage’s model (T_d is often less and or very close to T_o) may be invalid in some cases. For both species, the base temperature (T_b) and T_o were not affected by ψ and were constant while there was an exception only for T_c for which the value declined with decreasing ψs (more negative). In general, the estimated T_b, T_o and T_c were 9.64, 21.3 and 33.0 °C for radish and 11.8, 28.3 and 45.7 °C for cantaloupe in the control condition (ψ = 0 MPa), respectively. The HTT models used here and their parameters, each with strengths and weaknesses, can be used as a predictive tool in both cantaloupe and radish SG simulation models. However, at first, we need to select an appropriate HTT model based on SG behavior of plant species and then use the best model for quantifying the response of SG across Ts and ψs.

     

DNA structure-induced recruitment and activation of the Fanconi anemia pathway protein FANCD2

The Fanconi anemia (FA) pathway proteins are thought to be involved in the repair of irregular DNA structures including those encountered by the moving replication fork. However, the nature of the DNA structures that recruit and activate the FA proteins is not known. Because FA proteins function within an extended network of proteins, some of which are still unknown, we recently established cell-free assays in Xenopus laevis egg extracts to deconstruct the FA pathway in a fully replication-competent context. Here we show that the central FA pathway protein, xFANCD2, is monoubiquitinated (xFANCD2-L) rapidly in the presence of linear and branched double-stranded DNA (dsDNA) structures but not single-stranded or Y-shaped DNA. xFANCD2-L associates with dsDNA structures in an FA core complex-dependent manner but independently of xATRIP, the regulatory subunit of xATR. Formation of xFANCD2-L is also triggered in response to circular dsDNA, suggesting that dsDNA ends are not required to trigger monoubiquitination of FANCD2. The induction of xFANCD2-L in response to circular dsDNA is replication and checkpoint independent. Our results provide new evidence that the FA pathway discriminates among DNA structures and demonstrate that triggering the FA pathway can be uncoupled from DNA replication and ATRIP-dependent activation.     

LARGE SCALE BIOSYNTHESIS OF GANGLIOSIDE ANALOGUES BY RERF-LC-AI CELLS CULTURED IN HYPERFlask

The efficient production of ganglioside analogues was accomplished using RERF-LC-AI cells cultured in HYPERFlask (High Yield PERformance Flask). Eight kinds of ganglioside analogues (GM3, GM2, sialylparagloboside, GD3, di-sialylated lacto-N-tetraose, and another three kinds of analogues with intricate structures) were synthesized by the saccharide primer method using lung squamous-cell carcinoma line RERF-LC-AI and 12-azidododecyl β-lactoside primer. The yield for each analogue obtained using HYPERFlask was higher than yields obtained from 100-mm dishes.     

Development of a scale-up strategy for Chinese hamster ovary cell culture processes using the kLa ratio as a direct indicator of gas stripping conditions

Herein, we described a scale-up strategy focused on the dissolved carbon dioxide concentration (dCO₂) during fed-batch cultivation of Chinese hamster ovary cells. A fed-batch culture process for a 2000-L scale stainless steel (SS) bioreactor was scaled-up from similarly shaped 200-L scale bioreactors based on power input per unit volume (P/V). However, during the 2000-L fed-batch culture, the dCO₂ was higher compared with the 200-L scale bioreactor. Therefore, we developed an alternative approach by evaluating the k_La values of O₂ (k_La[O₂]) and CO₂ [k_La(CO₂)] in the SS bioreactors as a scale-up factor for dCO₂ reduction. The k_La ratios [k_La(CO₂)/k_La(O₂)] were different between the 200-L and 2000-L bioreactors under the same P/V condition. When the agitation conditions were changed, the k_La ratio of the 2000-L scale bioreactor became similar and the P/V value become smaller compared with those of the 200-L SS bioreactor. The dCO₂ trends in fed-batch cultures performed in 2000-L scale bioreactors under the modified agitation conditions were similar to the control. This k_La ratio method was used for process development in single-use bioreactors (SUBs) with shapes different from those of the SS bioreactor. The k_La ratios for the SUBs were evaluated and conditions that provided k_La ratios similar to the 200-L scale SS bioreactors were determined. The cell culture performance and product quality at the end of the cultivation process were comparable for all tested SUBs. Therefore, we concluded that the k_La ratio is a powerful scale-up factor useful to control dCO₂ during fed-batch cultures.     

LEAF GAS EXCHANGE IN QUERCUS MACROCARPA (FAGACEAE): RAPID STOMATAL RESPONSES TO VARIABILITY IN SUNLIGHT IN A TREE GROWTH FORM

Responses in net photosynthesis (A), stomatal conductance to water vapor (g), and leaf xylem pressure potential (ψ) were measured in the deciduous tree Quercus macrocarpa during alternating periods of sun (photosynthetic photon flux, PPF > 1,500 μmol m^-2 sec^-1) and shade (ca. 350 μmol m^-2 sec^-1 simulating cloud cover). Measurements were made on trees growing at the gallery forest-prairie edge on the Konza Prairie Research Natural Area in northeast Kansas. The region is near the westernmost extension of the range of Q. macrocarpa where this species experiences significant seasonal water stress (minimum ψ < -2.9 MPa). Quercus macrocarpa was chosen for study because it has relatively high A (15 μmol m^-2 sec^-1) and g (300 mmol m^-2 sec^-1) in contrast to the deciduous and evergreen subalpine trees previously studied. Both trees and large saplings of Q. macrocarpa responded to alternating several minute periods of sun and shade with relatively rapid changes in A and g. Reductions in g (110 mmol m^-2 sec^-1) during shade periods lowered transpirational water losses (E) by 13% (and reduced A by 5%) relative to estimates of A and E made assuming g remained constant. Partial stomatal closure during shade was correlated with moderate enhancement in ψ (0.31 MPa) in Q. macrocarpa. However, greater increases in ψ were measured in adjacent prairie grasses exposed to similar periods of shade (0.72 MPa in Andropogon gerardii, 0.61 MPa in Sorghastrum nutans). Reduced variability in ψ in tree growth forms may reflect greater buffering of water relations associated with the large size of trees, the amount of tissue devoted to water storage, and differences in hydraulic resistance relative to herbs. Nonetheless, the gas exchange and water relations responses in Q. macrocarpa were much more similar to those previously measured in herbaceous subalpine and grassland species than to those documented for subalpine trees. Thus, rapid gas exchange responses to variable PPF may also occur in tree growth forms.     

Laser desorption ionisation-time of flight mass spectrometry of the tolyporphins, bioactive metabolites from the cyanobacterium Tolypothrix nodosa

Introduction – The tolyporphins are metabolites isolated from the cyanobacterium Tolypothrix nodosa, comprising a porphyrin‐like macrocycle with C‐glycoside, hydroxide or acetate substituents. Previous studies of porphyrins by MALDI/LDI‐TOF MS indicate that strong radical cations and anions are usually observed in the parent spectra with little fragmentation of the macrocycle. The spectra of the tolyporphins were obtained and trends in the series utilised to partially characterise two new analogues. Objective – To examine tolyporphins by LDI‐TOF MS and utilise trends observed to partially characterise two new analogues. Methodology – The tolyporphins were analysed by LDI‐TOF MS in positive and negative ion mode and by a post source decay method (LIFT) in positive ion mode. Tolyporphin A was also analysed by MALDI‐TOF MS for comparison. Results were analysed and used to obtain structural information on two new analogues. Results and Discussion – The resulting spectra generally contained intense radical cations or anions, with little fragmentation of the macrocyclic core or the C‐glycosides observed. These results are consistent with previous studies of porphyrins. Major fragment ions observed in LIFT spectra yielded key structural information. An inseparable mixture of two tolyporphins was also examined. Analysis of the LIFT spectrum of the parent ion resulted in the postulation of structures of these two new analogues. Conclusions – Tolyporphins yield LDI‐TOF mass spectra somewhat analogous to those of porphyrins; furthermore, the substituents fragment in a characteristic manner permitting partial characterisation of the new analogues tolyporphins L and M by comparison of their LDI‐TOF mass spectra with those of the known analogues. Copyright © 2011 John Wiley & Sons, Ltd.     

Synthesis of amino acid conjugates of 1,1′-dimethylferrocene: New chiral conjugates

Syntheses of diastereomeric mixtures of 1,1′-dimethylferrocene-2-Ala-OMe (3) and 1,1′-dimethylferrocene-3-Ala-OMe (4) are reported by peptide coupling of L-Ala-OMe to the enantiomeric mixtures of the corresponding acids, 1,1′-dimethylferrocene-2-carboxylic acid (1) and 1,1′-dimethylferrocene-3-carboxylic acid (2).