Folding type-specific secondary structure propensities of amino acids,derived from α-helical, β-sheet, α/β, and α+β proteins of known structures

Folding type-specific secondary structure propensities of 20 naturally occurring amino acids have been derived from α-helical, β-sheet, α/β, and α+β proteins of known structures. These data show that each residue type of amino acids has intrinsic propensities in different regions of secondary structures for different folding types of proteins. Each of the folding types shows markedly different rank ordering, indicating folding type-specific effects on the secondary structure propensities of amino acids. Rigorous statistical tests have been made to validate the folding type-specific effects. It should be noted that α and β proteins have relatively small α-helices and β-strands forming propensities respectively compared with those of α+β and α/β proteins. This may suggest that, with more complex architectures than α and β proteins, α+β and α/β proteins require larger propensities to distinguish from interacting α-helices and β-strands. Our finding of folding type-specific secondary structure propensities suggests that sequence space accessible to each folding type may have differing features. Differing sequence space features might be constrained by topological requirement for each of the folding types. Almost all strong β-sheet forming residues are hydrophobic in character regardless of folding types, thus suggesting the hydrophobicities of side chains as a key determinant of β-sheet structures. In contrast, conformational entropy of side chains is a major determinant of the helical propensities of amino acids, although other interactions such as hydrophobicities and charged interactions cannot be neglected. These results will be helpful to protein design, class-based secondary structure prediction, and protein folding. © 1998 John Wiley & Sons, Inc. Biopoly 45: 35–49, 1998     

IL‐23 drives differentiation of peripheral γδ17 T cells from adult bone marrow‐derived precursors

Pro‐inflammatory interleukin (IL)‐17‐producing γδ (γδ17) T cells are thought to develop exclusively in the thymus during fetal/perinatal life, as adult bone marrow precursors fail to generate γδ17 T cells under homeostatic conditions. Here, we employ a model of experimental autoimmune encephalomyelitis (EAE) in which hematopoiesis is reset by bone marrow transplantation and demonstrate unequivocally that Vγ4⁺ γδ17 T cells can develop de novo in draining lymph nodes in response to innate stimuli. In vitro, γδ T cells from IL‐17 fate‐mapping reporter mice that had never activated the Il17 locus acquire IL‐17 expression upon stimulation with IL‐1β and IL‐23. Furthermore, IL‐23R (but not IL‐1R1) deficiency severely compromises the induction of γδ17 T cells in EAE, demonstrating the key role of IL‐23 in the process. Finally, we show, in a composite model involving transfers of both adult bone marrow and neonatal thymocytes, that induced γδ17 T cells make up a substantial fraction of the total IL‐17‐producing Vγ4⁺ T‐cell pool upon inflammation, which attests the relevance of this novel pathway of peripheral γδ17 T‐cell differentiation.     

The effect of polyelectrolyte counterion specificity, charge density, and conformation on polyelectrolyte-amphiphile interaction: the carrageenan/furcellaran-amitriptyline system

The effect of polyelectrolyte cation specificity, charge density, and conformation on the interaction between furcelleran, kappa, iota, and lambda-carrageenan, respectively, and amitriptyline, an amphiphilic cationic drug molecule, was studied by means of a dialysis equilibrium technique. The carrageenans used in this study-furcelleran, kappa, iota, and lambda-carrageenan-had a charge density corresponding to 0.69, 0.92, 1.53, and 2.07 sulfate groups per disaccharide. In general, the binding isotherms followed the order Li(+) < Na(+) < N(CH3)(4)(+) < K(+) < or = Cs(+) approximately Rb(+), i.e., the binding isotherms were shifted to higher concentrations of free amphiphile according to the sequence indicated. This affinity sequence correlates well with that found for the dextran sulfate-amitriptyline system (A. Hugerth and L.-O. Sundel?f, Langmuir 2000, 16, 313-317). The factor determining the critical aggregation concentration in the presence of Na(+) compared to K(+) was found to be as follows: the flexibility (conformation) in the case of the lower charged carrageenans, i.e., furcelleran and kappa-carrageenan, charge density for iota-carrageenan, and in the lambda-carrageenan case the difference in the ROSO(3)(-)-alkali ion specificity.     

δ18O‐derived incubation temperatures of oviraptorosaur eggs

In order to determine the incubation temperature of eggs laid by non‐avian dinosaurs, we analysed the oxygen isotope compositions of both eggshell carbonate (δ¹⁸O_c) and embryo bone phosphate (δ¹⁸O_p) from seven oviraptorosaur eggs with preserved in ovo embryo bones. These eggs come from the Upper Cretaceous Nanxiong Formation of Jiangxi Province, China. Oviraptorosaur theropods were selected because of their known brooding behaviour as evidenced by preserved adult specimens fossilized in brooding posture on their clutch. Incubation temperature of these embryos was estimated based on the following considerations: eggshell δ¹⁸O_c value reflects the oxygen isotope composition of egg water fluid; embryo bones precipitate from the same egg fluid; and oxygen isotope fractionation between phosphate and water is controlled by the egg temperature. A time‐dependent model predicting the δ¹⁸O_p evolution of the embryo skeleton during incubation as a function of egg temperature was built, and measured δ¹⁸O_c and δ¹⁸O_p values used as boundary conditions. According to the model outputs, oviraptorosaurs incubated their eggs within a 35–40°C range, similar to extant birds and compatible with the known active brooding behaviour of these theropod dinosaurs. Provided that both eggshell and embryo bones preserved their original oxygen isotope compositions, this method could be extended to investigate some reproductive traits of other extinct groups of oviparous amniotes.     

The α6β4 Integrin Is a Receptor for both Laminin and Kalinin

Previously, we have established K562 transfectants that express either α6Aβ1 or α6Bβ1 (Kα6A or Kα6B) on their surface. Both cell lines bind to laminin and kalinin after treatment with the β1-stimulatory antibody TS2/16. Here we introduce the full-length β4 cDNA into the α6A- and α6B-expressing K562 cells and selected stably transfected cells. The β4 subunit was expressed on the surface of both transfectants and it formed dimers with the α6A or α6B subunits. Immunoprecipitation and preclearing analyses revealed that both transfectants expressed α6β1, in addition to α6β4. While Kα6A and Kβ6B cells required TS2/16 stimulation for binding to laminin or kalinin, adhesion of the unstimulated β4-transfected Kα6A and Kα6B cells to these matrix components was already substantial. This adhesion was mediated by both α6β1 and α6β4 since it was completely blocked by an α6-specific antibody or by a combination of anti-β1 and anti-β4 antibodies, but only partially by either of these latter two antibodies alone. Adhesion to laminin was completely blocked by an antiserum to laminin fragment E8 as was the adhesion to kalinin by an antibody to kalinin, demonstrating the specificity of adhesion. Both transfectants always adhered more strongly to kalinin than to laminin. Furthermore, binding to kalinin was less well blocked by antibodies to β4 than binding to laminin, indicating that the affinity of α6β4 for kalinin is higher than that for laminin. The fact that α6β1 mediated adhesion without TS2/16 stimulation on the β4-transfected Kα6A and Kα6B cells suggests that some activation of α6β1 had occurred in these cells, even though binding was increased when they were actively stimulated by the antibody TS2/16. Finally, we show that Mn²⁺ induced binding of solubilized α6β4 to matrix containing kalinin, deposited by the murine cell line RAC-11P/SD. This binding was inhibited by the anti-α6 mAb GoH3. Together, these results indicate that both α6β1 and α6β4 are receptors for laminin and kalinin and that there are no differences in ligand specificity between the A and B variants of the α6 subunit when associated with either β1 or β4.     

The legacy of enhanced N and S deposition as revealed by the combined analysis of δ13C, δ18O and δ15N in tree rings

This study aimed to evaluate the effects of long‐term repeated aerial nitrogen (N) and sulphur (S) misting over tree canopies of a Sitka spruce plantation in Scotland. We combined δ¹³C and δ¹⁸O in tree rings to evaluate the changes in CO₂ assimilation (A) and stomatal conductance (g_s) and to assess their contribution to variations in the intrinsic water‐use efficiency (WUE_i, i.e., the A/g_s ratio). Measurements of δ¹⁵N enabled shifts in the ecosystem N cycling following misting to be assessed. We found that: (i) N applications, with or without S, increased the ratio between A and g_s in favour of A, thus supporting a fertilizer effect of added N. (ii) After the treatments ceased, the trees quickly adjusted to the reductions of N deposition, but not to the reduction in S deposition, which had a negative effect on WUE_i by reducing A. This indicates that the beneficial role of N deposition may be negated in forests that previously received a high load of acid rain. (iii) δ¹⁵N in tree rings reflected the N dynamics caused by canopy retention, with the fingerprint also present in the litter, after the experiment stopped. (iv) Both our results (obtained using canopy applications) and a collection of published data (obtained using soil applications) showed that generally WUE_i increased in response to an increase of N applications, with the magnitude of the changes related to soil conditions and the availability of other nutrients. The shifts observed in δ¹⁵N in tree rings also suggest that both the quantity of the applied N and its quality, mediated by processes occurring during canopy N retention, are important determinants of the interactions between N and C cycles. Stable isotopes are useful probes to understand these processes and to put the results of short‐term experiments into context.     

β‐Hairpin stabilization in a 28‐residue peptide derived from the β‐subunit sequence of human chorionic gonadotropin hormone

The β‐subunit of the human chorionic gonadotropin (hCG) hormone, which is believed to be related to certain types of cancer, contains three hairpin‐like fragments. To investigate the role of β‐hairpin formation in the early stages of the hCGβ folding, a 28‐residue peptide with the sequence RDVRFESIRLPGSPRGVNPVVSYAVALS, corresponding to the H3‐β hairpin fragment (residues 60–87) of the hCGβ subunit, was studied under various conditions using three optical spectroscopic methods: Fourier transform ir spectroscopy, electronic CD, and vibrational CD. Environmental conditions are critical factors for formation of secondary structure in this peptide. TFE : H₂O mixed solvents induced helical formation. Formation of β‐structure in this peptide, which may be related to the native β‐hairpin formation in the intact hormone, was found to be induced only under conditions such as high concentration, high temperature, and the presence of nonmicellar sodium dodecyl sulfate concentrations. These findings support a protein folding mechanism for the hCGβ subunit in which an initial hydrophobic collapse, which increases intermolecular interactions in hCGβ, is needed to induce the H3‐β hairpin formation. © 1999 John Wiley & Sons, Inc. Biopoly 50: 413–423, 1999     

Osteopontin mediates macrophage chemotaxis via α4 and α9 integrins and survival via the α4 integrin

Osteopontin (OPN) is highly expressed by macrophages and plays a key role in the pathology of several chronic inflammatory diseases including atherosclerosis and the foreign body reaction. However, the molecular mechanism behind OPN regulation of macrophage functions is not well understood. OPN is a secreted molecule and interacts with several integrins via two domains: the RGD sequence binding to α_v‐containing integrins, and the SLAYGLR sequence binding to α₄β₁, α₄β₇, and α₉β₁ integrins. Here we determined the role of OPN in macrophage survival, chemotaxis, and activation state. For survival studies, OPN treated‐bone marrow derived macrophages (BMDMs) were challenged with growth factor withdrawal and neutralizing integrin antibodies. We found that survival in BMDMs is mediated primarily through the α₄ integrin. In chemotaxis studies, we observed that migration to OPN was blocked by neutralizing α₄ and α₉ integrin antibodies. Further, OPN did not affect macrophage activation as measured by IL‐12 production. Finally, the relative contributions of the RGD and the SLAYGLR functional domains of OPN to leukocyte recruitment were evaluated in an in vivo model. We generated chimeric mice expressing mutated forms of OPN in myeloid‐derived leukocytes, and found that the SLAYGLR functional domain of OPN, but not the RGD, mediates macrophage accumulation in response to thioglycollate‐elicited peritonitis. Collectively, these data indicate that α₄ and α₉ integrins interacting with OPN via the SLAYGLR domain play a key role in macrophage biology by regulating migration, survival, and accumulation. J. Cell. Biochem. 114: 1194–1202, 2013. © 2012 Wiley Periodicals, Inc.     

An efficient and enantioselective Michael addition of aromatic oximes to α,β‐unsaturated aldehydes promoted by a chiral diamine catalyst derived from α,α‐diphenyl prolinol

Chiral diamine catalysts 11a–e derived from α ,α ‐diphenyl prolinol were prepared and successfully applied to the Michael addition of aromatic oximes to α ,β ‐unsaturated aldehydes in mediocre to good yields (up to 78%) and good to high enantioselectivities (up to 93% ee ).     

Biosynthesis of the leucine derived α‐, β‐ and γ‐hydroxynitrile glucosides in barley (Hordeum vulgare L.)

Barley (Hordeum vulgare L.) produces five leucine‐derived hydroxynitrile glucosides (HNGs), of which only epiheterodendrin is a cyanogenic glucoside. The four non‐cyanogenic HNGs are the β‐HNG epidermin and the γ‐HNGs osmaronin, dihydroosmaronin and sutherlandin. By analyzing 247 spring barley lines including landraces and old and modern cultivars, we demonstrated that the HNG level varies notably between lines whereas the overall ratio between the compounds is constant. Based on sequence similarity to the sorghum (Sorghum bicolor) genes involved in dhurrin biosynthesis, we identified a gene cluster on barley chromosome 1 putatively harboring genes that encode enzymes in HNG biosynthesis. Candidate genes were functionally characterized by transient expression in Nicotiana benthamiana. Five multifunctional P450s, including two CYP79 family enzymes and three CYP71 family enzymes, and a single UDP‐glucosyltransferase were found to catalyze the reactions required for biosynthesis of all five barley HNGs. Two of the CYP71 enzymes needed to be co‐expressed for the last hydroxylation step in sutherlandin synthesis to proceed. This observation, together with the constant ratio between the different HNGs, suggested that HNG synthesis in barley is organized within a single multi‐enzyme complex.     

Glacial–interglacial deep-water changes in the NW Pacific inferred from single foraminiferal δO and δC

Oxygen and carbon isotope values of single benthic foraminiferal tests in a core from the Shatsky Rise, NW Pacific Ocean, show greater intra-horizon variance during the Holocene than during the Last Glacial Maximum (LGM). This greater variance is caused by the introduction of glacial specimens some 20 cm upward from their original deposition layer due to bioturbation. In contrast, foraminiferal populations belonging to glacial layers do not include Holocene specimens. The difference in direction of bioturbation greatly modifies climate information in horizons formed during and after deglacial events. After omitting glacial specimens from Holocene sediments, the glacial–interglacial difference in δ¹⁸O suggests that Pacific deep-water temperature changed by 2.4–3.8°C at the most. The δ¹³C values suggest that nutrient concentration was higher during the LGM than the Holocene. The glacial deep North Pacific Ocean apparently was influenced by cold deep waters of southern origin.     

Comparative response of δ13C, δ18O and δ15N in durum wheat exposed to salinity at the vegetative and reproductive stages

This study compared the performance of the stable isotope composition of carbon (δ¹³C), oxygen (δ¹⁸O) and nitrogen (δ¹⁵N) by tracking plant response and genotypic variability of durum wheat to different salinity conditions. To that end, δ¹³C, δ¹⁸O and δ¹⁵N were analysed in dry matter (dm) and the water‐soluble fraction (wsf) of leaves from plants exposed to salinity, either soon after plant emergence or at anthesis. The δ¹³C and δ¹⁸O of the wsf recorded the recent growing conditions, including changes in evaporative conditions. Regardless of the plant part (dm or wsf), δ¹³C and δ¹⁸O increased and δ¹⁵N decreased in response to stress. When the stress conditions were established just after emergence, δ¹⁵N and δ¹³C correlated positively with genotypic differences in biomass, whereas δ¹⁸O correlated negatively in the most severe treatment. When the stress conditions were imposed at anthesis, relationships between the three isotope signatures and biomass were only significant and positive within the most severe treatments. The results show that nitrogen metabolism, together with stomatal limitation, is involved in the genotypic response to salinity, with the relative importance of each factor depending on the severity and duration of the stress as well as the phenological stage that the stress occurs.     

Dehalogenation Activity of Selected Fungi Toward δ‐Iodo‐γ‐Lactone Derived from trans,trans‐Farnesol

Time‐course of biotransformation of racemic trans‐4‐((E)‐4′,8′‐dimethylnona‐3′,7′‐dien‐1‐yl)‐5‐iodomethyl‐4‐methyldihydrofuran‐2‐one ( 1 ) in fungal and yeast cultures was investigated. In these conditions, the substrate 1 was enantioselectively dehalogenated yielding 4‐((E)‐4′,8′‐dimethylnona‐3′,7′‐dien‐1‐yl)‐4‐methyl‐5‐methylenedihydrofuran‐2‐one ( 2 ) and its structure was established based on the spectroscopic data. The most effective biocatalyst used was Didymosphaeria igniaria, which catalyzed the process with highest rate and enantioselectivity (ee of product = 76%). The antiproliferative activity of δ‐iodo‐γ‐lactone 1 , product of its biotransformation 2 , and starting substrate (farnesol) were evaluated toward two cancer cell lines: A549 (human lung adenocarcinoma) and HL‐60 (human promyelocytic leukemia).     

HLA‐DQ7 β1 and β2 derived peptides as immunomodulators

Modulation of protein–protein interactions involved in the immune system by using small molecular mimics of the contact interfaces may lead to the blockage of the autoimmune response and the development of drugs for immunotherapy. The nonpolymorphic β‐regions, exposed to the microenvironment, of the modeled HLA‐DQ7, which is genetically linked to autoimmune diseases, were determined. Peptides 132–141 and 58–67, located at the β₁ and β₂ domains of HLA‐DQ7, respectively, were tested for their involvement in the interactions with CD4⁺ T lymphocytes. Linear, cyclic, and dimeric analogs that mimic the exposed surfaces of HLA‐DQ7 were designed and synthesized. Their immunosuppressory activities, found in the secondary, humoral immune response to sheep erythrocytes (SRBC) in mice in vitro, ranged from 11% to 53%. The significance of the total charge of the peptides, the pattern of the hydrogen bonding, and the presence of secondary structure were investigated in relation to the immunomodulatory effect of the peptides. Two dimeric analogs of the HLA‐DQ7 58–67 fragment, consisting of the two monomers covalently linked by a polyethylene glycol (PEG) spacer, able to mimic the superdimers, were also synthesized and studied. As the 58–67 segment is located at the β₁ region of HLA‐DQ7, close to the major histocompatibility complex (MHC) groove, one may assume that the 58–67 peptide could accommodate the association between T‐cell receptor (TCR) and human leukocyte antigen (HLA) by activating a co‐stimulatory molecule of the TCR/HLA interaction. This hypothesis is supported by the confocal laser image of the fluorescein‐labeled 58–67 peptide and by the fact that it is an immunostimulator at low concentration. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.     

The effects of Paraloid B‐72 and Butvar B‐98 treatment and organic solvent removal on δ13C, δ15N,and δ18O values of collagen and hydroxyapatite in a modern bone

Stable isotopes in bones are a powerful tool for diet, provenance, climate, and physiological reconstructions, but necessarily require well‐preserved specimens unaltered by postmortem diagenesis or conservation practices. This study examines the effects of Paraloid B‐72 and Butvar B‐98, two common consolidants used in field and museum conservation, on δ¹³C, δ¹⁵N, and δ¹⁸O values from bone collagen and hydroxyapatite. The effects of solvent removal (100% acetone, 100% ethanol, 9:1 acetone:xylenes, 9:1 ethanol:xylenes) and drying methods (ambient air, vacuum, oven drying at 80°C) were also examined to determine if bones treated with these consolidants can successfully be cleaned and used for stable isotope analyses. Results show that introduction of Paraloid B‐72 or Butvar B‐98 in 100% acetone or 100% ethanol, respectively, with subsequent removal by the same solvents and drying at 80°C facilitates the most successful removal of consolidants and solvents. The δ¹³C values in collagen, δ¹⁵N in collagen, δ¹⁸O in hydroxyapatite phosphate, and δ¹³C in hydroxyapatite structural carbonate were unaltered by treatments with Paraloid or Butvar and subsequent solvent removal. The δ¹⁸O in hydroxyapatite structural carbonate showed nonsystematic variability when bones were treated with Paraloid and Butvar, which is hypothesized to be a result of hydroxyl exchange when bones are exposed to consolidants in solution. It is therefore recommended that δ¹⁸O in hydroxyapatite structural carbonate should not be used in stable isotope studies if bones have been treated with Paraloid or Butvar. Am J Phys Anthropol 157:330–338, 2015. © 2015 Wiley Periodicals, Inc.     

Low-molecular-weight chitosans derived from β-chitin: preparation, molecular characteristics and aggregation activity

Preparation, molecular characteristics, and aggregation activity of low-molecular-weight chitosans derived from β-chitin have been studied in comparison with those of chitosans from -chitin. Chitosan derived from β-chitin was partially degraded with alkali and acid to prepare chitosans with reduced molecular weights. The reaction was also conducted with chitosan from -chitin, but it was less susceptible to the degradation than chitosan from β-chitin. The resulting two series of chitosans had molecular weights ranging from 11 to 436 kDa. GPC analysis showed similar changes in the molecular weight distribution in the progress of main chain cleavage of the two kinds of chitosans. The polydispersity values were 2.01–4.16, indicating relatively narrow molecular weight distributions. These chitosans aggregated bovine serum albumin efficiently, and the aggregation behavior was dependent on the molecular weight and concentration of chitosan in addition to the pH of the media and concentration of sodium chloride. The aggregation activity of chitosans from β-chitin was found to be somewhat higher than that of chitosans from -chitin.     

α-, β-, and γ-Tubulin Polymerization in Response to DNA Damage

Microtubules provide structural support for a cell and play key roles in cell motility, mitosis, and meiosis. They are also the targets of several anticancer agents, indicating their importance in maintaining cell viability. We have investigated the possibility that alterations in microtubule structure and tubulin polymerization may be part of the cellular response to DNA damage. In this report, we find that γ-radiation stimulates the production and polymerization of α-, β-, and γ- tubulin in hematopoeitic cell lines (Ramos, DP16), leading to visible changes in microtubule structures. We have found that this microtubule reorganization can be prevented by caffeine, a drug that concomitantly inhibits DNA damage-induced cell cycle arrest and apoptosis. Our results support the idea that microtubule polymerization is an important facet of the mammalian response to DNA damage.