α/β-Peptide foldamers: state of the art

Interplay between proteins, nucleic acids, carbohydrates and/or lipids is involved in almost every process in life on earth. As a consequence, a wide range of diseases results from abnormal interactions of such biomolecules. The main motivation of foldamer science is the development of scaffolds that are capable of adopting defined structures, mimicking parts of biological protagonists in their function. Among the most fundamental interactions in living beings are those between proteins, the so called protein–protein interactions (PPIs). Therefore, peptidic foldamers bear the promise to be an important tool for the inhibition of PPIs, as they are structurally most similar to the original proteins. The great number of possible permutations given by the combination of proteinogenic α-amino acid residues along with β-amino acids opens the door for a larger pool of accessible structures with potential applications. Despite the increasing amount of new secondary structure motifs, only few examples for tertiary and quaternary structure design, as well as inhibition of PPIs, have been realized so far. In this review, we summarize the current knowledge and recent progress made in the field of α/β-peptide foldamers beginning from secondary structure design up to highly sophisticated biological applications, such as protein surface recognition and inhibition of HIV cell entry.     

Ectodermal Wnt/β-catenin signaling shapes the mouse face

The canonical Wnt/β-catenin pathway is an essential component of multiple developmental processes. To investigate the role of this pathway in the ectoderm during facial morphogenesis, we generated conditional β-catenin mouse mutants using a novel ectoderm-specific Cre recombinase transgenic line. Our results demonstrate that ablating or stabilizing β-catenin in the embryonic ectoderm causes dramatic changes in facial morphology. There are accompanying alterations in the expression of Fgf8 and Shh, key molecules that establish a signaling center critical for facial patterning, the frontonasal ectodermal zone (FEZ). These data indicate that Wnt/β-catenin signaling within the ectoderm is critical for facial development and further suggest that this pathway is an important mechanism for generating the diverse facial shapes of vertebrates during evolution.     

Zn Binding Disrupts the Asp-Lys Salt Bridge without Altering the Hairpin-Shaped Cross-β Structure of Aβ42 Amyloid Aggregates

Observations like high Zn²⁺ concentrations in senile plaques found in the brains of Alzheimer's patients and evidences emphasizing the role of Zn²⁺ in amyloid-β (Aβ)-induced toxicity have triggered wide interest in understanding the nature of Zn²⁺-Aβ interaction. In vivo and in vitro studies have shown that aggregation kinetics, toxicity, and morphology of Aβ aggregates are perturbed in the presence of Zn²⁺. Structural studies have revealed that Zn²⁺ has a binding site in the N-terminal region of monomeric Aβ, but not much is precisely known about the nature of binding of Zn²⁺ with aggregated forms of Aβ or its effect on the molecular structure of these aggregates. Here, we explore this aspect of the Zn²⁺-Aβ interaction using one- and two-dimensional ¹³C and ¹⁵N solid-state NMR. We find that Zn²⁺ causes major structural changes in the N-terminal and the loop region connecting the two β-sheets. It breaks the salt bridge between the side chains of Asp²³ and Lys²⁸ by driving these residues into nonsalt-bridge-forming conformations. However, the cross-β structure of Aβ₄₂ aggregates remains unperturbed though the fibrillar morphology changes distinctly. We conclude that the salt bridge is not important for defining the characteristic molecular architecture of Aβ₄₂ but is significant for determining its fibrillar morphology and toxicity.     

Evolution of the βGRP/GNBP/β-1,3-glucanase family of insects

The βGRP/GNBP/β-1,3-glucanase protein family of insects includes several proteins involved in innate immune recognition, such as the β-glucan recognition proteins of Lepidoptera and the Gram-negative bacteria-binding proteins of Drosophila. A phylogenetic analysis supported the existence of two distinct subfamilies, designated the pattern recognition receptor (PRR) and glucanase subfamilies, which originated by gene duplication prior to the origin of the Holometabola. In the C-terminal region (CTR) shared by both subfamilies, the PRR subfamily has evolved significantly more rapidly at the amino acid sequence level than has the glucanase subfamily, implying a relative lack of constraint on the amino acid sequence of this region in the PRR subfamily. PRR subfamily members also include an N-terminal region (NTR), involved in carbohydrate recognition, which is not shared by glucanase subfamily members. In comparisons between paralogous PRR subfamily members, there were no conserved amino acid residues in the NTR. However, when pairs of putatively orthologous PRR subfamily members were compared, the NTR was most often as conserved as the CTR or more so. This pattern suggests that the NTR may be important in functions specific to the different paralogs, while amino acid sequence changes in the NTR may have been important in functional differentiation among paralogs, specifically with regard to the types of carbohydrates that they recognize.     

Flow-Induced β-Hairpin Folding of the Glycoprotein Ibα β-Switch

Flow-induced shear has been identified as a regulatory driving force in blood clotting. Shear induces β-hairpin folding of the glycoprotein Ibα β-switch which increases affinity for binding to the von Willebrand factor, a key step in blood clot formation and wound healing. Through 2.1-μs molecular dynamics simulations, we investigate the kinetics of flow-induced β-hairpin folding. Simulations sampling different flow velocities reveal that under flow, β-hairpin folding is initiated by hydrophobic collapse, followed by interstrand hydrogen-bond formation and turn formation. Adaptive biasing force simulations are employed to determine the free energy required for extending the unfolded β-switch from a loop to an elongated state. Lattice and freely jointed chain models illustrate how the folding rate depends on the entropic and enthalpic energy, the latter controlled by flow. The results reveal that the free energy landscape of the β-switch has two stable conformations imprinted on it, namely, loop and hairpin—with flow inducing a transition between the two.     

The biphasic effects of the oxLDL/β2GPI/anti-β2GPI complex on VSMC proliferation and apoptosis

In our previous study, the oxLDL/β₂GPI/anti-β₂GPI complex was demonstrated to further enhance the foam cell formation and migration of VSMC, as well as the expression of inflammatory cytokines, via the TLR4/NF-κB pathway. However, sparse information is available on other pro-atherogenic pathogenic effects of the oxLDL/β₂GPI/anti-β₂GPI complex, such as effects on proliferation and apoptosis. In the present study, we focused on the biphasic effects and underlying mechanisms of the oxLDL/β₂GPI/anti-β₂GPI complex on VSMC survival. The data showed that short exposure to the oxLDL/β₂GPI/anti-β₂GPI complex could activate NF-κB and ERK1/2 pathways and stimulate cell proliferation in VSMC. In contrast, longer exposure increased the level of p38 pathway activation and cell apoptosis. Additionally, the promotion effect of the oxLDL/β₂GPI/anti-β₂GPI complex on both proliferation and apoptosis, as well as signaling pathway activation, was stronger than that of the other control groups. The use of selective blockers showed that TLR4/NF-κB and ERK1/2 partly mediated oxLDL/β₂GPI/anti-β₂GPI complex-induced proliferation and had an inhibitory effect on complex-stimulated apoptosis. Conversely, TLR2/p38 partly mediated oxLDL/β₂GPI/anti-β₂GPI complex-induced apoptosis and had a negative effect on complex-stimulated proliferation. Specific inhibitors of NF-κB and ERK1/2 activation could augment the oxLDL/β₂GPI/anti-β₂GPI complex-induced phosphorylation of p38 and vice versa. Under pretreatment with NADPH oxidase inhibitors, intracellular ROS generation was confirmed to participate in oxLDL/β₂GPI/anti-β₂GPI complex-induced proliferation and apoptosis, as well as the phosphorylation of NF-κB and MAPKs. Taken together, our data clearly revealed that the oxLDL/β₂GPI/anti-β₂GPI complex had biphasic effects on VSMC survival, partly mediated by ROS-induced NF-κB and MAPKs activation. The TLR4/NF-κB and TLR2/p38 pathways played supporting roles in this dual effects-initiated signal network, and there is a trade-off relationship between the phosphorylation of NF-κB, ERK1/2 and p38. The dual effects of the oxLDL/β₂GPI/anti-β₂GPI complex on VSMC survival contribute to the development of the structure typical of atherosclerotic lesions, particularly focal excessive growth alternating with necrosis.     

β-galactosidase activity in the germinating seeds of Vigna sinensis

The β-galactosidase activity in cotyledons of Vigna sinensis increases during seed germination and is inhibited by cycloheximide. The increasing activity may be due to the de novo synthesis of enzyme protein. The enzyme has been partially purified by gel filtration and characterized with respect to some biochemical parameters. The optimum pH and optimum temperature are 4.5 and 55°, respectively and the enzymes follows typical Michaelis kinetics with K_m and V_max of 4.5 x 10^?4 M and 2.0 x 10^?5 mol/hr respectively. K_i for galactose and lactose are 4.5 and 220 mM, respectively. The energy of activation of the enzyme for p-nitrophenyl β-D-galactoside is 9.83 kcal/mol. The apparent relative MW of the enzyme as determined by gel filtration was 56000.     

On the role of Wnt/β-catenin signaling in stem cells

Background

Stem cells are mainly characterized by two properties: self-renewal and the potency to differentiate into diverse cell types. These processes are regulated by different growth factors including members of the Wnt protein family. Wnt proteins are secreted glycoproteins that can activate different intracellular signaling pathways.

Scope of review

Here we summarize our current knowledge on the role of Wnt/β-catenin signaling with respect to these two main features of stem cells.

Major conclusions

A particular focus is given on the function of Wnt signaling in embryonic stem cells. Wnt signaling can also improve reprogramming of somatic cells towards iPS cells highlighting the importance of this pathway for self-renewal and pluripotency. As an example for the role of Wnt signaling in adult stem cell behavior, we furthermore focus on intestinal stem cells located in the crypts of the small intestine.

General significance

A broad knowledge about stem cell properties and the influence of intrinsic and extrinsic factors on these processes is a requirement for the use of these cells in regenerative medicine in the future or to understand cancer development in the adult. This article is part of a Special Issue entitled Biochemistry of Stem Cells.     

Roles for the two N-terminal (β/α) modules in the folding of a (β/α)₈-barrel protein as studied by fragmentation analysis

The (β/α)₈‐barrel is one of the most abundant folds found in enzymes. To identify the independent folding units and the segment(s) that correspond to a minimum core structure within a (β/α)₈‐barrel protein, fragmentation experiments were performed with Escherichia coli phosphoribosylanthranilate isomerase, which has a single (β/α)₈‐barrel domain. Our previous studies indicated that the central four β/α segments comprise an independent folding unit; whereas, the role(s) of the first two β/α segments in folding had not been clarified prior to this report. Herein, we report the design and synthesis of a series of N‐terminally deleted fragments starting with (β/α)_1–5β₆ as the parent construct. Analytical gel filtration and urea‐induced equilibrium unfolding experiments indicated that deletions within the N‐terminal region, that is, within the first two β/α modules, resulted in reduced stability or aggregation of the remaining segments. The (β/α)_3–5β₆ segment appeared to fold into a stable structure and deletion of β₆ from (β/α)_3–5β₆ yielded (β/α)_3–5, which did not form native‐like secondary structures. However, urea‐induced unfolding of (β/α)_3–5, monitored by reduction of tryptophan fluorescence, indicated that the fragment contained a loosely packed hydrophobic core. Taken together, the results of our previous and present fragmentation experiments suggest the importance of the central (β/α)_3–4β₅ module in folding, which is a finding that is compatible with our simulated unfolding study performed previously. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Wnt/β-catenin signaling induces the aging of mesenchymal stem cells through the DNA damage response and the p53/p21 pathway

Recent studies have demonstrated the importance of cellular extrinsic factors in the aging of adult stem cells. However, the effects of an aged cell-extrinsic environment on mesenchymal stem cell (MSC) aging and the factors involved remain unclear. In the current study, we examine the effects of old rat serum (ORS) on the aging of MSCs, and explore the effects and mechanisms of Wnt/β-catenin signaling on MSC aging induced by ORS treatment. Senescence-associated changes in the cells are examined with SA-β-galactosidase staining and ROS staining. The proliferation ability is detected by MTT assay. The surviving and apoptotic cells are determined using AO/EB staining. The results suggest that ORS promotes MSC senescence and reduces the proliferation and survival of cells. The immunofluorescence staining shows that the expression of β-catenin increases in MSCs of old rats. To identify the effects of Wnt/β-catenin signaling on MSC aging induced with ORS, the expression of β-catenin, GSK-3β, and c-myc are detected. The results show that the Wnt/β-catenin signaling in the cells is activated after ORS treatment. Then we examine the aging, proliferation, and survival of MSCs after modulating Wnt/β-catenin signaling. The results indicate that the senescence and dysfunction of MSCs in the medium containing ORS is reversed by the Wnt/β-catenin signaling inhibitor DKK1 or by β-catenin siRNA. Moreover, the expression of γ-H2A.X, a molecular marker of DNA damage response, p16(INK4a), p53, and p21 is increased in senescent MSCs induced with ORS, and is also reversed by DKK1 or by β-catenin siRNA. In summary, our study indicates the Wnt/β-catenin signaling may play a critical role in MSC aging induced by the serum of aged animals and suggests that the DNA damage response and p53/p21 pathway may be the main mediators of MSC aging induced by excessive activation of Wnt/β-catenin signaling.     

Regulation of cadherin expression in the chicken neural crest by the Wnt/β-catenin signaling pathway

In neural crest cell development, the expression of the cell adhesion proteins cadherin-7 and cadherin-11 commences after delamination of the neural crest cells from the neuroepithelium. The canonical Wnt signaling pathway is known to drive this delamination step and is a candidate for inducing expression of these cadherins at this time. This project was initiated to investigate the role of canonical Wnt signaling in the expression of cadherin-7 and cadherin-11 by treating neural crest cells with Wnt3a ligand. Expression of cadherin-11 was first confirmed in the neural crest cells for the chicken embryo. The changes in the expression level of cadherin-7 and -11 following the treatment with Wnt3a were studied using real-time RT-PCR and immunostaining. Statistically significant upregulation in the mRNA expression of cadherin-7 and cadherin-11 and in the amount of cadherin-7 and cadherin-11 protein found in cell-cell interfaces between neural crest cells was observed in response to Wnt, demonstrating that cadherin-7 and cadherin-11 expressed by the migrating neural crest cells can be regulated by the canonical Wnt pathway.Key words: neural crest, Wnt, cadherin-7, cadherin-11