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.     

The outs and the ins of sphingosine-1-phosphate in immunity

The potent lipid mediator sphingosine-1-phosphate (S1P) is produced inside cells by two closely related kinases, sphingosine kinase 1 (SPHK1) and SPHK2, and has emerged as a crucial regulator of immunity. Many of the actions of S1P in innate and adaptive immunity are mediated by its binding to five G protein-coupled receptors, designated S1PR1-5, but recent findings have also identified important roles for S1P as a second messenger during inflammation. In this Review, we discuss recent advances in our understanding of the roles of S1P receptors and describe the newly identified intracellular targets of S1P that are crucial for immune responses. Finally, we discuss the therapeutic potential of new drugs that target S1P signalling and functions.     

Involvement of Acid ��-Glucosidase 1 in the Salvage Pathway of Ceramide Formation

Activation of protein kinase C (PKC) promotes the salvage pathway of ceramide formation, and acid sphingomyelinase has been implicated, in part, in providing substrate for this pathway (Zeidan, Y. H., and Hannun, Y. A. (2007) J. Biol. Chem. 282, 11549–11561). In the present study, we examined whether acid β-glucosidase 1 (GBA1), which hydrolyzes glucosylceramide to form lysosomal ceramide, was involved in PKC-regulated formation of ceramide from recycled sphingosine. Glucosylceramide levels declined after treatment of MCF-7 cells with a potent PKC activator, phorbol 12-myristate 13-acetate (PMA). Silencing GBA1 by small interfering RNAs significantly attenuated acid glucocerebrosidase activity and decreased PMA-induced formation of ceramide by 50%. Silencing GBA1 blocked PMA-induced degradation of glucosylceramide and generation of sphingosine, the source for ceramide biosynthesis. Reciprocally, forced expression of GBA1 increased ceramide levels. These observations indicate that GBA1 activation can generate the source (sphingosine) for PMA-induced formation of ceramide through the salvage pathway. Next, the role of PKCδ, a direct effector of PMA, in the formation of ceramide was determined. By attenuating expression of PKCδ, cells failed to trigger PMA-induced alterations in levels of ceramide, sphingomyelin, and glucosylceramide. Thus, PKCδ activation is suggested to stimulate the degradation of both sphingomyelin and glucosylceramide leading to the salvage pathway of ceramide formation. Collectively, GBA1 is identified as a novel source of regulated formation of ceramide, and PKCδ is an upstream regulator of this pathway.Sphingolipids are abundant components of cellular membranes, many of which are emerging as bioactive lipid mediators thought to play crucial roles in cellular responses (1, 2). Ceramide, a central sphingolipid, serves as the main precursor for various sphingolipids, including glycosphingolipids, gangliosides, and sphingomyelin. Regulation of formation of ceramide has been demonstrated through the action of three major pathways: the de novo pathway (3, 4), the sphingomyelinase pathway (5), and the salvage pathway (6–8). The latter plays an important role in constitutive sphingolipid turnover by salvaging long-chain sphingoid bases (sphingosine and dihydrosphingosine) that serve as sphingolipid backbones for ceramide and dihydroceramide as well as all complex sphingolipids (Fig. 1A).Open in a separate windowFIGURE 1.The scheme of the sphingosine salvage pathway of ceramide formation and inhibition of PMA induction of ceramide by fumonisin B1. A, the scheme of the sphingosine salvage pathway of ceramide formation. B, previously published data as to effects of fumonisin B1 on ceramide mass profiles (23) are re-plotted as a PMA induction of ceramide. In brief, MCF-7 cells were pretreated with or without 100 μm fumonisin B1 for 2 h followed by treatment with 100 nm PMA for 1 h. Lipids were extracted, and then the levels of ceramide species were determined by high-performance liquid chromatography-tandem mass spectrometry. Results are expressed as sum of increased mass of ceramide species. Dotted or open columns represents C₁₆-ceramide or sum of other ceramide species (C₁₄-ceramide, C₁₈-ceramide, C_18:1-ceramide, C₂₀-ceramide, C₂₄-ceramide, and C_24:1-ceramide), respectively. The data represent mean ± S.E. of three to five values.Metabolically, ceramide is also formed from degradation of glycosphingolipids (Fig. 1A) usually in acidic compartments, the lysosomes and/or late endosomes (9). The stepwise hydrolysis of complex glycosphingolipids eventually results in the formation of glucosylceramide, which in turn is converted to ceramide by the action of acid β-glucosidase 1 (GBA1)² (9, 10). Severe defects in GBA1 activity cause Gaucher disease, which is associated with aberrant accumulation of the lipid substrates (10–14). On the other hand, sphingomyelin is cleaved by acid sphingomyelinase to also form ceramide (15, 16). Either process results in the generation of lysosomal ceramide that can then be deacylated by acid ceramidase (17), releasing sphingosine that may escape the lysosome (18). The released sphingosine may become a substrate for either sphingosine kinases or ceramide synthases, forming sphingosine 1-phosphate or ceramide, respectively (3, 19–21).In a related line of investigation, our studies (20, 22, 23) have begun to implicate protein kinase Cs (PKC) as upstream regulators of the sphingoid base salvage pathway resulting in ceramide synthesis. Activation of PKCs by the phorbol ester (PMA) was shown to stimulate the salvage pathway resulting in increases in ceramide. All the induced ceramide was inhibited by pretreatment with a ceramide synthase inhibitor, fumonisin B1, but not by myriocin, thus negating acute activation of the de novo pathway and establishing a role for ceramide synthesis (20, 23). Moreover, labeling studies also implicated the salvage pathway because PMA induced turnover of steady state-labeled sphingolipids but did not affect de novo labeled ceramide in pulse-chase experiments.Moreover, PKCδ, among PKC isoforms, was identified as an upstream molecule for the activation of acid sphingomyelinase in the salvage pathway (22). Interestingly, the PKCδ isoform induced the phosphorylation of acid sphingomyelinase at serine 508, leading to its activation and consequent formation of ceramide. The activation of acid sphingomyelinase appeared to contribute to ∼50% of the salvage pathway-induced increase in ceramide (28) (also, see Fig. 4C). This raised the possibility that distinct routes of ceramide metabolism may account for the remainder of ceramide generation. In this study, we investigated glucocerebrosidase GBA1 as a candidate for one of the other routes accounting for PKC-regulated salvage pathway of ceramide formation.Open in a separate windowFIGURE 4.Effects of knockdown of lysosomal enzymes on the generation of ceramide after PMA treatment. A, MCF-7 cells were transfected with 5 nm siRNAs of each of four individual sequences (SCR, GBA1-a, GBA1-b, and GBA1-c) for 48 h and then stimulated with 100 nm PMA for 1 h. Lipids were extracted, and then the levels of the C₁₆-ceramide species were determined by high-performance liquid chromatography-tandem mass spectrometry. The data represent mean ± S.E. of three to nine values. B, MCF-7 cells were transfected with 5 nm siRNAs of SCR or GBA1-a (GBA1) for 48 h and then stimulated with 100 nm PMA for 1 h. Lipids were extracted, and then the levels of individual ceramide species were determined by high-performance liquid chromatography-tandem mass spectrometry. The data represent mean ± S.E. of three to five values. C₁₄-Cer, C₁₄-ceramide; C₁₆-Cer, C₁₆-ceramide; C₁₈-Cer; C₁₈-ceramide; C_18:1-Cer, C_18:1-ceramide; C₂₀-Cer, C₂₀-ceramide; C₂₀-Cer, C₂₄-ceramide; C_24:1-Cer, C_24:1-ceramide. C, MCF-7 cells were transfected with 5 nm siRNAs of SCR, acid sphingomyelinase (ASM), or GBA1-a (GBA1) for 48 h following stimulation with (PMA) or without (Control) 100 nm PMA for 1 h. Lipids were extracted, and then the levels of ceramide species were determined by high-performance liquid chromatography-tandem mass spectrometry. Levels of C₁₆-ceramide are shown. The data represent mean ± S.E. of four to five values. Significant changes from SCR-transfected cells treated with PMA are shown in A–C (^*, p < 0.02; ^**, p < 0.05; ^***, p < 0.01).     

The Diverse Bacterial Community in Intertidal, Anaerobic Sediments at Sapelo Island, Georgia

The phylogenetic diversity and composition of the bacterial community in anaerobic sediments from Sapelo Island, GA, USA were examined using 16S rRNA gene libraries. The diversity of this community was comparable to that of soil, and 1,186 clones formed 817 OTUs at 99% sequence similarity. Chao1 estimators for the total richness were also high, at 3,290 OTUs at 99% sequence similarity. The program RDPquery was developed to assign clones to taxonomic groups based upon comparisons to the RDP database. While most clones could be assigned to describe phyla, fewer than 30% of the clones could be assigned to a described order. Similarly, nearly 25% of the clones were only distantly related (<90% sequence similarity) to other environmental clones, illustrating the unique composition of this community. One quarter of the clones were related to one or more undescribed orders within the γ-Proteobacteria. Other abundant groups included the δ-Proteobacteria, Bacteroidetes, and Cyanobacteria. While these phyla were abundant in other estuarine sediments, the specific members at Sapelo Island appeared to be different from those previously described in other locations, suggesting that great diversity exists between as well as within estuarine intertidal sediments. In spite of the large differences in pore water chemistry with season and depth, differences in the bacterial community were modest over the temporal and spatial scales examined and generally restricted to only certain taxa. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Structural coupling between FKBP12 and buried water

Globular proteins often contain structurally well-resolved internal water molecules. Previously, we reported results from a molecular dynamics study that suggested that buried water (Wat3) may play a role in modulating the structure of the FK506 binding protein-12 (FKBP12) (Park and Saven, Proteins 2005; 60:450-463). In particular, simulations suggested that disrupting a hydrogen bond to Wat3 by mutating E60 to either A or Q would cause a structural perturbation involving the distant W59 side chain, which rotates to a new conformation in response to the mutation. This effectively remodels the ligand-binding pocket, as the side chain in the new conformation is likely to clash with bound FK506. To test whether the protein structure is in effect modulated by the binding of a buried water in the distance, we determined high-resolution (0.92-1.29 A) structures of wild-type FKBP12 and its two mutants (E60A, E60Q) by X-ray crystallography. The structures of mutant FKBP12 show that the ligand-binding pocket is indeed remodeled as predicted by the substitution at position 60, even though the water molecule does not directly interact with any of the amino acids of the binding pocket. Thus, these structures support the view that buried water molecules constitute an integral, noncovalent component of the protein structure. Additionally, this study provides an example in which predictions from molecular dynamics simulations are experimentally validated with atomic precision, thus showing that the structural features of protein-water interactions can be reliably modeled at a molecular level.