Coassembly of enantiomeric amphipathic peptides into amyloid-inspired rippled β-sheet fibrils

Amphipathic peptides composed of alternating hydrophobic and hydrophilic amino acids self-assemble into amyloid-inspired, β-sheet nanoribbon fibrils. Herein, we report a new fibril type that is formed from equimolar mixtures of enantiomeric amphipathic peptides (L- and D-(FKFE)(2)). Spectroscopic analysis indicates that these peptides do not self-sort and assemble into enantiomeric fibrils composed of all-l and all-d peptides, but rather coassemble into fibrils that contain alternating L- and D-peptides in a "rippled β-sheet" orientation. Isothermal titration calorimetry indicates an enthalpic advantage for rippled β-sheet coassembly compared to self-sorted β-sheet assembly of enantiomeric peptides.     

Fundamental studies on the electrokinetic transfer of net cationic peptides across supported liquid membranes

By the application of an electrical potential difference (25 V), 37 different peptides were extracted from 500 μL aqueous sample (10 mM formic acid, positive electrode), through a supported liquid membrane (SLM) impregnated in the walls of a porous hollow fiber, and into 25 μL aqueous acceptor solution (100 mM formic acid, negative electrode) present inside the lumen of the fiber. Most of the peptides were obtained by tryptic digestion of cytochrome c and bovine serum albumin, which yielded complex samples for extraction. Three different SLMs were utilized to correlate the peptides extractability with the highly variable physical-chemical properties of the peptides. The first SLM (pure eugenol) provided an electromembrane extraction system for hydrophobic and intermediate peptides (hydrophilicity values below 0.2), where the extraction of peptides into the SLM was mainly based on solvent interactions. The second SLM (1-octanol/di-isobutylketone/di-(2-ethylhexyl) phosphate) extracted both hydrophobic and hydrophilic peptides (hydrophilicity values in the range from -2 to+1) successfully, and the transfer of peptides was principally based on ionic interactions with di-(2-ethylhexyl) phosphate. The third SLM (1-octanol/15-crown-5 ether) was selective for hydrophobic peptides (negative hydrophilicity values), and complexation of the peptides with the crown ether was important for the migration of peptides into the acceptor solution.     

Structural variety of membrane permeable peptides

Peptide-mediated protein delivery into living cells has been attracting our attention. Among the peptides that have been reported to have carrier activity, the one from the human immunodeficient virus (HIV)-1 Tat has been most often used for the introduction of exogenous macromolecules into cells. We have shown that not only the Tat peptide, but also various arginine-rich peptides showed very similar characteristics in translocation, and the possible presence of ubiquitous internalization mechanisms among the arginine-rich peptides has also been suggested. These arginine-rich peptides includes ones derived from HIV-1 Rev and flock house virus coat proteins. The linear- and branched-chain peptides containing approximately 8 residues of arginine also show a similar ability. In this review, we present the structural variety of membrane permeable peptides and provide a survey of the findings on the translocation of these peptides through the cell membranes.     

Synthesis of Sulfotyrosine‐Containing Peptides by Incorporating Fluorosulfated Tyrosine Using an Fmoc‐Based Solid‐Phase Strategy

Tyrosine O‐sulfation is a common protein post‐translational modification that regulates many biological processes, including leukocyte adhesion and chemotaxis. Many peptides with therapeutic potential contain one or more sulfotyrosine residues. We report a one‐step synthesis for Fmoc‐fluorosulfated tyrosine. An efficient Fmoc‐based solid‐phase peptide synthetic strategy is then introduced for incorporating the fluorosulfated tyrosine residue into peptides of interest. Standard simultaneous peptide‐resin cleavage and removal of the acid‐labile side‐chain protecting groups affords the crude peptides containing fluorosulfated tyrosine. Basic ethylene glycol, serving both as solvent and reactant, transforms the fluorosulfated tyrosine peptides into sulfotyrosine peptides in high yield.     

Application of mass spectrometry to the characterization and quantification of food-derived bioactive peptides

Biologically active peptides are of particular interest in food science and nutrition because they have been shown to play different physiological roles, including antihypertensive, opioid, antimicrobial, and immunostimulating activities. Because these peptides are generated by protein hydrolysis or fermentation, they can represent only minor constituents in a highly complex matrix and therefore, identification of biologically active peptides in food matrixes is a challenging task in food technology. In this context, mass spectrometry (MS) has developed into a necessary tool to assess quality and safety of food and, more recently, to determine the presence and behavior of functional components such as these bioactive peptides. This review highlights the existing methods based on MS to identify, characterize, and quantify food-derived biologically active peptides, taking into account the different ionization sources used for the analysis of these high-value food components. The quantitative determination of bioactive peptides in food products or biological fluids is also discussed.     

Controlling Peptide Self‐Assembly through a Native Chemical Ligation/Desulfurization Strategy

Self‐assembled peptides were synthesized by using a native chemical ligation (NCL)/desulfurization strategy that maintained the chemical diversity of the self‐assembled peptides. Herein, we employed oxo‐ester‐mediated NCL reactions to incorporate cysteine, a cysteine‐based dipeptide, and a sterically hindered unnatural amino acid (penicillamine) into peptides. Self‐assembly of the peptides resulted in the formation of self‐supporting gels. Microscopy analysis indicated the formation of helical nanofibers, which were responsible for the formation of gel matrices. The self‐assembly of the ligated peptides was governed by covalent and non‐covalent interactions, as confirmed by FTIR, CD, fluorescence spectroscopy, and MS (ESI) analyses. Peptide disassembly was induced by desulfurization reactions with tris(2‐carboxyethyl)phosphine (TCEP) and glutathione at 80 °C. Desulfurization reactions of the ligated peptides converted the Cys and penicillamine functionalities into Ala and Val moieties, respectively. The self‐supporting gels showed significant shear‐thinning and thixotropic properties.     

Lasso peptides: structure, function, biosynthesis, and engineering

Covering: up to May 2012Lasso peptides are a class of ribosomally-synthesized and posttranslationally-modified natural products with diverse bioactivities. This review describes the structure and function of all known lasso peptides (as of mid-2012) and covers our current knowledge about the biosynthesis of those molecules. The isolation and characterization of lasso peptides are also covered as are bioinformatics strategies for the discovery of new lasso peptides from genomic sequence data. Several studies on the engineering of new or improved function into lasso peptides are highlighted, and unanswered questions in the field are also described.     

Amphiphilic peptides as models for protein-membrane interactions: interfacial behaviour of sequential Lys- and Leu-based peptides and their penetration into lipid monolayers

Synthetic peptides constructed with doublets of hydrophobic residues tandemly repeated with doublets of positively charged residues, (Leu-Lys-Lys-Leu)_n, were used as models for the study of protein-membrane interactions. Their behaviour has been compared with that of their strictly alternating iso peptides, (Leu-Lys)_n. Both peptides present a random coil structure in pure water. In saline solutions, (Leu-Lys-Lys-Leu)_n peptides adopt an α-helical structure whereas (Leu-Lys)_n transit into a β-sheet structure. These peptides form multilayer assemblies on a pure water subphase but they are organized in monomolecular films on a saline aqueous subphase. The stability of these films increases with the peptide length. Structured peptides (α helices and β sheets) penetrate readily into lipid monolayers, whereas the penetration of unordered peptides is very slow. We have not observed any significant difference between the behaviour of a helices and β-sheet structures.     

基于细胞穿膜肽的药物递送研究进展

从细胞穿膜肽(CPP)的分类、内化机制、与货物的连接和应用四个方面讲述目前人们在对细胞穿膜肽的研究上已经取得的成果。细胞穿膜肽是一种能穿过细胞膜的短肽,可分为阳离子型肽、两亲性肽和疏水性肽。细胞穿膜肽的内化机制主要有内吞作用、直接渗透、依赖于糖蛋白的内化机制和依赖于浓度的内化机制等。近年来,人们合成了多种有实际应用价值的CPP-货物复合物,在细胞穿膜肽的应用上,取得了很多进展和突破。科学家们主要研究将细胞穿膜肽应用于药物递送和细胞成像。     

Hydrolytic reaction by zinc finger mutant peptides: successful redesign of structural zinc sites into catalytic zinc sites

To redesign a metal site originally required for the stabilization of a folded protein structure into a functional metal site, we constructed a series of zinc finger mutant peptides such as zf(CCHG) and zf(GCHH), in which one zinc-coordinating residue is substituted into a noncoordinating one. The mutant peptides having water bound to the zinc ion catalyzed the hydrolysis of 4-nitrophenyl acetate as well as the enantioselective hydrolysis of amino acid esters. All the zinc complexes of the mutant peptides showed hydrolytic activity, depending on their peptide sequences. In contrast, the zinc complex of the wild-type, zf(CCHH), and zinc ion alone exhibited no hydrolytic ability. These results clearly indicate that the catalytic abilities are predominantly attributed to the zinc center in the zinc complexes of the mutant peptides. Kinetic studies of the mutant peptides demonstrated that the catalytic hydrolysis is affected by the electron-donating ability of the protein ligands and the coordination environment. In addition, the pH dependence of the hydrolysis strongly suggests that the zinc-coordinated hydroxide ion participates the catalytic reaction. This report is the first successful study of catalytically active zinc finger peptides.     

多肽分子自组装

源于自然界中广泛存在的蛋白质自组装现象,近年来多肽的自组装逐渐成为材料学和生物医学等领域的研究热点.通过合理调控多肽的分子结构以及改变外界的环境,多肽分子可以利用氢键、疏水性作用、π-π堆积作用等非共价键力自发或触发地自组装形成形态与结构特异的组装体.由于多肽自身具有良好的生物相容性和可控的降解性能,利用多肽自组装技术构建的各种功能性材料在药物控制释放、组织工程支架材料以及生物矿化等领域内有着巨大的应用前景.本文总结了近年来多肽自组装研究的进展,介绍了多肽自组装技术常见的几种结构模型,概括了多肽自组装的机理,并进一步阐述多肽自组装形成的组装体形态及其在材料学和生物医学等领域里的应用.     

Design of self-assembling surfactant-like peptides and their applications

A surfactant is briefly defined as a material that can greatly reduce the surface tension of water when used in very low concentrations. Surfactants are usually organic compounds that are amphiphilic, containing both hydrophobic groups and hydrophilic groups. Therefore, they are soluble in both organic solvents and water. Many surfactants can also assemble in the bulk solution into aggregates such as vesicles and micelles. Self-assembling peptides are a novel category of designer peptides that can undergo spontaneous organization into well-ordered nanostructures with the great potentials in nanotechnology, nanomedicine including 3-dimensional (3-D) cell culture, drug delivery, wound repair, and so on. In this review, we introduce a family of designer surfactant-like peptides: the self-assembling peptides which have been derived by mimicking the structure of traditional surfactants.     

An Optimized Protocol for the Synthesis of Peptides Containing trans-Cyclooctene and Bicyclononyne Dienophiles as Useful Multifunctional Bioorthogonal Probes

Despite the great advances in solid-phase peptide synthesis (SPPS), the incorporation of certain functional groups into peptide sequences is restricted by the compatibility of the building blocks with conditions used during SPPS. In particular, the introduction of highly reactive groups used in modern bioorthogonal reactions into peptides remains elusive. Here, we present an optimized synthetic protocol enabling installation of two strained dienophiles, trans-cyclooctene (TCO) and bicyclononyne (BCN), into different peptide sequences. The two groups enable fast and modular post-synthetic functionalization of peptides, as we demonstrate in preparation of peptide-peptide and peptide-drug conjugates. Due to the excellent biocompatibility, the click-functionalization of the peptides can be performed directly in live cells. We further show that the introduction of both clickable groups into peptides enables construction of smart, multifunctional probes that can streamline complex chemical biology experiments such as visualization and pull-down of metabolically labeled glycoconjugates. The presented strategy will find utility in construction of peptides for diverse applications, where high reactivity, efficiency and biocompatibility of the modification step is critical.     

Disulfide Click Reaction for Stapling of S-terminal Peptides

A disulfide click strategy is disclosed for stapling to enhance the metabolic stability and cellular permeability of therapeutic peptides. A 17-membered library of stapling reagents with adjustable lengths and angles was established for rapid double/triple click reactions, bridging S-terminal peptides from 3 to 18 amino acid residues to provide 18- to 48-membered macrocyclic peptides under biocompatible conditions. The constrained peptides exhibited enhanced anti-HCT-116 activity with a locked α-helical conformation (IC₅₀=6.81 μM vs. biological incompetence for acyclic linear peptides), which could be unstapled for rehabilitation of the native peptides under the assistance of tris(2-carboxyethyl)phosphine (TCEP). This protocol assembles linear peptides into cyclic peptides controllably to retain the diverse three-dimensional conformations, enabling their cellular uptake followed by release of the disulfides for peptide delivery.     

Fluorous Tagged Peptides for Intracellular Delivery and Biomedical Imaging

Fluorous tagged peptides have shown promising features for biomedical applications such as drug delivery and multimodal imaging. The bioconjugation of fluoroalkyl ligands onto cargo peptides greatly enhances their proteolytic stability and membrane penetration via a proposed “fluorine effect”. The tagged peptides also efficiently deliver other biomolecules such as DNA and siRNA into cells via a co-assembly strategy. The fluoroalkyl chains on peptides with antifouling properties enable efficient gene delivery in the presence of serum proteins. Besides intracellular biomolecule delivery, the amphiphilic peptides can be used to stabilized perfluorocarbon-filled microbubbles for ultrasound imaging. The fluorine nucleus on fluoroalkyls provides intrinsic probes for background-free magnetic resonance imaging. Labeling of fluorous tags with radionuclide ¹⁸F also allows tracing the biodistribution of peptides via positron emission tomography imaging. This mini-review will discuss properties and mechanism of the fluorous tagged peptides in these applications.     

Perfluoroaryl Bicyclic Cell‐Penetrating Peptides for Delivery of Antisense Oligonucleotides

Exon‐skipping antisense oligonucleotides are effective treatments for genetic diseases, yet exon‐skipping activity requires that these macromolecules reach the nucleus. While cell‐penetrating peptides can improve delivery, proteolytic instability often limits efficacy. It is hypothesized that the bicyclization of arginine‐rich peptides would improve their stability and their ability to deliver oligonucleotides into the nucleus. Two methods were introduced for the synthesis of arginine‐rich bicyclic peptides using cysteine perfluoroarylation chemistry. Then, the bicyclic peptides were covalently linked to a phosphorodiamidate morpholino oligonucleotide (PMO) and assayed for exon skipping activity. The perfluoroaryl cyclic and bicyclic peptides improved PMO activity roughly 14‐fold over the unconjugated PMO. The bicyclic peptides exhibited increased proteolytic stability relative to the monocycle, demonstrating that perfluoroaryl bicyclic peptides are potent and stable delivery agents.     

The interaction of helical polypeptides with biological model membranes

Proton-decoupled solid-state ¹⁵N NMR spectroscopy was used to investigate helical peptides reconstituted into oriented phospholipid bilayers. Hydrophobic channel peptides such as the N-terminal region of Vpu of human immunodeficiency virus (HIV-1) adopt transmembrane orientations, whereas amphipathic peptide antibiotics are oriented parallel to the bilayer surface. The alignment of helical peptides in lipid membranes was analysed in some detail using model peptides. In particular, peptides with pH-dependent topology and a series of peptides that allow one to study the contributions of specific interactions were designed. The energies of transfer of several amino acids from the in-plane to transmembrane localisation were determined. In addition, the alignment of peptides and phospholipids under conditions of hydrophobic mismatch have been investigated in considerable detail.     

Peptide Nanotubes

The self‐assembly of different classes of peptide, including cyclic peptides, amyloid peptides and surfactant‐like peptides into nanotube structures is reviewed. The modes of self‐assembly are discussed. Additionally, applications in bionanotechnology and synthetic materials science are summarized.     

A critical cross-validation of high throughput structural binding prediction methods for pMHC

T-cells recognize antigens via their T-cell receptors. The major histocompatibility complex (MHC) binds antigens in a specific way, transports them to the surface and presents the peptides to the TCR. Many in silico approaches have been developed to predict the binding characteristics of potential T-cell epitopes (peptides), with most of them being based solely on the amino acid sequence. We present a structural approach which provides insights into the spatial binding geometry. We combine different tools for side chain substitution (threading), energy minimization, as well as scoring methods for protein/peptide interfaces. The focus of this study is on high data throughput in combination with accurate results. These methods are not meant to predict the accurate binding free energy but to give a certain direction for the classification of peptides into peptides that are potential binders and peptides that definitely do not bind to a given MHC structure. In total we performed approximately 83,000 binding affinity prediction runs to evaluate interactions between peptides and MHCs, using different combinations of tools. Depending on the tools used, the prediction quality ranged from almost random to around 75% of accuracy for correctly predicting a peptide to be either a binder or a non-binder. The prediction quality strongly depends on all three evaluation steps, namely, the threading of the peptide, energy minimization and scoring.