β-Glutamine-mediated self-association of transmembrane β-peptides within lipid bilayers

10-Residue MyD88-Peptide Adopts β-Sheet Structure, Self-Assembles, Binds to Lipopolysaccharides, and Rescues Mice from Endotoxin-Mediated Lung-Infection and Death

Naturally occurring cationic antimicrobial peptides (AMPs) mostly adopt α-helical structures in bacterial membrane mimetic environments. To explore the design of novel β-sheet AMPs, we identified two short cationic amphipathic β-strand segments from the crystal structure of the innate immune protein, MyD88. Interestingly, of these, the 10-residue arginine-valine-rich synthetic MyD88-segment, KRCRRMVVVV (M3), exhibited β-sheet structure when bound to the outer membrane Gram-negative bacterial component, LPS. Isothermal titration calorimetric data showed that M3 bound to LPS with high affinity, and the interaction was hydrophobic in nature. Supporting these observations, computational studies indicated strong interactions of multiple and consecutive valine residues of M3 with the acyl chain of LPS. Moreover, M3 adopted nanosheet and nanofibrillar structure in 25% acetonitrile/water and isopropanol, respectively. M3 showed substantial antibacterial activities against both Gram-positive and Gram-negative bacteria which it appreciably retained in the presence of human serum and physiological salts. M3 was non-hemolytic against human red blood cells and non-cytotoxic to 3T3 cells up to 200 μM and to mice in vivo at a dose of 40 mg/kg. Furthermore, M3 neutralized LPS-induced pro-inflammatory responses in THP-1 cells and rat bone marrow-derived macrophages. Consequently, M3 attenuated LPS-mediated lung inflammation in mice and rescued them (80% survival at 10 mg/kg dose) against a lethal dose of LPS. The results demonstrate the identification of a 10-mer LPS-interacting, β-sheet peptide from MyD88 with the ability to form nanostructures and in vivo activity against LPS challenge in mice. The identified M3-template provides scope for designing novel bioactive peptides with β-sheet structures and self-assembling properties.

Chalcogen bonding mediates the formation of supramolecular helices of azapeptides in crystals

To explore whether chalcogen bonding was able to drive the formation of supramolecular helices, alanine-based azapeptides containing a β-turn structure, with a thiophene group, respectively, incorporated in the N- or C-terminus, were employed as helical building blocks. While the former derivative formed a supramolecular M-helix via intermolecular SS chalcogen bonding in crystals, the latter formed P-helix via intermolecular SO chalcogen bonding.

Transmembrane β-peptide helices as molecular rulers at the membrane surface

β-Peptides are known to form 14-helices with high conformational rigidity, helical persistence length, and well-defined spacing and orientation regularity of amino acid side chains. Therefore, β-peptides are well suited to serve as backbone structures for molecular rulers. On the one hand, they can be functionalized in a site-specific manner with molecular probes or fluorophores, and on the other hand, the β-peptide helices can be recognized and anchored in a biological environment of interest. In this study, the β-peptide helices were anchored in lipid bilayer membranes, and the helices were elongated in the outer membrane environment. The distances of the covalently bound probes to the membrane surface were determined using graphene-induced energy transfer (GIET) spectroscopy, a method based on the distance-dependent quenching of a fluorescent molecule by a nearby single graphene sheet. As a proof of principle, the predicted distances were determined for two fluorophores bound to the membrane-anchored β-peptide molecular ruler.

The Landscape of Pseudomonas aeruginosa Membrane-Associated Proteins

Background: Pseudomonas aeruginosa cell envelope-associated proteins play a relevant role in infection mechanisms. They can contribute to the antibiotic resistance of the bacterial cells and be involved in the interaction with host cells. Thus, studies contributing to elucidating these key molecular elements are of great importance to find alternative therapeutics. Methods: Proteins and peptides were extracted by different methods and analyzed by Multidimensional Protein Identification Technology (MudPIT) approach. Proteomic data were processed by Discoverer2.1 software and multivariate statistics, i.e., Linear Discriminant Analysis (LDA), while the Immune Epitope Database (IEDB) resources were used to predict antigenicity and immunogenicity of experimental identified peptides and proteins. Results: The combination of 29 MudPIT runs allowed the identification of 10,611 peptides and 2539 distinct proteins. Following application of extraction methods enriching specific protein domains, about 15% of total identified peptides were classified in trans inner-membrane, inner-membrane exposed, trans outer-membrane and outer-membrane exposed. In this scenario, nine outer membrane proteins (OprE, OprI, OprF, OprD, PagL, OprG, PA1053, PAL and PA0833) were predicted to be highly antigenic. Thus, they were further processed and epitopes target of T cells (MHC Class I and Class II) and B cells were predicted. Conclusion: The present study represents one of the widest characterizations of the P. aeruginosa membrane-associated proteome. The feasibility of our method may facilitates the investigation of other bacterial species whose envelope exposed protein domains are still unknown. Besides, the stepwise prioritization of proteome, by combining experimental proteomic data and reverse vaccinology, may be useful for reducing the number of proteins to be tested in vaccine development.

Supramolecular Self-Assembly of β3 -Peptides Mediated by Janus-Type Recognition Units

To gain mechanistic insights, natural systems with biochemical relevance are inspiring for the creation of new biomimetics with unique properties and functions. Despite progress in rational design and protein engineering, folding and intramolecular organization of individual components into supramolecular structures remains challenging and requires controlled methods. Foldamers, such as β-peptides, are structurally well defined with rigid conformations and suitable for the specific arrangement of recognition units. Herein, we show the molecular arrangement and aggregation of β3 -peptides into a hexameric helix bundle. For this purpose, β-amino acid side chains were modified with cyanuric acid and triamino-s-triazine as complementary recognition units. The pre-organization of the β3 -peptides leads these Janus molecule pairs into a hexameric arrangement and a defined rosette nanotube by stacking. The helical conformation of the subunits was indicated by circular dichroism spectroscopy, while the supramolecular arrangement was detected by dynamic light scattering and confirmed by high-resolution electrospray ionization mass spectrometry (ESI-HRMS).

Membrane-Associated Nucleobase-Functionalized β-Peptides (β-PNAs) Affecting Membrane Support and Lipid Composition

Protein-membrane interactions are essential to maintain membrane integrity and control membrane morphology and composition. Cytoskeletal proteins in particular are known to interact to a high degree with lipid bilayers and to line the cytoplasmic side of the plasma membrane with an extensive network structure. In order to gain a better mechanistical understanding of the protein-membrane interplay and possible membrane signaling, we started to develop a model system based on β-peptide nucleic acids (β-PNAs). These β-peptides are known to form stable hydrogen-bonded aggregates due to their helical secondary structure, which serve to pre-organize the attached nucleobases. After optimization of the β-PNA solid-phase peptide synthesis and validation of helix formation, the ability of the novel β-PNAs to dimerize and interact with lipid bilayers was investigated by both fluorescence and circular dichroism spectroscopy. It was shown that duplex formation occurs rapidly and with high specificity and could also be detected on the surfaces of the lipid bilayers. Hereby, the potential of a β-PNA-based peptide system to mimic membrane-associated protein networks could be demonstrated.

Synthesis and characterization of β-peptide helices as transmembrane domains in lipid model membranes

Aggregation, orientation and dynamics of transmembrane helices are of relevance for protein function and transmembrane signaling. To explore the interactions of transmembrane helices and the interdependence of peptide structure and lipid composition of the membranes, β-peptides were explored as model transmembrane domains. Various hydrophobic β-peptide sequences were synthesized by solid phase peptide synthesis. Conformational analyses of β-peptide helices were performed in organic solvents (methanol and 2,2,2-trifluoroethanol) and in large unilamellar liposomes (dimyristoylphosphatidylcholine, dipalmitoylphosphatidylcholine and dioleoylphosphatidylcholine) indicating 12- and 14-helix conformations, depending on β³ -amino acid sequences. The intrinsic tryptophan fluorescence of β³ -homotryptophan units inserted in the center or near the end of the sequence was used to verify the membrane insertion of the β-peptides. A characteristic blue shift with peripheral β³ -homotryptophan compared with β-peptides with central tryptophan served as indication for a transmembrane orientation of the β-peptides within the lipid bilayer. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.