Self-assembly of diphenylalanine with preclick components as capping groups.

Alkyne and azide, which are commonly used in the cycloaddition reaction recognized as "click chemistry", have been used as capping groups of two engineered diphenylalanine (FF) derivatives due to their ability to form weak intermolecular interactions (i.e. dipole-π and π-π stacking). In Poc-FF-N3, alkyne and azide act as N- and C-terminal capping groups, respectively, while such positions are exchanged in N3-FF-OPrp. The self-assembly of such two synthesized peptides has been extensively studied in their "pre-click" state, considering the influence of three different factors: the peptide concentration, the polarity of the medium, and the nature of the substrate. Poc-FF-N3 assembles into microfibers that, depending on the medium and the substrate, can aggregate hierarchically in supramolecular structures with different morphologies. The most distinctive one corresponds to very stable birefringent dendritic-like microstructures, which are derived from the ordered agglomeration of microfibers. These branched supramolecular structures, which are observed under a variety of conditions, are relatively uncommon in short FF sequences. At the molecular level, Poc-FF-N3 organizes in antiparallel ß-sheets stabilized by N-HO intermolecular hydrogen bonds and re-enforced by weak interactions between the azide and alkyne groups of neighbouring molecules. In contrast, N3-FF-OPrp exhibits a very poor tendency to organize into structures with a well-defined morphology. Theoretical calculations on model complexes indicate that the tendency of the latter peptide to organize into small amorphous agglomerates is due to its poor ability to form specific intermolecular interactions in comparison with Poc-FF-N3. The implications of the weak interactions induced by the alkyne and azide groups, which strengthen peptidepeptide hydrogen bonds and π-ladders due to the stacked aromatic phenyl side groups, are discussed.

Effect of Solvent Choice on the Self-Assembly Properties of a Diphenylalanine Amphiphile Stabilized by an Ion Pair.

A diphenylalanine (FF) amphiphile blocked at the C terminus with a benzyl ester (OBzl) and stabilized at the N terminus with a trifluoroacetate (TFA) anion was synthetized and characterized. Aggregation of peptide molecules was studied by considering a peptide solution in an organic solvent and adding pure water, a KCl solution, or another organic solvent as co-solvent. The choice of the organic solvent and co-solvent and the solvent/co-solvent ratio allowed the mixture to be tuned by modulating the polarity, the ionic strength, and the peptide concentration. Differences in the properties of the media used to dissolve the peptides resulted in the formation of different self-assembled microstructures (e.g. fibers, branched-like structures, plates, and spherulites). Furthermore, crystals of TFA⋅FF-OBzl were obtained from the aqueous peptide solutions for X-ray diffraction analysis. The results revealed a hydrophilic core constituted by carboxylate (from TFA), ester, and amide groups, and the core was found to be surrounded by a hydrophobic crown with ten aromatic rings. This segregated organization explains the assemblies observed in the different solvent mixtures as a function of the environmental polarity, ionic strength, and peptide concentration.

Alamethicin Supramolecular Organization in Lipid Membranes from 19F Solid-State NMR.

Alamethicins (ALMs) are antimicrobial peptides of fungal origin. Their sequences are rich in hydrophobic amino acids and strongly interact with lipid membranes, where they cause a well-defined increase in conductivity. Therefore, the peptides are thought to form transmembrane helical bundles in which the more hydrophilic residues line a water-filled pore. Whereas the peptide has been well characterized in terms of secondary structure, membrane topology, and interactions, much fewer data are available regarding the quaternary arrangement of the helices within lipid bilayers. A new, to our knowledge, fluorine-labeled ALM derivative was prepared and characterized when reconstituted into phospholipid bilayers. As a part of these studies, C19F3-labeled compounds were characterized and calibrated for the first time, to our knowledge, for 19F solid-state NMR distance and oligomerization measurements by centerband-only detection of exchange (CODEX) experiments, which opens up a large range of potential labeling schemes. The 19F-19F CODEX solid-state NMR experiments performed with ALM in POPC lipid bilayers and at peptide/lipid ratios of 1:13 are in excellent agreement with molecular-dynamics calculations of dynamic pentameric assemblies. When the peptide/lipid ratio was lowered to 1:30, ALM was found in the dimeric form, indicating that the supramolecular organization is tuned by equilibria that can be shifted by changes in environmental conditions.

Hierarchical self-assembly of di-, tri- and tetraphenylalanine peptides capped with two fluorenyl functionalities: from polymorphs to dendrites.

Homopeptides with 2, 3 and 4 phenylalanine (Phe) residues and capped with fluorenylmethoxycarbonyl and fluorenylmethyl esters at the N-terminus and C-terminus, respectively, have been synthesized to examine their self-assembly capabilities. Depending on the conditions, the di- and triphenylalanine derivatives self-organize into a wide variety of stable polymorphic structures, which have been characterized: stacked braids, doughnut-like shapes, bundled arrays of nanotubes, corkscrew-like shapes and spherulitic microstructures. These highly aromatic Phe-based peptides also form incipient branched dendritic microstructures, even though they are highly unstable, making their manipulation very difficult. Conversely, the tetraphenylalanine derivative spontaneously self-assembles into stable dendritic microarchitectures made of branches growing from nucleated primary frameworks. The fractal dimension of these microstructures is ∼1.70, which provides evidence for self-similarity and two-dimensional diffusion controlled growth. DFT calculations at the M06L/6-31G(d) level have been carried out on model ß-sheets since this is the most elementary building block of Phe-based peptide polymorphs. The results indicate that the antiparallel ß-sheet is more stable than the parallel one, with the difference between them growing with the number of Phe residues. Thus, the cooperative effects associated with the antiparallel disposition become more favorable when the number of Phe residues increases from 2 to 4, while those of the parallel disposition remained practically constant.

Synthesis of α-aminoboronic acids.

This review describes available methods for the preparation of α-aminoboronic acids in their racemic or in their enantiopure form. Both, highly stereoselective syntheses and asymmetric procedures leading to the stereocontrolled generation of α-aminoboronic acid derivatives are included. The preparation of acyclic, carbocyclic and azacyclic α-aminoboronic acid derivatives is covered. Within each section, the different synthetic approaches have been classified according to the key bond which is formed to complete the α-aminoboronic acid skeleton.

Self-Assembly of Tetraphenylalanine Peptides.

Three different tetraphenylalanine (FFFF) based peptides that differ at the N- and C-termini have been synthesized by using standard procedures to study their ability to form different nanoassemblies under a variety of conditions. The FFFF peptide assembles into nanotubes that show more structural imperfections at the surface than those formed by the diphenylalanine (FF) peptide under the same conditions. Periodic DFT calculations (M06L functional) were used to propose a model that consists of three FFFF molecules defining a ring through head-to-tail NH3(+)⋅⋅⋅(-)OOC interactions, which in turn stack to produce deformed channels with internal diameters between 12 and 16 Å. Depending on the experimental conditions used for the peptide incubation, N-fluorenylmethoxycarbonyl (Fmoc) protected FFFF self-assembles into a variety of polymorphs: ultra-thin nanoplates, fibrils, and star-like submicrometric aggregates. DFT calculations indicate that Fmoc-FFFF prefers a parallel rather than an antiparallel ß-sheet assembly. Finally, coexisting multiple assemblies (up to three) were observed for Fmoc-FFFF-OBzl (OBzl = benzyl ester), which incorporates aromatic protecting groups at the two peptide terminals. This unusual and noticeable feature is attributed to the fact that the assemblies obtained by combining the Fmoc and OBzl groups contained in the peptide are isoenergetic.

The fluorescence and infrared absorption probe para-cyanophenylalanine: Effect of labeling on the behavior of different membrane-interacting peptides.

Total syntheses and complete characterizations of singly substituted PheCN -based analogs of alamethicin AlaP, which is active on model and natural membranes, and the TM peptide, which inserts in a transmembrane orientation in lipid bilayers, are reported. The syntheses of the AlaP analogs were performed in solution, while those of TM and its analogs were carried out by solid phase. Using the cyanophenyl fluorescence and infrared (IR) absorption probe, an in-depth investigation of the self-association, membrane-interacting, permeabilizing, and orientation properties of these peptides were conducted. The aromatic residue incorporated induces only a negligible modification to the properties of the parent peptides. The PheCN IR absorption band was located between 2228 and 2230 cm(-1) for all peptides, irrespective of the position of labeling. By contrast, as the width of this band varied significantly with the depth of probe insertion in the bilayer, it could represent a good marker of the PheCN position in phospholipid membranes.

Solution synthesis, conformational analysis, and antimicrobial activity of three alamethicin F50/5 analogs bearing a trifluoroacetyl label.

We prepared, by solution-phase methods, and fully characterized three analogs of the membrane-active peptaibiotic alamethicin F50/5, bearing a single trifluoroacetyl (Tfa) label at the N-terminus, at position 9 (central region) or at position 19 (C-terminus), and with the three Gln at positions 7, 18, and 19 replaced by Glu(OMe) residues. To add the Tfa label at position 9 or 19, a γ-trifluoroacetylated α,γ-diaminobutyric acid (Dab) residue was incorporated as a replacement for the original Val(9) or Glu(OMe)(19) amino acid. We performed a detailed conformational analysis of the three analogs (using FT-IR absorption, CD, 2D-NMR, and X-ray diffraction), which clearly showed that Tfa labeling does not introduce any dramatic backbone modification in the predominantly α-helical structure of the parent peptaibiotic. The results of an initial solid-state (19)F-NMR study on one of the analogs favor the conclusion that the Tfa group is a very promising reporter for the analysis of peptaibioticmembrane interactions. Finally, we found that the antimicrobial activities of the three newly synthesized analogs depend on the position of the Tfa label in the peptide sequence.

Electro-biocompatibility of conjugates designed by chemical similarity.

The roughness and thickness of films formed by hybrid conjugates prepared by coupling poly(3,4-ethylenedioxythiophene) and synthetic amino acids bearing a 3,4-ethylenedioxythiophene group in the side chain have been significantly increased using a new synthetic approach. This procedure also provoked a more effective incorporation of the amino acid at the end of the polymer chains, as has been reflected by the electronic and electrochemical properties. Although the surface polarity of all these materials is similar to that of formamide, the hydrophilicity of the conjugates is higher than that of the conducting polymer. The surface energy of all the investigated systems is dominated by the dispersive component, even though the role played by the polar contribution is more important for the conjugates than for the conducting polymer. On the other hand, all the prepared materials behave as bioactive matrices. The electrochemical response of the conjugates coated with cells reflects the electro-compatibility of these two-component substrates. Thus, the ability to exchange charge reversibly of all conjugates increases considerably when they are coated with cellular monolayers, which has attributed to favorable interactions at the interface formed by the conjugate surface and the cellular monolayer.

A single-residue substitution inhibits fibrillization of Ala-based pentapeptides. A spectroscopic and molecular dynamics investigation.

The aggregation properties of two Ala-based pentapeptides were investigated by spectroscopic techniques and molecular dynamics (MD) simulations. The two peptides, both functionalized at the N-terminus with a pyrenyl group, differ in the insertion of an α-aminoisobutyric acid residue at position 4. We showed that this single modification of the homo-peptide sequence inhibits the aggregation of the pentapeptide in aqueous solutions. Atomic force microscopy imaging revealed that the two peptides form mesoscopic aggregates of very different morphologies when deposited on mica. MD experiments showed that the two peptides have a very different propensity to form ß-pleated sheet structures, as confirmed by our spectroscopic measurements. The implications of these findings for our understanding of the mechanism leading to the formation of amyloid structures, primary responsible for numerous neurodegenerative diseases, are also discussed.

Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing.

We present a chemical strategy to engineer analogs of the tumor-homing peptide CREKA (Cys-Arg-Glu-Lys-Ala), which binds to fibrin and fibrin-associated clotted plasma proteins in tumor vessels (Simberg et al. in Proc Natl Acad Sci USA 104:932-936, 2007) with improved ability to inhibit tumor growth. Computer modeling using a combination of simulated annealing and molecular dynamics were carried out to design targeted replacements aimed at enhancing the stability of the bioactive conformation of CREKA. Because this conformation presents a pocket-like shape with the charged groups of Arg, Glu and Lys pointing outward, non-proteinogenic amino acids α-methyl and N-methyl derivatives of Arg, Glu and Lys were selected, rationally designed and incorporated into CREKA analogs. The stabilization of the bioactive conformation predicted by the modeling for the different CREKA analogs matched the tumor fluorescence results, with tumor accumulation increasing with stabilization. Here we report the modeling, synthetic procedures, and new biological assays used to test the efficacy and utility of the analogs. Combined, our results show how studies based on multi-disciplinary collaboration can converge and lead to useful biomedical advances.

Novel peptide foldameric motifs: a step forward in our understanding of the fully-extended conformation/3(10)-helix coexistence.

The fully-extended, multiple C(5), conformation or 2.0(5) helix is a very appealing peptide secondary structure, in particular for its potential use as a molecular spacer, as it is characterized by the longest elevation (as high as 3.62 Å) between the α-carbon atoms of two consecutive α-amino acids. Despite this intriguing property, however, it is only poorly investigated and understood. Here, using a complete series of C(α,α)-diethylglycine (Deg) homo-oligopeptide esters to the pentamer level, we exploited the properties of a fluorophore and a quencher, synthetically positioned at the N- and C-termini of the main chain, respectively, to check the applicability of the fully-extended conformation as a rigid molecular spacer. The fluorescence study was complemented by FT-IR absorption and NMR conformational investigations. The X-ray diffraction structures of selected compounds are also reported. Unfortunately, we find that, even in a solvent of low polarity, such as chloroform, in this peptide series an equilibrium does take place between the fragile fully-extended conformation and the 3(10)-helical structure, the latter becoming more and more stable as the main chain is elongated. Since the Deg homo-peptide esters lacking any terminal aromatic group, previously investigated, are known to adopt a stable fully-extended conformation in chloroform solution, we tend to attribute the 3D-structure instability observed in this work to the presence of multiple aromatic rings in their blocking groups.

Linear and two-dimensional infrared spectroscopic study of the amide I and II modes in fully extended peptide chains.

We have carried out structural determination of capped C(α,α)-diethylglycine (Deg) homopeptides with different chain lengths, Ac-(Deg)(n)-OtBu (n = 2-5), solvated in CDCl(3), and investigated vibrational properties of the amide I and II modes by linear and 2D IR spectroscopy, ONIOM calculations, and molecular dynamics simulations. 2D IR experiments were performed in the amide I region using the rephasing pulse sequence under the double-crossed polarization and the nonrephasing sequence under a new polarization configuration to measure cross-peak patterns in the off-diagonal regions. The 2D IR spectra measured in the amide I and II regions reveal complex couplings between these modes. Model spectral calculations finely reproduced the measured spectral profiles by using vibrational parameters that were very close to the values predicted by the ONIOM method. The agreement led to a conclusion that peptide backbones are fully extended with the dihedral angles (ϕ,ψ) ≈ (±180°,±180°) and that a sequence of intramolecular C(5) hydrogen bonds forms along the entire chain regardless of the chain length. This conclusion was endorsed by analysis of the molecular dynamics trajectories for n = 3 and 5 that showed an exclusive population of the C(5) conformation. The conformationally well-restrained Deg homopeptides serve as an ideal linear exciton chain, which is scarcely obtainable by protein amino acids. We investigated excitonic properties of the linear chain through analytic modeling and compared the measurement and calculation results of the amide I and II modes. The integrated intensity of the amide II band is larger than that of the amide I for the C(5) structure, untypical behavior in contrast with other secondary structures. This comprehensive study characterized the amide I and II spectral signatures of the fully extended conformation, which will facilitate the conformational analysis of artificial oligopeptides that contain such structural motifs.

Synthesis, preferred conformation, and membrane activity of medium-length peptaibiotics: tylopeptin B.

The solid-phase synthesis and full chemical characterization of the medium-length (14-amino acid residues) peptaibol with antibiotic properties of tylopeptin B, originally extracted from the fruiting body of the mushroom Tylopilus neofelleus, are described. These data are accompanied by the results on the solution-phase synthesis via the segment condensation approach of a selected, side-chain protected, analog. A solution conformational analysis, performed by the combined use of FTIR absorption, circular dichroism, and 2D-NMR (the latter technique coupled to molecular dynamics calculations), favors the conclusion that the 3D-structure of tylopeptin B is largely helical with a preference for the alpha- or the 3(10)-helix type depending upon the nature of the solvent. Helix topology and (partial) amphiphilic character are responsible for the observed membrane-modifying properties of this peptaibiotic.

Structure of N,N'-bis(amino acids) in the solid state and in solution. A 13C and 15N CPMAS NMR study.

Three bis(amino acids) linked by the amino groups have been prepared and structurally characterized. We have named them Gly-Gly, Ala-Ala and Gly-Ala (or Ala-Gly). These compounds have been characterized by NMR both in solution and in the solid state. They exist as zwitterions with the ammonium group proximal to the carboxylate anion. In the case of Gly-Ala, a dynamic situation is observed by CPMAS NMR ((13)C and (15)N) corresponding to a double proton migration between two proximal tautomers.

Structural analysis of a beta-helical protein motif stabilized by targeted replacements with conformationally constrained amino acids.

Here we study conformational stabilization induced in a beta-helical nanostructure by position-specific mutations. The nanostructure is constructed through the self-assembly of the beta-helical building block excised from E. coli galactoside acetyltransferase (PDB code 1krr , chain A; residues 131-165). The mutations involve substitutions by cyclic, conformationally constrained amino acids. Specifically, a complete structural analysis of the Pro-Xaa-Val sequence [with Xaa being Gly, Ac 3c (1-aminocyclopropane-1-carboxylic acid) and Ac 5c (1-aminocyclopentane-1-carboxylic acid)], corresponding to the 148-150 loop region in the wild-type (Gly) and mutated (Ac 3c and Ac 5c) 1krr , has been performed using Molecular Dynamics simulations and X-ray crystallography. Simulations have been performed for the wild-type and mutants of three different systems, namely the building block, the nanoconstruct and the isolated Pro-Xaa-Val tripeptide. Furthermore, the crystalline structures of five peptides of Pro-Xaa-Val or Xaa-Val sequences have been solved by X-ray diffraction analysis and compared with theoretical predictions. Both the theoretical and crystallographic studies indicate that the Pro-Ac n c-Val sequences exhibit a high propensity to adopt turn-like conformations, and this propensity is little affected by the chemical environment. Overall, the results indicate that replacement of Gly149 by Ac 3c or Ac 5c significantly reduce the conformational flexibility of the target site enhancing the structural specificity of the building block and the nanoconstruct derived from the 1krr beta-helical motif.