Nucleation of the β-hairpin structure in a linear hybrid peptide containing α-, β- and γ-amino acids

Synthesis and conformational studies of a short linear peptide containing a pyrrole amino acid (1, Paa) and a furan amino acid (2, Faa), namely Boc-hGly-Faa-d-Pro-Gly-Paa-hGly-Faa-OMe (3), were carried out in which it was established that peptide 3 adopted a well-defined β-hairpin structure in DMSO-d₆.     

Supramolecular peptide helix from a novel double turn forming peptide containing a β-amino acid

A single-crystal X-ray diffraction study of the terminally protected tetrapeptide Boc-β-Ala-Aib-Leu-Aib-OMe 1 (Aib: α-aminoisobutyric acid; β-Ala: β-Alanine) reveals that it adopts a new type of double turn structure which self-associates to form a unique supramolecular helix through intermolecular hydrogen bonds. Scanning electron microscopic studies show that peptide 1 exhibits amyloid-like fibrillar morphology in the solid state.     

Metadynamics study of a β-hairpin stability in mixed solvents

Understanding the molecular mechanisms that allow some organisms to survive in extremely harsh conditions is an important achievement that might disclose a wide range of applications and that is constantly drawing the attention of many research fields. The high adaptability of these living creatures is related to the presence in their tissues of a high concentration of osmoprotectants, small organic, highly soluble molecules. Despite osmoprotectants having been known for a long time, a full disclosure of the machinery behind their activity is still lacking. Here we describe a computational approach that, taking advantage of the recently developed metadynamics technique, allows one to fully describe the free energy surface of a small β-hairpin peptide and how it is affected by an osmoprotectant, glycine betaine (GB) and for comparison by urea, a common denaturant. Simulations led to relevant thermodynamic information, including how the free energy difference of denaturation is affected by the two cosolvents; unlike urea, GB caused a considerable increase of the folded basin stability, which transposes into a higher melting temperature. NMR experiments confirmed the picture derived from the theoretical study. Further molecular dynamics simulations of selected conformations allowed investigation into deeper detail the role of GB in folded state protection. Simulations of the protein in GB solutions clearly showed an excess of osmoprotectant in the solvent bulk, rather than in the protein domain, confirming the exclusion from the protein surface, but also highlighted interesting features on its interactions, opening to new scenarios besides the classic "indirect mechanism" hypothesis.     

The design and synthesis of a novel organophosphorus compound containing the structure of both β-amino acid and β-aminophosphonate

<正>A novel organophosphorus compound containing the structure of bothβ-amino acid andβ-aminophosphonate is designed and synthesized.Arbuzov reaction with P(OEt)_3,the N-Boc protected iodide 3 cannot provide the desired product but 2-oxazolidinone 4 because of the neighboring-group participation of the Boc moiety.To avoid the intramolecular participation of the carbamates,the Ts protecting group is employed and the Ts-protected iodide 5 affords the target product successfully.     

Evaluating force field accuracy with long-time simulations of a β-hairpin tryptophan zipper peptide

We have combined graphics processing unit-accelerated all-atom molecular dynamics with parallel tempering to explore the folding properties of small peptides in implicit solvent on the time scale of microseconds. We applied this methodology to the synthetic β-hairpin, trpzip2, and one of its sequence variants, W2W9. Each simulation consisted of over 8 μs of aggregated virtual time. Several measures of folding behavior showed good convergence, allowing comparison with experimental equilibrium properties. Our simulations suggest that the intramolecular interactions of tryptophan side chains are responsible for much of the stability of the native fold. We conclude that the ff99 force field combined with ff96 φ and ψ dihedral energies and an implicit solvent can reproduce plausible folding behavior in both trpzip2 and W2W9.     

Stereo-regulated synthesis of peptides containing a β-trifluoromethyl-β-amino acid

For the chemical conversions of a β-trifluoromethyl-β-amino acid ((S)-4,4,4-trifluoro-3-aminobutyric acid, 1), such as the N-terminus protection with benzyloxycarbonyl or tert-butoxycarbonyl group, the C-terminus protection with benzyl or tert-butyl group, and peptide elongation at the both termini, highly practical protocols were established. Through these conversions, the stereochemistry of 1 and/or its condensation counterpart was maintained. Because the protocols developed here are indispensable for the application of 1 in peptide engineering, they would expand the utility of 1 and its derivatives.     

Thermophysical property characterization of aqueous amino acid salt solutions containing α-aminobutyric acid

In this study, density, electrical conductivity, refractive index and viscosity of aqueous potassium and sodium salt solutions of α-aminobutyric acid were presented. Measurements were done over the temperature range (303.15 to 343.15) K and atmospheric pressure for salt compositions from x₁ = 0.009 to 0.062. A modified Graber et al. equation was used to correlate the density, electrical conductivity, and refractive index with temperature and composition leading to average absolute deviations (AAD) between the predicted and calculated values of 0.04%, 0.7%, and 0.01%, respectively. The viscosity data were represented as a function of temperature and composition via Vogel–Tamman–Fulcher (VTF) type equation at an AAD of 0.6%.     

Identification of α- and β-hydroxy acid containing cyclodepsipeptides in natural peptide mixtures using negative ion mass spectrometry

Natural peptide libraries often contain cyclodepsipeptides containing α- or β-hydroxy residues. Extracts of fungal hyphae of Isaria yield a microheterogenous cyclodepsipeptide mixture in which two classes of molecules can be identified by mass spectral fragmentation of negative ions. In the case of isaridins, which contain an α-hydroxy residue and a β-amino acid residue, a characteristic product ion corresponding to a neutral loss of 72 Da is obtained. In addition, neutral loss of water followed by a 72 Da loss is also observed. Two distinct modes of fragmentation rationalize the observed product ion distribution. The neutral loss of 72 Da has also been obtained for a roseotoxin component, which is also an α-hydroxy residue containing cyclodepsipeptide. In the case of isariins, which contain a β-hydroxy acid residue, ring opening and subsequent loss of the terminal residue as an unsaturated ketene fragment, rationalizes the observed product ion formation. Fragmentation of negative ions provide characteristic neutral losses, which are diagnostic of the presence of α-hydroxy or β-hydroxy residues.     

Active-site structure of a β-hydroxylase in antibiotic biosynthesis

X-ray absorption and resonance Raman spectroscopies show that CmlA, the β-hydroxylase of the chloramphenicol biosynthetic pathway, contains a (μ-oxo)-(μ-1,3-carboxylato)diiron(III) cluster with 6-coordinate iron centers and 3 - 4 His ligands. This active site is found within a unique β-lactamase fold and is distinct from those of soluble methane monooxygenase and related enzymes that utilize a highly conserved diiron cluster with a 2-His-4-carboxylate ligand set within a 4-helix bundle motif. These structural differences may have an impact on the nature of the activated oxygen species of the reaction cycle.     

Enhancement of sortase A-mediated protein ligation by inducing a β-hairpin structure around the ligation site

A Staphylococcus aureus transpeptidase, sortase A (SrtA), catalyzes selective peptide/protein ligations that have been applied to cell imaging and protein engineering, while the ligations do not proceed to completion due to their reversibility. We successfully enhanced SrtA-mediated protein ligation through the formation of a β-hairpin around the ligation site.     

Polyelectrolyte microcapsules containing molecules of sulfated β-cyclodextrin in the structure of nanosized shell

Alternate adsorption of the molecules of poly(allylamine hydrochloride) (PAA) and sulfated β-cyclodextrin (sulfo-β-CD) is studied by piezoelectric microweighing upon the formation of coatings of nanosized thicknesses by the polyionic assembly procedure. The thickness of planar coatings on the surface of single-crystalline silicon is determined by ellipsometry. The layer-by-layer character of the formation of planar nanosized coating is revealed and assumptions about the structure of the PAA and sulfo-β-CD bilayers are stated. A comparison of the spherical microparticles of polystyrene, as well as manganese and calcium carbonates, demonstrated that it is feasible to use microparticles of calcium carbonate as a template for producing microcapsules. Microcapsules with shells containing five (PAA/sulfo-β-CD) layers are prepared and studied by confocal fluorescent microscopy.     

Site specificity of OH α-H abstraction reaction for a β-hairpin peptide: an ab initio study

A β-hairpin peptide (PDB ID 1UAO) was modeled to explore the backbone oxidation of a protein by an OH radical to abstract one α-H atom with ab initio calculation at the B3LYB/6-31G(d) without any constraint. Three glycine residues located at three different sites in 1UAO were used to examine the possible site specificity of this backbone oxidation. The pre- and post-reactive complexes along with their associated transition states were located and verified by the intrinsic reaction coordinate method. The reaction profile of these α-H abstraction reactions was constructed. The effects of the aqueous solution were estimated by the conductor-like polarizable continuum model (CPCM) model. Rate constants were calculated with transition state theory. The reaction rate of the OH α-H abstraction varies among these three different sites. The differences among these three sites were rationalized in terms of the molecular and electronic structures of the reactive complexes along the reaction pathway. The explicit solvation effect was estimated through the similar abstraction of a zwitterionic glycine with the combination of microsolvation and a CPCM model. Our results indicate that the α-H abstraction at certain sites requires explicit salvation to obtain accurate results. A replica exchange molecular dynamics simulation was performed to demonstrate the structural change due to this type of abstraction.     

The intricacies of the stacking interaction in a pyrrole–pyrrole system

Extensive calculations of potential energy surfaces for parallel-displaced configurations of pyrrole–pyrrole systems have been carried out by the use of a dispersion-corrected density functional. System geometries associated with the energy minima have been found. The minimum interaction energy has been calculated as ?5.38 kcal/mol. However, bonding boundaries appeared to be relatively broad, and stacking interactions can be binding even for ring centroid distances larger than 6 Å. Though the contribution of the correlation energy to intermolecular interaction in pyrrole dimers appeared to be relatively small (around 1.6 smaller than it is in a benzene–benzene system), this system’s minimum interaction energy is lower than those calculated for benzene–benzene, benzene–pyridine and even pyridine–pyridine configurations. The calculation of the charges and energy decomposition analysis revealed that the specific charge distribution in a pyrrole molecule and its relatively high polarization are the significant source of the intermolecular interaction in pyrrole dimer systems.     

A novel conjugate of a cell-penetrating peptide and a ferrocenyl amino acid: a potential electrochemical sensor for living cells?

The conjugation of a ferrocenyl amino acid to the cell-penetrating peptide hCT(9-32) does not impair its ability to efficiently translocate into cells. Furthermore, the bioconjugate does not induce any cytotoxicity, thus presenting a potential electrochemical sensor suitable for the detection of living cells.     

Dynamic relaying properties of a β-turn peptide in long-range electron transfer

The relay stations play a significant role in long-range charge hopping transfer in proteins. Although studies have clarified that many more protein structural motifs can function as relays in charge hopping transfers by acting as intermediate charge carriers, the relaying properties are still poorly understood. In this work, taking a β-turn oligopeptide as an example, we report a dynamic character of a relay with tunable relaying properties using the density functional theory calculations. Our main finding is that a β-turn peptide can serve as an effective electron relay in facilitating long-range electron migration and its relay properties is vibration-tunable. The vibration-induced structural transient distortions remarkably affect the lowest occupied molecular orbital (LUMO) energy, vertical electron affinity and electron-binding mode of the β-turn oligopeptide and the singly occupied molecular orbital (SOMO) energy of the corresponding electron adduct and thus the relaying properties. Different vibration modes lead to different structural distortions and thus have different effects on the relaying properties and ability of the β-turn peptide. For the relaying properties, there approximately is a linear negative correlation of electron affinity with the LUMO energy of the β-turn or the SOMO energy of its electron adduct. Besides, such relaying properties also vary in the vibration evolution process, and the electron-binding modes may be tunable. As an important addition to the known static charge relaying properties occurring in various protein structural motifs, this work reports the dynamic electron-relaying characteristics of a β-turn oligopeptide with variable relaying properties governed by molecular vibrations which can be applied to different proteins in mediating long-range charge transfers. Clearly, this work reveals molecular vibration effects on the electron relaying properties of protein structural motifs and provides new insights into the dynamics of long-range charge transfers in proteins. © 2018 Wiley Periodicals, Inc.