Effect of the peptide secondary structure on the peptide amphiphile supramolecular structure and interactions

Bottom-up fabrication of self-assembled nanomaterials requires control over forces and interactions between building blocks. We report here on the formation and architecture of supramolecular structures constructed from two different peptide amphiphiles. Inclusion of four alanines between a 16-mer peptide and a 16 carbon long aliphatic tail resulted in a secondary structure shift of the peptide headgroups from α helices to β sheets. A concomitant shift in self-assembled morphology from nanoribbons to core-shell worm-like micelles was observed by cryogenic transmission electron microscopy (cryo-TEM) and atomic force microscopy (AFM). In the presence of divalent magnesium ions, these a priori formed supramolecular structures interacted in distinct manners, highlighting the importance of peptide amphiphile design in self-assembly.     

Metal compound-mediated hydrolytic cleavage of oxidized insulin B chain:Regioselectivity and influence of peptide secondary structure

The interaction of oxidized insulin B chain(B)with cis-[Pd-(en)Cl2](en=ethylenediamine),cis-[Pd-(dtco-3-OH)Cl2](dtco-3-OH=dithiacyclooctan-3-ol)and CuCl2 was studied by electrospray inass spectrometry.It is discovered that the binding of Pd(Ⅱ)complexes and the sites of cleavage are highly dependent on the secondary structure and local environment of B.The hydrolytic cleavage of denatured B by Pd(Ⅱ)complexes was monitored by HPLC.The reaction is regioselective and follows first order kinetics with half-life of 4.8 days at 40℃.Two amide bonds,i.e.at Leu6-Cys7 and at Gly8-Ser9,which are close to the two potential Pd(Ⅱ)binding sites His5 and His10,are selectively cleaved.In the case of Cu(Ⅱ)ion as promoter,only one cleavage site was observed which is located at Gly8-Ser9 bond.These results provide improved understanding on the design of artificial metallopeptidase.     

The structure of water surrounding a peptide: a theoretical approach

Recently developed integral equation methods for the evaluation of correlations of polar molecular solutes in polar solvent media have been solved for the alanine dipeptide in water. The results are compared with simulations of similar model systems. The use of the full molecular site-site correlations determined in this work can be used in approximate non-superposition theories for conformational populations in solution.     

The effect of the secondary structure on dissociation of peptide radical cations: fragmentation of angiotensin III and its analogues

Fragmentation of protonated RVYIHPF and RVYIHPF-OMe and the corresponding radical cations was studied using time- and collision energy-resolved surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially equipped to perform SID experiments. Peptide radical cations were produced by gas-phase fragmentation of Co (III)(salen)-peptide complexes. Both the energetics and the mechanisms of dissociation of even-electron and odd-electron angiotensin III ions are quite different. Protonated molecules are much more stable toward fragmentation than the corresponding radical cations. RRKM modeling of the experimental data suggests that this stability is largely attributed to differences in threshold energies for dissociation, while activation entropies are very similar. Detailed analysis of the experimental data obtained for radical cations demonstrated the presence of two distinct structures separated by a high free-energy barrier. The two families of structures were ascribed to the canonical and zwitterionic forms of the radical cations produced in our experiments.     

Solubility of small molecule in ionic liquids: a model study on the ionic size effect

Recently, the solvent power of ionic liquid (IL) has been described based on Flory-Huggins (FH) theory assuming that the volumes of the components are the same (J. Phys. Chem. B, 2006, 110, 16205). Here, we extended the FH theory to derive the solvent power in the case of different sizes (molar volumes) of the IL's components based on "polymer-like" model. Applying this model, the effect of ionic size on the solvent power of ionic liquids has been investigated. It was found that the effect of size can be characterized by introducing the effective volume (V+ and V-) of each site of the ion, and for the equivalent ionic liquid, the larger effective volume of the ionic liquid has the larger solvent power. Our results are in excellent agreement with the experimental solubility data in various ionic liquids.     

Protein-associated water and secondary structure effect removal of blood proteins from metallic substrates

Removing adsorbed protein from metals has significant health and industrial consequences. There are numerous protein-adsorption studies using model self-assembled monolayers or polymeric substrates but hardly any high-resolution measurements of adsorption and removal of proteins on industrially relevant transition metals. Surgeons and ship owners desire clean metal surfaces to reduce transmission of disease via surgical instruments and minimize surface fouling (to reduce friction and corrosion), respectively. A major finding of this work is that, besides hydrophobic interaction adhesion energy, water content in an adsorbed protein layer and secondary structure of proteins determined the access and hence ability to remove adsorbed proteins from metal surfaces with a strong alkaline-surfactant solution (NaOH and 5 mg/mL SDS in PBS at pH 11). This is demonstrated with three blood proteins (bovine serum albumin, immunoglobulin, and fibrinogen) and four transition metal substrates and stainless steel (platinum (Pt), gold (Au), tungsten (W), titanium (Ti), and 316 grade stainless steel (SS)). All the metallic substrates were checked for chemical contaminations like carbon and sulfur and were characterized using X-ray photoelectron spectroscopy (XPS). While Pt and Au surfaces were oxide-free (fairly inert elements), W, Ti, and SS substrates were associated with native oxide. Difference measurements between a quartz crystal microbalance with dissipation (QCM-D) and surface plasmon resonance spectroscopy (SPR) provided a measure of the water content in the protein-adsorbed layers. Hydrophobic adhesion forces, obtained with atomic force microscopy, between the proteins and the metals correlated with the amount of the adsorbed protein-water complex. Thus, the amount of protein adsorbed decreased with Pt, Au, W, Ti and SS, in this order. Neither sessile contact angle nor surface roughness of the metal substrates was useful as predictors here. All three globular proteins behaved similarly on addition of the alkaline-surfactant cleaning solution, in that platinum and gold exhibited an increase, while tungsten, titanium, and stainless steel showed a decrease in weight. According to dissipation measurements with the QCM-D, the adsorbed layer for platinum and gold was rigid, while that for the tungsten, titanium, and stainless steel was much more flexible. The removal efficiency of adsorbed-protein by alkaline solution of SDS depended on the water content of the adsorbed layers for W, Ti, and SS, while for Pt and Au, it depended on secondary structural content. When protein adsorption was high (Pt, Au), protein-protein interactions and protein-surface interactions were dominant and the removal of protein layers was limited. Water content of the adsorbed protein layer was the determining factor for how efficiently the layer was removed by alkaline SDS when protein adsorption was low. Hence, protein-protein and protein-surface interactions were minimal and protein structure was less perturbed in comparison with those for high protein adsorption. Secondary structural content determined the efficient removal of adsorbed protein for high adsorbed amount.     

Solution structure of the aqueous model peptide N-methylacetamide

Classical molecular dynamics simulations of aqueous N-methylacetamide (NMA) have been performed across a concentration range at 308 K. This peptidic fragment molecule is a useful model for investigating water/peptide hydrogen bond competition. The simulations predict considerable NMA self-association even at low concentrations with a concentration-dependent increase in the ratio of branched to linear clusters. Water-mediated NMA contacts are a feature of this regime, manifested by an unexpected increase in the number of short NMA oxygen contacts arising from water bridge motifs. In contrast, bulk water structure is significantly disrupted by the addition of even small quantities of NMA. With increases in NMA concentration water molecules become progressively more isolated, forming dimers and trimers hydrogen-bonded to NMA. The mixture in this concentration regime may therefore offer a minimal model system for certain structural properties of interior water buried in protein cavities and hydrogen-bonded to mainchain peptide groups.     

Theoretical investigation on electron transport through an organic molecule: effect of the contact structure

Knowing how the contact geometry influences the conductance of a molecular wire junction requires both a precise determination of the molecule/metallic-electrode interface structure and an evaluation of the conductance for different contact geometries with a fair accuracy. With a greatly improved method to solve the Lippmann-Schwinger equation, we are able to include at least one atomic layer of each electrode into the extended molecule. The artificial effect of the jellium model used for the electrodes is therefore significantly reduced. Our first-principles calculations on the transport properties of a single benzene dithiolate molecule sandwiched between Au(111) surfaces show that the transmission of the bridge site contact, which is the most stable adsorption configuration in equilibrium, displays different features from those of other configurations, and that the inclusion of the surface layers of Au electrodes into the extended molecule shifts and broadens the transmission peaks due to a stronger and more realistic S-Au bonding. We discuss the geometry dependence of the transport properties by analyzing the density of states of the molecular orbitals.     

Compatibility of the thioamide functional group with beta-sheet secondary structure: incorporation of a thioamide linkage into a beta-hairpin peptide

[structure: see text]. We report the incorporation of a thioamide linkage between the i + 2 and i + 3 residues of the type II' beta-turn of a peptide known to fold into a beta-hairpin conformation. Two-dimensional NMR spectroscopy and circular dichroism spectroscopy indicate that the thioxo peptide adopts a hairpin conformation similar to that of the oxo peptide and that the hairpin conformation persists at elevated temperatures. The results show that a thioamide linkage is compatible with beta-sheet secondary structure.     

The alpha-helical peptide nucleic acid concept: merger of peptide secondary structure and codified nucleic acid recognition

A novel platform for nucleic acid recognition that integrates the alpha-helix secondary structure of peptides with the codified base-pairing capability of nucleic acids is reported. The resulting alpha-helical peptide nucleic acids (alpha PNAs) are composed of a repeating tetrapeptidyl unit, aa(1)-aa(2)-aa(3)-Ser(B), where aa(1) through aa(3) represent generic ancillary amino acids and B = nucleobases linked to Ser via a methylene bridge. Effective syntheses of constituent Fmoc-protected nucleoamino acids (Fmoc-Ser(B)-OH, where B = thymine, cytosine, and uracil) are described along with a protocol for the solid-phase synthesis of 21mer alpha PNAs containing five such nucleobases. By varying the ancillary amino acids, two distinct classes of alpha PNAs were constructed, having a net charge of -1 or +6, respectively, at physiological pH. The modular nature of the alpha PNA platform was illustrated by the synthesis of symmetrical disulfide-bridged alpha PNA dimers containing 10 nucleobases. Hybridization of these alpha PNAs with ssDNA has been examined by thermal denaturation, gel electrophoresis, and circular dichroism (CD) and the data indicated that alpha PNA binds to ssDNA in a cooperative manner with high affinity and sequence specificity. In general, b2 alpha PNAs bind faster and more strongly with ssDNA than do the corresponding b1 alpha PNAs. Parallel alpha PNA-DNA complexes are more stable than their antiparallel counterparts. CD studies also revealed that the hybridization event involves the folding of both species into their helical conformations. Finally, NMR experiments provided conclusive evidence of Watson-Crick base pairing in alpha PNA-ssDNA hybrids.     

Small molecule directed aggregation of a heme peptide on gold: an STM study

Microperoxidase 11 was adsorbed on Au(111) from basic aqueous solutions containing pure heme peptide and co-added stoichiometric amounts of exogenous neutral and ionic ligands. The addition of small molecules to MP11 produced different aggregate structures that were easily differentiated by STM. In the absence of a complexing agent, the MP-11 formed large clusters of metallopeptide molecules on the gold surface. With neutral imidazole in solution the MP11 aggregated into regular elongated structures (nano-épis) on the substrate. When S(2-) is used as coupling agent, single heme peptide molecules are isolated with identifiable porphyrin ring and substructure in the peptide chain.     

Control of peptide chain conformation by photoisomerising chromophores: Enzymes and model compounds

Literature data about enzymatic proteins and synthetic polymers containing azo or spirobenzopyran photochromic compounds are discussed.In enzymes, the catalytic activity can be photomodulated by means of the attached photochromic molecules as well as by microenvironmental changes when they are embedded in photoresponsive membranes. In synthetic polymers, large light-induced conformational changes can be obtained in solution, the most pronounced effects being observed in systems with labile fold structures.The mechanisms responsible for the conformational variations can be the changes in intramolecular and solvational interactions brought about both by the structural change of the chromophore after photoisomerisation and by the charge separation.The data about enzymes, when brought into correlation with those about model compounds, support the hypothesis that the above mechanisms are also operative in the photomodulation of enzyme activity.     

The effect of water on the secondary dielectric relaxations in nylon 66

Dielectric data were taken on nylon 66 at several moisture levels at frequencies from 10 to 10⁵ Hz and temperatures from ?70°C to room temperature. Moisture increases the frequency and the peak height for the β relaxation and reduces its activation energy. The peak height of the γ relaxation is reduced by moisture and shifts to slightly higher frequencies with little change in activation energy. The β relaxation follows the pattern of Jonscher and Ngai for a cooperative many-body process. The γ relaxation is slightly broader than a Debye relaxation and approaches that model quite closely as the temperature is increased. The high-frequency end of the β relaxation overlaps the γ relaxation.     

Calculation of the effect of ions on the structure of water

Summary The discussion shows the fallaciousness of Mikhailov and Syrnikov's method of calculating the effect of an ionic field on the free energy of water.     

Synthesis of a cyclic peptide containing norlanthionine: effect of the thioether bridge on peptide conformation

Two diastereomeric analogues of ring C of nisin incorporating a novel norlanthionine residue have been synthesized via a triply orthogonal protecting group strategy. A full structural study was carried out by NMR, which elucidated the conformational properties of the two peptides and enabled the identity of each diastereoisomer to be proposed.