Vibrational spectroscopic detection of H-bonded β- and γ-turns in cyclic peptides and glycopeptides

Bifurcated hydrogen bonds stabilize fibrils of poly(L-glutamic) acid

Model fibrillating homopolypeptides have been providing many insightful analogies to the clinically important phenomena of protein misfolding and amyloidogenesis. Here we show that the beta(2) structural variant of poly(l-glutamic) acid forms fibrils with an amyloid-like morphology, ability to enhance fluorescence of thioflavin T, and seeding properties. The beta(2) fibrils are formed upon heating of aqueous solutions of alpha-helical poly(l-glutamic) acid, which leads to a significant increase of pD (pH) of unbuffered samples and a concomitant precipitation of fibrils with unusual infrared traits: amide I' band being dramatically red-shifted to 1596 cm(-1), and the -COOD stretching band split into two peaks around 1730 and 1719 cm(-1). We are proposing that formation of three-center hydrogen bonds involving bifurcated peptide carbonyl acceptors (>C=O) and main chains' NH, as well as side chains' -COOH proton donors is likely to underlie the observed infrared characteristics of beta(2) fibrils. Such bonds provide additional conformational constraints in a tightly packed environment around glutamate side chains resulting in the decreased overall acidity of the polypeptide. The presence of bifurcated hydrogen bonds in amyloid fibrils may be an overlooked factor in fibrils' robustness, thermodynamic stability and the ability to propagate their own growth.

Prediction of Folding Preference of 10 kDa Silk-like Proteins Using a Lego Approach and ab Initio Calculations

Because of their great flexibility and strength resistance, both spider silks and silkworm silks are of increasing scientific and commercial interest. Despite numerous spectroscopic and theoretical studies, several structural properties at the atomic level have yet to be identified. The present theoretical investigation focuses on these issues by studying three silk-like model peptides: (AG)(64), [(AG)(4)EG](16), and [(AG)(4)PEG](16), using a Lego-type approach to construct these polypeptides. On the basis of these examples it is shown that thermoneutral isodesmic reactions and ab initio calculations provide a capable method to investigate structural properties of repetitive polypeptides. The most probable overall fold schema of these molecules with respect to the type of embedded hairpin structures were determined at the ab initio level of theory (RHF/6-311++G(d,p)//RHF/3-21G). Further on, analysis is carried out on the possible hairpin and turn regions and on their effect on the global fold. In the case of the (AG)(64) model peptide, the optimal beta-sheet/turn ratio was also determined, which provided good support for experimental observations. In addition, lateral shearing of a hairpin "folding unit" was investigated at the quantum chemical level to explain the mechanical properties of spider silk. The unique mechanical characteristics of silk bio-compounds are now investigated at the atomic level.

Conformational study on glycosylated asparagine-oligopeptides by NMR spectroscopy and molecular dynamics calculations

The conformational properties of the homo oligomers of increasing chain length Boc-(Asn)(n)-NHMe (n = 2, 4, 5), (GlcNAc-beta-Asn)(n)-NHMe (n = 2, 4, 5, 8) and Boc-[GlcNAc(Ac)(3)-beta-Asn](n)-NHMe (n = 2, 4, 5) were studied by using NOE experiments and molecular dynamic calculations (MD). Sequential NOEs and medium range NOEs, including (i,i+2) interactions, were detected by ROESY experiments and quantified. The calculated inter-proton distances are longer than those characteristic of beta-turn secondary structures. Owing to the large conformational motions expected for linear peptides, MD simulations were performed without NMR constraints, with explicit water and by applying different treatments of the electrostatic interactions. In agreement with the NOE results, the simulations showed, for all peptides, the presence of both folded and unfolded structures. The existence of significant populations of beta-turn structures can be excluded for all the examined compounds, but two families of structures were more often recognized. The first one with sinusoidal or S-shaped forms, and another family of large turns together with some more extended conformations. Only the glycosylated pentapeptide shows in vacuo a large amount of structures with helical shaped form. The results achieved in water and in DMSO are compared and discussed, together with the effect of the glycosylation.

Genetically directed synthesis and spectroscopic analysis of a protein polymer derived from a flagelliform silk sequence

The flagelliform silk protein underlies the unique elastomeric properties displayed by the capture spiral of arachnid webs. To investigate molecular mechanism underlying the elastomeric recovery of the capture spiral, a model polypeptide based upon the elastomeric repeat sequence of Nephila clavipes flagelliform silk protein has been synthesized using recombinant DNA techniques. Polypeptide 1 contains 11 repeats of the 25 amino acid sequence [(Gly-Pro-Gly-Gly-Ser-Gly-Pro-Gly-Gly-Tyr)(2)-Gly-Pro-Gly-Gly-Lys] and was expressed in Escherichia coli strain BL21(DE3) as a C-terminal fusion to a decahistidine leader sequence. A combination of (1)H-(1)H COSY, DEPT, (1)H-(13)C HETCOR, and (1)H-(13)C HMBC NMR spectroscopy was employed on polypeptides 1 and the [1-(13)C]glycine-labeled analogue 1G to assign the (1)H and (13)C NMR resonances of the amino acid residues comprising the flagelliform silk repeat sequence. The conformational properties of 1 in aqueous solution were investigated using a combination of CD, FTIR, VT-NMR, and two-dimensional NOESY NMR. These techniques were consistent with the presence of small but detectable population of beta-turn conformers between Gly(1) and Gly(4) of the pentapeptide units of 1. FTIR and CD studies of solid films of 1 indicated an increase in beta-turn population in the solid state, which coincided with the decrease in hydration level of the polypeptide. The spectroscopic information suggests that the pentapeptide segments of the flagelliform silk protein adopt a beta-turn conformation in the fiber and that the mechanism of elasticity may resemble that proposed for other beta-turn forming polypeptides including elastin.

Conformational investigations on glycosylated asparagine-oligopeptides of increasing chain length

Stepwise solution syntheses of the homo-oligomers Boc-(Asn)n-NHCH3 (n = 1-5; I1-5), Boc-[[GlcNAc(Ac)3beta]Asn]n-NHCH3 (n = 1-8; II1-8), and Boc-[(GlcNAcbeta)Asn]n-NHCH3 (n = 1-8; III1-8) are described. Members of the series III were obtained by deacetylation of the corresponding members of the series II. The conformational preferences of the N-protected homo-peptides of the three series were investigated by spectroscopic techniques. 1H-NMR measurements were carried out in various solvents; the CD spectra were recorded in water, aqueous SDS and TFE. The poor solubility of the oligomers of the three series prevented FT-IR measurements in solution. NMR and IR measurements indicate the existence of unordered structures containing some gamma-turns in the carbohydrate-free oligomers and the presence of beta-turns in the glycosylated oligopeptides, whether acetylated or not. The CD spectra do not indicate the presence of organized structures. The sugar moieties apparently do not have a structure-inducing effect on the asparagine homo-oligomer main chain.

Structure determination and by-product profile of the NK(2) receptor antagonist nepadutant, a bicyclic glycopeptide

We have synthesized and fully characterized the NK(2) receptor antagonist nepadutant and its by-products using nuclear magnetic resonance (NMR) and restrained molecular dynamics. The agent consists of an active bicyclic hexapeptide combined with a sugar residue. Analysis of the high-performance liquid chromatogram and the mass spectroscopy spectra yields traces of three by-products with the same molecular weight as the main product. The conformation of the molecules in the bicyclic hexapeptide segment, the active region, is well defined, whereas the sugar moiety is disordered. For the peptide region of nepadutant and all of its by-products, the NMR observables can be described by a single backbone conformation, more specifically a betaI, betaII-turn arrangement. The active dipeptide unit Trp-Phe occupies the i+1 and i+2 position of a betaI-turn. The by-product profile is characterized by different forms of sugars which are caused mainly by isomerization in the process of ring opening.

Spectroscopic evidence of beta-turn in N-glycated peptidomimetics related to leucine-enkephalin

The conformational differences caused by N-glycation of the amide bond in endogenous opioid pentapeptide leucine-enkephalin (Tyr-Gly-Gly-Phe-Leu) have been explored in solution using FTIR spectroscopy, NMR and molecular modelling. The compounds studied include protected and unprotected enkephalin analogues N-alkylated at the second (Gly2) amino acid residue with a 6-deoxy-D-galactose moiety (1-3). Comparison of the amide I component bands in the FTIR spectra, measured in trifluoroethanol (TFE), CHCl3 and DMSO, revealed significant differences in the intensity as well as shifts in component band frequencies for glycopeptides 1-3. We found that only the FTIR spectrum of the fully protected compound 1 indicated the presence of a higher population of beta-turns, while the spectra of the partially protected and unprotected glycopeptides 2 and 3 reflected the dominance of unordered or open structures, with some low population of turns. The observed NOE connectivities in CDCl3 for both isomers of the fully protected compound 1, the all-trans one and another with Tyr1-Gly2 peptide bond in cis conformation, indicate the presence of a beta-like turn conformation. Molecular dynamics simulations of the glycopeptide 1 obtained by unconstrained energy minimization of trans- and cis-1 shows that one of trans form conformations is consistent with beta-turn whereas cis isomer has revealed less-compact turn.

Circular dichroism study of the carbohydrate-modified opioid peptides

The conformational preferences of enkephalins and the related glycoconjugates in which free or protected carbohydrate moieties were linked to the opioid peptides through an ether, ester or amide bond were investigated by circular dichroism spectroscopy in water, trifluoroethanol and water-trifluoroethanol mixtures. The analysis of the spectra revealed that the conformation of the enkephalin molecule is very sensitive to slight changes in the peptide structure around the C-terminal region. It was found that the type II beta-turn structures are populated in N-terminal tetrapeptide enkephalin fragment, while leucine-enkephalin amide feature a type I (III) beta-turn structure in solution. Incorporation of the sugar moiety into opioid peptide compound did not significantly influence the overall conformation of the peptide backbone, although minor intensity changes may reflect shifts in the population of the different turn systems. These small structural alterations can be responsible for the receptor-subtype selectivity of the various carbohydrate-modified enkephalin analogs.