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

Vass, Elemér; Lång, Emma; Samu, János; Májer, Zsuzsa; Kajtár-Peredy, Mária; Mak, Melody L; Radics, L.; Hollósi, Miklós

doi:10.1016/s0022-2860(97)00216-0

Cited by 14 publications

(9 citation statements)

References 39 publications

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“…Structure elucidation of the sugar moieties of nepadutant and its by‐products can be summarized as follows: nepadutant shows a transoid orientation of the two acetamido groups. This finding, and the intermediate temperature coefficient of the NH at C 2 , suggest the occurrence of a C7 H‐bound γ‐turn‐like structure, and corresponds with NMR studies on a variety of N ‐glycopeptide models [17]. NMR studies on MEN11420A demonstrate the β‐linkage of 2‐acetamido‐2‐deoxy‐ D ‐mannopyranose on Asn 1 .…”

Section: Resultssupporting

confidence: 75%

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Structure determination and by‐product profile of the NK₂ receptor antagonist nepadutant, a bicyclic glycopeptide

Weißhoff

Nagel²,

Hänsicke³

et al. 2001

FEBS Letters

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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 L LI, L LII-turn arrangement. The active dipeptide unit Trp^Phe occupies the i+1 and i+2 position of a L LI-turn. The byproduct profile is characterized by different forms of sugars which are caused mainly by isomerization in the process of ring opening. ß

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Section: Resultssupporting

confidence: 75%

“…The bicyclic glyco‐hexapeptide nepadutant was synthesized accordingly by coupling of β‐ D ‐GlcNAc‐NH 2 with the aspartic acid of the bicyclic peptide precursor MEN11282. NMR analyses with N ‐glycopeptides have suggested that the polypeptide and the oligosaccharide have little mutual effect on local conformations [17].…”

Section: Discussionmentioning

confidence: 99%

Structure determination and by‐product profile of the NK₂ receptor antagonist nepadutant, a bicyclic glycopeptide

Weißhoff

Nagel²,

Hänsicke³

et al. 2001

FEBS Letters

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“…First, seven-, six-, and five-residue-long oligoglycines, G 7 , G 6 , and G 5 , were optimized in various conformations incorporating different types of turns, namely, three-residue-long α-turns, , two-residue-long β-turns, , and one-residue-long γ-turns . To mimic the hairpin-like secondary structure, both the first two and the last two amino acid residues of these oligoglycines were set to have extended-like backbone structure (φ ∼180° and ψ ∼180°), or β l for short, with the typical interstrand H-bonds of antiparallel β-pleated sheets.…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2006

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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.

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“…In some cases, they can be discriminated by labeling with stable isotopes and identified in the IR and VCD spectra. − Structural fluctuations lead to complex perturbations of the spectra and difficulties in interpretation. Some peptides can be induced to have relatively stable structures, such as the Ala-rich α-helical models, Aib-containing 3 10 helices, high Pro content 3 1 -helices, and hydrophobically or turn-stabilized β-hairpins. − As another option, modeling small structural elements with cyclic peptides enables one to study specific peptide segments on a conformationally restricted system that is accessible to relatively precise computations. − In the past we used the cyclo-(Phe- d -Pro-Gly-Arg-Gly-Asp) molecule to investigate the structure, flexibility, and the IR and VCD spectral components related to the β-turn induced by the d -Pro-Gly moiety . The type I′ turn was determined as the most reasonable conformation of this sequence, although the peptide exhibited unexpected flexibility that caused a broadening of the spectral bands.…”

Section: Introductionmentioning

confidence: 99%

Side Chain and Flexibility Contributions to the Raman Optical Activity Spectra of a Model Cyclic Hexapeptide

Hudecová

Kapitán²,

Baumruk

et al. 2010

J. Phys. Chem. A

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A model peptide, cyclo-(Phe-d-Pro-Gly-Arg-Gly-Asp), with a distinct folded structure containing short beta-hairpin and beta-sheet patterns was studied by Raman and Raman optical activity (ROA) spectroscopies. Unlike for previously analyzed vibrational circular dichroism of the same compound (Chirality 2008, 20, 1104), the Raman spectrum is dominated by side chain contributions and is more sensitive to their geometry fluctuations. The spectra and molecular motion were analyzed with the aid of the density functional theory simulations combined with molecular dynamics (MD). The side chain geometry fluctuations were found to significantly contribute to the broadening of the spectral bands, while dynamics of the backbone is rather restricted. According to our MD results, the side chains do not move freely but largely oscillate around preferred conformations. Averaging of computed spectra for many structures derived from the MD trajectories provided better spectral profiles than did a fixed geometry. The Raman and ROA scattering is dominated by the more polarizable phenylalanine and proline groups, as could be verified both by the computations and by comparison to experiments with a model Phe-d-Pro dipeptide. Computational analyses suggest that the ROA spectrum mostly senses local side chain conformation, whereas a vibrational coupling between different side chains contributes less. The coupling is mostly mediated by the peptide backbone and is restricted to specific vibrational region. The ROA spectroscopic technique thus provides important local structural information that needs, however, to be extracted by multiscale (QM/MM) simulation techniques.

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

Cited by 14 publications

References 39 publications

Structure determination and by‐product profile of the NK₂ receptor antagonist nepadutant, a bicyclic glycopeptide

Structure determination and by‐product profile of the NK₂ receptor antagonist nepadutant, a bicyclic glycopeptide

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

Side Chain and Flexibility Contributions to the Raman Optical Activity Spectra of a Model Cyclic Hexapeptide

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

Cited by 14 publications

References 39 publications

Structure determination and by‐product profile of the NK2 receptor antagonist nepadutant, a bicyclic glycopeptide

Structure determination and by‐product profile of the NK2 receptor antagonist nepadutant, a bicyclic glycopeptide

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

Side Chain and Flexibility Contributions to the Raman Optical Activity Spectra of a Model Cyclic Hexapeptide

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Product

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Structure determination and by‐product profile of the NK₂ receptor antagonist nepadutant, a bicyclic glycopeptide

Structure determination and by‐product profile of the NK₂ receptor antagonist nepadutant, a bicyclic glycopeptide