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3. 13C18O/15N Isotope Dependence of the Amide-I/II 2D IR Cross Peaks for the Fully Extended Peptides

Author

Maekawa, Hiroaki, Ballano, Gema, Formaggio, Fernando, Toniolo, Claudio, and Ge, Nien-Hui

Subjects
Chemical Sciences, Engineering, Technology, Physical Chemistry
Abstract

We have used a combination of 2D IR spectroscopy with 13C=18O labeled amide-I and 15N-labeled amide-II modes to reveal how vibrational coupling between labeled peptide units depends on secondary structure. Linear and 2D IR measurements and simulations of Cα,α-diethylglycine homotetrapeptide show that this compound adopts the fully extended (2.05-helical) conformation in CDCl3, consistent with previous work on the Ac-capped peptide. The amide-I/II cross peaks of isotopomers exhibit only a marginal isotope frequency shift between labeled modes that are separated by two peptide units, indicating a very weak coupling. This result is in sharp contrast with a large cross-peak shift observed in 310-helical peptides, in which the labeled amide-I and -II modes are connected through an inter-residue C=O···H-N hydrogen bond. The discovered 3D-structural dependence indicates that the 13C=18O/15N labeled amide-I/II cross peaks can distinguish the formation of a single 310-helical turn from the fully extended polypeptide chain and increase the versatility of 2D IR spectroscopy as a conformational analysis tool of biomolecules.

Published
2014

5. Sensitivity of 2D IR Spectra to Peptide Helicity: A Concerted Experimental and Simulation Study of an Octapeptide

Author

Sengupta, Neelanjana, Maekawa, Hiroaki, Zhuang, Wei, Toniolo, Claudio, Mukamel, Shaul, Tobias, Douglas J, and Ge, Nien-Hui

Subjects
Computer Simulation, Crystallography, X-Ray, Hydrogen Bonding, Models, Chemical, Models, Statistical, Molecular Conformation, Peptides, Protein Conformation, Spectrophotometry, Spectrophotometry, Infrared, Spectroscopy, Fourier Transform Infrared, Static Electricity, Time Factors, Physical Sciences, Chemical Sciences, Engineering
Abstract

We have investigated the sensitivity of two-dimensional infrared (2D IR) spectroscopy to peptide helicity with an experimental and theoretical study of Z-[l-(alphaMe)Val](8)-OtBu in CDCl(3). 2D IR experiments were carried out in the amide-I region under the parallel and the double-crossed polarization configurations. In the latter polarization configuration, the 2D spectra taken with the rephasing and nonrephasing pulse sequences exhibit a doublet feature and a single peak, respectively. These cross-peak patterns are highly sensitive to the underlying peptide structure. Spectral calculations were performed on the basis of a vibrational exciton model, with the local mode frequencies and couplings calculated from snapshots of molecular dynamics (MD) simulation trajectories using six different models for the Hamiltonian. Conformationally variant segments of the MD trajectory, while reproducing the main features of the experimental spectra, are characterized by extraneous features, suggesting that the structural ensembles sampled by the simulation are too broad. By imposing periodic restraints on the peptide dihedral angles with the crystal structure as a reference, much better agreement between the measured and the calculated spectra was achieved. The result indicates that the structure of Z-[l-(alphaMe)Val](8)-OtBu in CDCl(3) is a fully developed 3(10)-helix with only a small fraction of alpha-helical or nonhelical conformations in the middle of the peptide. Of the four different combinations of pulse sequences and polarization configurations, the nonrephasing double-crossed polarization 2D IR spectrum exhibits the highest sensitivity in detecting conformational variation. Of the six local mode frequency models tested, the electrostatic maps of Mukamel and Cho perform the best. Our results show that the high sensitivity of 2D IR spectroscopy can provide a useful basis for developing methods to improve the sampling accuracy of force fields and for characterizing the relative merits of the different protocols for the Hamiltonian calculation.

Published
2009

12. Energy transport in peptide helices around the glass transition

Author

Backus, Ellen H. G., Nguyen, Phuong H., Botan, Virgiliu, Pfister, Rolf, Moretto, Alessandro, Crisma, Marco, Toniolo, Claudio, Stock, Gerhard, Hamm, Peter, Corkum, Paul, editor, Silvestri, Sandro, editor, Nelson, Keith A., editor, Riedle, Eberhard, editor, and Schoenlein, Robert W., editor

Published
2009
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15. Energy Transport in a Peptide Helix

Author

Botan, Virgiliu, Backus, Ellen H. G., Moretto, Alessandro, Toniolo, Claudio, Hamm, Peter, Castleman, A. W., Jr., editor, Toennies, J. P., editor, Zinth, W., editor, Yamanouchi, K., editor, Corkum, Paul, editor, Jonas, David M., editor, Miller, R. J. Dwayne., editor, and Weiner, Andrew M., editor

Published
2007
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24. Isolated α-turn and incipient γ-helix† †Electronic supplementary information (ESI) available: General information, experimental procedures, compounds characterization, crystallographic data, 1H, 13C and 2D NMR spectra, FT-IR absorption spectra. CCDC 1906513, 1906514, 1906515, 1906516 and 1906517. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c9sc01683j

Author

Mir, Fatemeh M., Crisma, Marco, Toniolo, Claudio, and Lubell, William D.

Subjects
Chemistry
Abstract

The unique abilities of homo-oligo-adamantyl peptides to adopt α- and γ-turn conformations are demonstrated by X-ray diffraction, and NMR and FT-IR absorption spectroscopies., The unique abilities of homo-oligo-adamantyl peptides to adopt α- and γ-turn conformations are demonstrated by X-ray diffraction, and NMR and FT-IR absorption spectroscopies. Assembled by an Ugi multiple component reaction strategy, Nα-formyl-adamantyl tripeptide iso-propyl and tert-butyl amides are respectively found to adopt an isolated α-turn and an incipient γ-helix conformation by X-ray diffraction crystallography. The shortest example of a single α-turn with ideal geometry is observed in the crystalline state. In solution both peptides predominantly assume γ-helical structures.

Published
2019

43. Peptide [alpha]/[3.sub.10]-helix dimorphism in the crystal state

Author

Crisma, Marco, Saviano, Michele, Moretto, Alessandro, Broxterman, Quirinus B., Kaptein, Bernard, and Toniolo, Claudio

Subjects
Crystalline polymers -- Research, Crystalline polymers -- Chemical properties, Proteins -- Structure, Proteins -- Observations, Proteins -- Properties, Chemistry
Abstract

An example of a solvent-driven [alpha]/[3.sub.10]-helix dimorphismis described for a peptide molecule in the crystalline state. The studies have shown that the interconversion between [alpha]- and [3.sub.10]-helices might be allowed even in peptides composed by [C.sup.[alpha]]-tetrasubstituted [alpha]-amino acids and has provided clues for understanding the interactions of 1,1,1,3,3,3-hexafluoropropan-2-ol (HFIP) with helical peptides.

Published
2007

44. Unraveling solvent-driven equilibria between [alpha]- and [3.sub.10]-helices through an integrated spin labeling and computational approach

Author

Carlotto, Silvia, Cimino, Paola, Zerbetto, Mirco, Franco, Lorenzo, Corvaja, Carlo, Crisma, Marco, Formaggio, Fernando, Toniolo, Claudio, Polimeno, Antonio, and Barone, Vincenzo

Subjects
Polypeptides -- Chemical properties, Computational chemistry -- Research, Spin labeling -- Usage, Chemistry
Abstract

An effective and flexible computational approach is described and its usefulness and reliability is demonstrated by the tuning of the equilibrium between [3.sub.10] and [alpha]-helices of polypeptides by different solvents. The generality of this computational strategy and its applicability in effective and user-friendly computer codes have paved the way toward applications in the field of biomolecules and other complex systems.

Published
2007

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