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8. Controlling the Formation of Peptide Films: Fully Developed Helical Peptides are Required to Obtain a Homogenous Coating over a Large Area

Author

De Zotti, Marta, primary, Corvi, Gabriele, additional, Gatto, Emanuela, additional, Di Napoli, Benedetta, additional, Mazzuca, Claudia, additional, Palleschi, Antonio, additional, Placidi, Ernesto, additional, Biondi, Barbara, additional, Crisma, Marco, additional, Formaggio, Fernando, additional, Toniolo, Claudio, additional, and Venanzi, Mariano, additional

Published
2019
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12. Conformational properties, membrane interaction, and antibacterial activity of the peptaibiotic chalciporin A: Multitechnique spectroscopic and biophysical investigations on the natural compound and labeled analogs

Author

Biondi, Barbara, primary, Peggion, Cristina, additional, De Zotti, Marta, additional, Pignaffo, Chiara, additional, Dalzini, Annalisa, additional, Bortolus, Marco, additional, Oancea, Simona, additional, Hilma, Geta, additional, Bortolotti, Annalisa, additional, Stella, Lorenzo, additional, Pedersen, Jens Z., additional, Syryamina, Victoria N., additional, Tsvetkov, Yuri D., additional, Dzuba, Sergei A., additional, Toniolo, Claudio, additional, and Formaggio, Fernando, additional

Published
2018
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17. 4‐Cyano‐ α ‐methyl‐ l‐ phenylalanine as a Spectroscopic Marker for the Investigation of PeptaibioticMembrane Interactions

Author

De Zotti, Marta, primary, Bobone, Sara, additional, Bortolotti, Annalisa, additional, Longo, Edoardo, additional, Biondi, Barbara, additional, Peggion, Cristina, additional, Formaggio, Fernando, additional, Toniolo, Claudio, additional, Dalla Bona, Andrea, additional, Kaptein, Bernard, additional, and Stella, Lorenzo, additional

Published
2015
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29. Conformational properties, membrane interaction, and antibacterial activity of the peptaibiotic chalciporin A: Multitechnique spectroscopic and biophysical investigations on the natural compound and labeled analogs.

Author

Biondi B, Peggion C, De Zotti M, Pignaffo C, Dalzini A, Bortolus M, Oancea S, Hilma G, Bortolotti A, Stella L, Pedersen JZ, Syryamina VN, Tsvetkov YD, Dzuba SA, Toniolo C, and Formaggio F

Abstract

In this work, an extensive set of spectroscopic and biophysical techniques (including FT-IR absorption, CD, 2D-NMR, fluorescence, and CW/PELDOR EPR) was used to study the conformational preferences, membrane interaction, and bioactivity properties of the naturally occurring synthetic 14-mer peptaibiotic chalciporin A, characterized by a relatively low (≈20%), uncommon proportion of the strongly helicogenic Aib residue. In addition to the unlabeled peptide, we gained in-depth information from the study of two labeled analogs, characterized by one or two residues of the helicogenic, nitroxyl radical-containing TOAC. All three compounds were prepared using the SPPS methodology, which was carefully modified in the course of the syntheses of TOAC-labeled analogs in view of the poorly reactive α-amino function of this very bulky residue and the specific requirements of its free-radical side chain. Despite its potentially high flexibility, our results point to a predominant, partly amphiphilic, α-helical conformation for this peptaibiotic. Therefore, not surprisingly, we found an effective membrane affinity and a remarkable penetration propensity. However, chalciporin A exhibits a selectivity in its antibacterial activity not in agreement with that typical of the other members of this peptide class., (© 2017 Wiley Periodicals, Inc.)

Published
2017
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30. Endothioxopeptides: A conformational overview.

Author

De Zotti M, Peggion C, Biondi B, Crisma M, Formaggio F, and Toniolo C

Subjects
Protein Structure, Secondary, Chemistry Techniques, Synthetic methods, Peptides chemical synthesis, Peptides chemistry, Sulfhydryl Compounds chemistry
Abstract

Although thionamides would have been first prepared two centuries ago and their chemical and spectroscopic properties extensively investigated, only much more recently (since about 1985) a well deserved but still insufficient attention has been paid to their endothioxopeptide subfamily which nonetheless currently represents a rapidly emerging area of great scientific interest in the broader field of foldameric compounds based on biologically relevant building blocks. After two brief sections offering information on the unfortunately still limited number of endothioxopeptides discovered from natural sources but also on the impressive advancements registered in the last few years in their synthetic methods, this review article outlines the results of a detailed literature survey on the ongoing great, but not systematic, progress related to the conformational consequences generated by incorporating one (or more) thionamide group(s) into a polypeptide chain. Finally, a short discussion of the growing, but still in its infancy, class of the endoselenoxopeptide congeners is also presented., (© 2016 Wiley Periodicals, Inc.)

Published
2016
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31. The fluorescence and infrared absorption probe para-cyanophenylalanine: Effect of labeling on the behavior of different membrane-interacting peptides.

Author

Bobone S, De Zotti M, Bortolotti A, Biondi B, Ballano G, Palleschi A, Toniolo C, Formaggio F, and Stella L

Subjects
Alamethicin chemistry, Alanine chemistry, Fluorescent Dyes chemical synthesis, Phospholipids chemistry, Spectroscopy, Fourier Transform Infrared, Alanine analogs & derivatives, Fluorescent Dyes chemistry, Membranes chemistry, Nitriles chemistry, Peptides metabolism
Abstract

Total syntheses and complete characterizations of singly substituted PheCN -based analogs of alamethicin AlaP, which is active on model and natural membranes, and the TM peptide, which inserts in a transmembrane orientation in lipid bilayers, are reported. The syntheses of the AlaP analogs were performed in solution, while those of TM and its analogs were carried out by solid phase. Using the cyanophenyl fluorescence and infrared (IR) absorption probe, an in-depth investigation of the self-association, membrane-interacting, permeabilizing, and orientation properties of these peptides were conducted. The aromatic residue incorporated induces only a negligible modification to the properties of the parent peptides. The PheCN IR absorption band was located between 2228 and 2230 cm(-1) for all peptides, irrespective of the position of labeling. By contrast, as the width of this band varied significantly with the depth of probe insertion in the bilayer, it could represent a good marker of the PheCN position in phospholipid membranes., (© 2015 Wiley Periodicals, Inc.)

Published
2015
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32. Isovaline in naturally occurring peptides: A nondestructive methodology for configurational assignment.

Author

De Zotti M, Biondi B, Crisma M, Hjørringgaard CU, Berg A, Brückner H, and Toniolo C

Subjects
Amino Acid Sequence, Amino Acids chemistry, Stereoisomerism, Peptides chemistry, X-Ray Diffraction
Abstract

The nonproteinogenic, C(α)-tetrasubstituted, helicogenic, chiral α-amino acid isovaline (Iva) is remarkably spread in the biosphere. Together with its achiral, lower homolog α-aminoisobutyric acid (Aib), it represents a characteristic marker of a class of naturally occurring peptide antibiotics, for which the acronym "peptaibiotics" became established. In these peptides, Iva occurs as the (S)-(= L) or the (R)-(= D) enantiomer, but peptide sequences containing both Iva enantiomers are also common. Here, we applied our recently developed (1)H-NMR method, which enables the nondestructive assignment of the configuration of each Iva residue in a peptide of known helical screw sense, to natural and synthetic peptaibiotics. Our method proved to be generally applicable and provided evidence that, in the peptaibiotic bergofungin A, the Iva(12) configuration is (R) and not (S) as reported previously. Moreover, we extended our NMR method by including a (13)C-NMR parameter. A statistical analysis of the preferred main- and side-chain conformations of the Iva residues in peptides, performed based on their published X-ray diffraction structures, allowed us to provide a sound rationale to the NMR criteria exploited to establish the configuration of this amino acid., (Copyright © 2011 Wiley Periodicals, Inc.)

Published
2012
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33. Conformational constraints of tyrosine in protein tyrosine kinase substrates: Information about preferred bioactive side-chain orientation.

Author

Ruzza P, Calderan A, Donella-Deana A, Biondi B, Cesaro L, Osler A, Elardo S, Guiotto A, Pinna LA, and Borin G

Subjects
Amino Acid Sequence, Kinetics, Magnetic Resonance Spectroscopy, Models, Chemical, Molecular Sequence Data, Peptide Biosynthesis, Peptides chemistry, Phosphorylation, Protein Binding, Protein Conformation, Protein-Tyrosine Kinases metabolism, Substrate Specificity, Time Factors, Tyrosine chemistry, Protein-Tyrosine Kinases chemistry
Abstract

The side-chain orientation of a tyrosine residue located in a peptide, which is an excellent substrate of Syk tyrosine kinase (A. M. Brunati, A. Donella-Deana, M. Ruzzene, O. Marin, L. A. Pinna, FEBS Letters, 1995, Vol. 367, pp. 149-152), was fixed in the gauche (+) or gauche (-) conformation by using the 7-hydroxy-1,2,3,4-tetrahydro isoquinoline-3-carboxylic (Htc) structure. The tyrosine trans conformation was blocked by using an aminobenzazepine-type (Hba) structure. The proposed side-chain orientations were confirmed by the analysis of the (1)H-NMR parameters: chemical shifts, coupling constants, and nuclear Overhauser effects to the tyrosine constraints in the different analogs. This "rotamer scan" of the phosphorylatable residue allowed us to generate optimal substrates in terms of both phosphorylation efficiency and selectivity for Syk tyrosine kinase. In contrast, these conformationally restricted tyrosine analogs were not tolerated by the Src-related tyrosine kinases Lyn and c-Fgr., (Copyright 2003 Wiley Periodicals, Inc.)

Published
2003
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