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Biondi B, Formaggio F, Toniolo C, Peggion C, Crisma M. Isolated α-turns in peptides: a selected literature survey. J Pept Sci 2023:e3476. [PMID: 36603599 DOI: 10.1002/psc.3476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/21/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023]
Abstract
The results of classifying into various types the 68 examples of isolated α-turns in the X-ray diffraction crystal structures of peptides documented in the literature are presented and discussed in this review article. α-Turns characterized by the trans disposition of all ω torsion angles are common for the backbone linear peptides investigated. In contrast, the cis arrangement of the N-terminal (ωi + 1 ) torsion angle, among those generated by the three residues internal to the α-turn, is a peculiar feature of 65% of the cyclic peptides. Among linear and cyclic peptides featuring the all-trans disposition of the ω torsion angles, only one third of the α-turns display φ,ψ values not too far from those characterizing regular α-helices. In general, our findings, taken together, suggest that a significant conformational diversity is compatible with the formation of an intramolecularly H-bonded C13 -member pseudocycle (α-turn) in linear and cyclic peptides.
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Affiliation(s)
- Barbara Biondi
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy
| | - Fernando Formaggio
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Claudio Toniolo
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Cristina Peggion
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Marco Crisma
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy
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Crisma M, Toniolo C. Helical screw-sense preferences of peptides based on chiral, Cα-tetrasubstituted α-amino acids. Biopolymers 2016; 104:46-64. [PMID: 25363510 DOI: 10.1002/bip.22581] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 10/14/2014] [Accepted: 10/24/2014] [Indexed: 01/09/2023]
Abstract
The preferred helical screw senses of chiral α-amino acids with a C(α)-tetrasubstituted α-carbon atom, as determined in the crystal state by X-ray diffraction analyses on derivatives and peptides, are reviewed. This survey covers C(α)-methylated and C(α)-ethylated α-amino acids, as well as α-amino acids cyclized on the α-carbon, including those characterized by the combination of lack of chirality at the α-carbon with either side-chain or axial chirality. Although, in general, chiral C(α)-tetrasubstituted α-amino acids show a less pronounced bias toward a single helical screw sense than their proteinogenic (C(α)-trisubstituted) counterparts, our analysis highlights significant differences in terms of magnitude and direction of such a bias among the various sub-families of residues, and between individual amino acids within each sub-family as well. The experimental findings can be rationalized, at least in part, on the basis of steric considerations.
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Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131, Padova, Italy
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Tumminakatti S, Reddy DN, Prabhakaran EN. Exploring the consequences of a representative "disallowed" conformation of Aib on a 3₁₀-helical fold. Biopolymers 2014; 104:21-36. [PMID: 25488434 DOI: 10.1002/bip.22599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 11/28/2014] [Accepted: 12/01/2014] [Indexed: 01/24/2023]
Abstract
The structural effects of a representative "disallowed" conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D ((1)H, (13)C) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)-helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib*-Oxa) of 2, in a conformation (ϕ, ψ = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)-helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations.
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Affiliation(s)
- Shama Tumminakatti
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
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Casanovas J, Revilla-López G, Crisma M, Toniolo C, Alemán C. Factors Governing the Conformational Tendencies of Cα-Ethylated α-Amino Acids: Chirality and Side-Chain Size Effects. J Phys Chem B 2012; 116:13297-307. [DOI: 10.1021/jp3045115] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jordi Casanovas
- Departament
de Química, Escola Politècnica Superior, Universitat de Lleida, 25001 Lleida, Spain
| | - Guillermo Revilla-López
- Departament d’Enginyeria Química,
E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, 08028
Barcelona, Spain
| | - Marco Crisma
- ICB, Padova
Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy
| | - Claudio Toniolo
- ICB, Padova
Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy
| | - Carlos Alemán
- Departament d’Enginyeria Química,
E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, 08028
Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, 08028 Barcelona, Spain
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De Zotti M, Biondi B, Crisma M, Hjørringgaard CU, Berg A, Brückner H, Toniolo C. Isovaline in naturally occurring peptides: A nondestructive methodology for configurational assignment. Biopolymers 2011; 98:36-49. [DOI: 10.1002/bip.21679] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2011] [Revised: 05/03/2011] [Accepted: 05/10/2011] [Indexed: 11/08/2022]
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6
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Corzana F, Busto JH, García de Luis M, Fernández-Tejada A, Rodríguez F, Jiménez-Barbero J, Avenoza A, Peregrina JM. Dynamics and Hydration Properties of Small Antifreeze-Like Glycopeptides Containing Non-Natural Amino Acids. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000375] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Fernández-Tejada A, Corzana F, Busto JH, Avenoza A, Peregrina JM. Conformational effects of the non-natural alpha-methylserine on small peptides and glycopeptides. J Org Chem 2010; 74:9305-13. [PMID: 19924838 DOI: 10.1021/jo901988w] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis and the conformational analysis in aqueous solution of a peptide and a glycopeptide containing the sequence threonine-alanine-alanine (Thr-Ala-Ala) are reported. Furthermore, the threonine residue has been replaced by the quaternary amino acid alpha-methylserine (MeSer) and their corresponding non-natural peptide and glycopeptide are also studied. The conformational analysis in aqueous solution combines NOEs and coupling constants data with Molecular Dynamics (MD) simulations with time-averaged restraints. The study reveals that the beta-O-glycosylation produces a remarkable and completely different effect on the backbone of the peptide derived from Thr and MeSer. In the former, the beta-O-glycosylation is responsible for the experimentally observed shift from extended conformations (peptide) to folded ones (glycopeptide). In contrast, the beta-O-glycosylation of the MeSer-containing peptide, which clearly shows two main conformations in aqueous solution [extended ones (70%) and beta-turn (30%)], causes a high degree of flexibility for the backbone.
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Affiliation(s)
- Alberto Fernández-Tejada
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Sintesis Química, Grupo de Sintesis Química de La Rioja, UA-CSIC, 26006 Logroño, Spain
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Fernández-Tejada A, Corzana F, Busto JH, Avenoza A, Peregrina JM. Stabilizing unusual conformations in small peptides and glucopeptides using a hydroxylated cyclobutane amino acid. Org Biomol Chem 2009; 7:2885-93. [DOI: 10.1039/b907091p] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Moretto A, Formaggio F, Kaptein B, Broxterman QB, Wu L, Keiderling TA, Toniolo C. First homo-peptides undergoing a reversible 310-helix/α-helix transition: Critical main-chain length. Biopolymers 2008; 90:567-74. [DOI: 10.1002/bip.21016] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Crisma M, Saviano M, Moretto A, Broxterman QB, Kaptein B, Toniolo C. Peptide alpha/3(10)-helix dimorphism in the crystal state. J Am Chem Soc 2007; 129:15471-3. [PMID: 18027948 DOI: 10.1021/ja076656a] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy.
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Crisma M, Moretto A, Formaggio F, Kaptein B, Broxterman QB, Toniolo C. Meteoritic Cα-Methylated α-Amino Acids and the Homochirality of Life: Searching for a Link. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200460908] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Crisma M, Moretto A, Formaggio F, Kaptein B, Broxterman QB, Toniolo C. Meteoritic C?-Methylated ?-Amino Acids and the Homochirality of Life: Searching for a Link. Angew Chem Int Ed Engl 2004; 43:6695-9. [PMID: 15593146 DOI: 10.1002/anie.200460908] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, CNR and Department of Chemistry, University of Padova via Marzolo 1, 35131 Padova, Italy
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Formaggio F, Peggion C, Crisma M, Kaptein B, Broxterman QB, Mazaleyrat JP, Wakselman M, Toniolo C. Recent contributions of electronic circular dichroism to the investigation of oligopeptide conformations. Chirality 2004; 16:388-97. [PMID: 15190584 DOI: 10.1002/chir.20051] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Recent applications in our laboratories of electronic circular dichroism to the study of peptide secondary structures and their changes under external stimuli are briefly reviewed. More specifically, this article deals with: 1). characterization of a novel peptide conformation; 2). origin of amino acid homo-chirality on Earth; 3). bend and helical peptides as spacers; and 4). transfer and propagation of chirality in peptides.
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Affiliation(s)
- Fernando Formaggio
- Institute of Biomolecular Chemistry, CNR, Department of Chemistry, University of Padova, Padova, Italy.
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