Isolated α-turn and incipient γ-helix

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

doi:10.1039/c9sc01683j

Cited by 7 publications

(4 citation statements)

References 58 publications

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“…Thus, only prolyl acetamide N–H’s of 3a – 3d / 4a – 4d are involved in the intramolecular hydrogen bonding in solution (CDCl 3 ), possibly with the NBoc carbonyl group. In literature, the prolyl dipeptides (X aa -Pro/Pro-X aa ) reportedly form the β-/γ-turn and open-type conformations in solid states. ,, Hence, we proposed that the possible intramolecular hydrogen bonding (N–H···OC) in control peptides ( 3a – 3d ) forms γ-turn (Figure A), while etpro -peptides ( 4a – 4d ) form β-turn types structure in chloroform (CDCl 3 ) solution (Figure B).…”

Section: Resultsmentioning

confidence: 90%

“…In literature, the prolyl dipeptides (X aa -Pro/Pro-X aa ) reportedly form the β-/γ-turn and open-type conformations in solid states. 25,35,37 Hence, we proposed that the possible intramolecular hydrogen bonding (N−H•••OC) in control peptides (3a−3d) forms γ-turn (Figure 3A), while etpropeptides (4a−4d) form β-turn types structure in chloroform (CDCl 3 ) solution (Figure 3B).…”

Section: ■ Results and Discussionmentioning

confidence: 98%

“…Moreover the amide bonds/functional side-chain of peptides are natural ligands of coordinating metals. For example, peptide–metal complexes of metal ions (Fe/Cu/Zn ions) have significant roles in regulating the essential biological processes . Metallopeptides are primarily engaged in a redox reaction, including regulating reactive oxygen species (ROS) production in living systems, the emerging area of biochemical research for developing therapeutic drugs and diagnosis probes. , For example, the most common copper-peptide as GHK-Cu(II) is considered as natural antioxidant and collagen stimulating agents, which are found in human plasma and saliva. , Other copper peptides (Cu(II)-amyloid β-peptides) are associated with ROS regulation in Alzheimer’s disease (AD) .…”

Section: Introductionmentioning

confidence: 99%

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Unusual Pseudopeptides: Syntheses and Structural Analyses of Ethylenediprolyl Peptides and Their Metal Complexes with Cu(II) Ion

et al. 2021

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The synthetic unnatural amino acids and their peptides as peptidomimetics have shown remarkable structural and functional properties. In the repertoire of synthetic peptides, pseudopeptides have emerged as attractive small peptidomimetics that are capable of forming the characteristic secondary structures in the solid/solution phase, as in natural peptides. This report describes the synthesis and structural analyses of novel pseudopeptides as ethylenediprolyl (etpro) tetra/hexapeptides, comprising a chiral diaminedicarboxylate scaffold. Their NMR and CD spectral analyses strongly support the formation of the β-turn-type structures in organic solvents (ACN/MeOH). Further, the single-crystal X-ray studies of tetrapseudopeptide confirm the formation of a unique self-assembly structure as β-strand type in the solid state through hydrogen bonding. Importantly, their diamine moiety influences the formation of Cu-complexes with Cu(II) ions. A tetrapseudopeptide monocarboxylate-Cu(II) complex forms the single crystal that is studied by the single-crystal X-ray diffractometer. The crystal structure of the tetrapseudopeptide-Cu(II) complex confirms the formation of the distorted square planar geometry structure, almost like the amyloid β(Aβ)-peptide-Cu(II) complex structural geometry. Hence, these etpro-pseudopeptides are emerging peptidomimatics that form β-turn types of structures and metal complexes mainly with Cu(II) ions. These molecules could be considered for the development of peptide-based catalysts and peptide-based therapeutic drug candidates.

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Section: Resultsmentioning

confidence: 90%

Section: ■ Results and Discussionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

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Unusual Pseudopeptides: Syntheses and Structural Analyses of Ethylenediprolyl Peptides and Their Metal Complexes with Cu(II) Ion

et al. 2021

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“…A fully developed γ-helix is generated by three or more consecutive γ-turns . It is a tight helix characterized by 2.2 amino acids per turn and a rise per residue of 2.75 Å. γ-Helices are very rare in naturally occurring proteins, but they have been observed in some synthetic peptides. − Consequently, very few methods identify γ-helices where SCOT is one example. PSIQUE also detects γ-helices using a minimum length of three residues as in SCOT.…”

Section: Resultsmentioning

confidence: 99%

PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations

Adasme‐Carreño

Caballero

Ireta

2021

J. Chem. Inf. Model.

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The secondary structure is important in protein structure analysis, classification, and modeling. We have developed a novel method for secondary structure assignment, termed PSIQUE, based on the potential energy surface (PES) of polyalanine obtained using an infinitely long chain model and density functional theory calculations. First, uniform protein segments are determined in terms of a difference of quaternions between neighboring amino acids along the protein backbone. Then, the identification of the secondary structure motifs is carried out based on the minima found in the PES. PSIQUE shows good agreement with other secondary structure assignment methods. However, it provides better discrimination of subtle secondary structures (e.g., helix types) and termini and produces more uniform segments while also accounting for local distortions. Overall, PSIQUE provides a precise and reliable assignment of secondary structures, so it should be helpful for the detailed characterization of the protein structure.

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Isolated α‐turns in peptides: a selected literature survey

Biondi¹,

Formaggio

Toniolo

et al. 2023

Journal of Peptide Science

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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 (ω i + 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 alltrans 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 C 13 -member pseudocycle (α-turn) in linear and cyclic peptides.

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Isolated α-turn and incipient γ-helix

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.

Cited by 7 publications

References 58 publications

Unusual Pseudopeptides: Syntheses and Structural Analyses of Ethylenediprolyl Peptides and Their Metal Complexes with Cu(II) Ion

Unusual Pseudopeptides: Syntheses and Structural Analyses of Ethylenediprolyl Peptides and Their Metal Complexes with Cu(II) Ion

PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations

Isolated α‐turns in peptides: a selected literature survey

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