Dataset Information

?,?-Hybrid Peptide Foldamers: Self-Assembly of Peptide with Trans Carbon-Carbon Double Bonds in the Backbone and Its Saturated Analogue.

ABSTRACT: The effect of geometrically rigid trans ?,?-unsaturated ?-amino acids on the structure, folding, and assembly of ?,?-hybrid peptide foldamers has been reported. From single-crystal diffraction analysis, the unsaturated tetrapeptide 1 has stapler-pin-like structure but without intramolecular hydrogen bond. The asymmetric unit has two molecules that are stabilized by multiple intermolecular hydrogen bonding interactions as well as ?-? stacking interactions between the aromatic rings of 3-aminocinnamic acid. Peptide 1 does not form organogel. But on hydrogenation, peptide 1 provides the saturated ?,?-hybrid peptide foldamer 2, which forms instant gel in most of the aromatic solvents. The gel exhibits high stability. The unsaturated peptide 1 has porous microsphere morphology, but saturated analogue 2 has ribbonlike morphology. The gel has been used efficiently for removal of cationic organic pollutants from waste water.

SUBMITTER: Debnath M

PROVIDER: S-EPMC6644893 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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Publications

α,ε-Hybrid Peptide Foldamers: Self-Assembly of Peptide with Trans Carbon-Carbon Double Bonds in the Backbone and Its Saturated Analogue.

Debnath Mintu M Das Tanmay T Podder Debasish D Haldar Debasish D

ACS omega 20180808 8

The effect of geometrically rigid trans α,β-unsaturated ε-amino acids on the structure, folding, and assembly of α,ε-hybrid peptide foldamers has been reported. From single-crystal diffraction analysis, the unsaturated tetrapeptide <b>1</b> has stapler-pin-like structure but without intramolecular hydrogen bond. The asymmetric unit has two molecules that are stabilized by multiple intermolecular hydrogen bonding interactions as well as π-π stacking interactions between the aromatic rings of 3-am ...[more]

PMID: 31459008

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Project description:An algorithm is proposed for the conversion of a virtual-bond polypeptide chain (connected C alpha atoms) to an all-atom backbone, based on determining the most extensive hydrogen-bond network between the peptide groups of the backbone, while maintaining all of the backbone atoms in energetically feasible conformations. Hydrogen bonding is represented by aligning the peptide-group dipoles. These peptide groups are not contiguous in the amino acid sequence. The first dipoles to be aligned are those that are both sufficiently close in space to be arranged in approximately linear arrays termed dipole paths. The criteria used in the construction of dipole paths are: to assure good alignment of the greatest possible number of dipoles that are close in space; to optimize the electrostatic interactions between the dipoles that belong to different paths close in space; and to avoid locally unfavorable amino acid residue conformations. The equations for dipole alignment are solved separately for each path, and then the remaining single dipoles are aligned optimally with the electrostatic field from the dipoles that belong to the dipole-path network. A least-squares minimizer is used to keep the geometry of the alpha-carbon trace of the resulting backbone close to that of the input virtual-bond chain. This procedure is sufficient to convert the virtual-bond chain to a real chain; in applications to real systems, however, the final structure is obtained by minimizing the total ECEPP/2 (empirical conformational energy program for peptides) energy of the system, starting from the geometry resulting from the solution of the alignment equations. When applied to model alpha-helical and beta-sheet structures, the algorithm, followed by the ECEPP/2 energy minimization, resulted in an energy and backbone geometry characteristic of these alpha-helical and beta-sheet structures. Application to the alpha-carbon trace of the backbone of the crystallographic 5PTI structure of bovine pancreatic trypsin inhibitor, followed by ECEPP/2 energy minimization with C alpha-distance constraints, led to a structure with almost as low energy and root mean square deviation as the ECEPP/2 geometry analog of 5PTI, the best agreement between the crystal and reconstructed backbone being observed for the residues involved in the dipole-path network.

Dataset Information

?,?-Hybrid Peptide Foldamers: Self-Assembly of Peptide with Trans Carbon-Carbon Double Bonds in the Backbone and Its Saturated Analogue.

Publications

α,ε-Hybrid Peptide Foldamers: Self-Assembly of Peptide with Trans Carbon-Carbon Double Bonds in the Backbone and Its Saturated Analogue.

Similar Datasets

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