Molecular modeling of conformational properties of oligodepsipeptides.

Molecular modeling of conformational properties of oligodepsipeptides. Research Abstract Details 

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Molecular modeling of conformational properties of oligodepsipeptides. Abstract Text:

Jiajing Zhang,Michael King,Laura Suggs,Pengyu Ren,Jiajing Zhang,Michael King,Laura Suggs,Pengyu Ren,Jiajing Zhang,Michael King,Laura Suggs,Pengyu Ren,

A depsipeptide is a chemical structure consisting of both ester and amide bonds. Quantum mechanics calculations have been performed to investigate the conformational properties of a depsidipeptide in the gas and solution phases. Similar to an alanine dipeptide, the depsidipeptide exhibits a strong preference for the polyproline II (PPII) helical conformation. Meanwhile, due to the changes in the intramolecular interaction, the propensity for beta-sheets and alpha-helices diminishes while an unusual inclination for the (phi,psi) = (-150 degrees ,0 degrees ) conformation was observed. A molecular mechanics model has been developed for polydepsipeptides based on the quantum mechanical study. Both simulated annealing and replica exchange molecular dynamics simulations have been carried out on oligodepsipeptide sequences with alternating depsi and natural residues in solution. Novel helical structures have been indicated from the simulations. When glycine is used as the alternating natural amino acid residue, the PPII conformation of a depsi residue stabilizes the peptide into a right-handed helical structure while the alpha-helical conformation of the depsi residue favors an overall left-handed helical structure. The free energy analysis indicates that both the left- and the right-handed helices are equally likely to exist. When charged lysine is introduced as the alternating natural residue, however, it is found that the depsipeptide sequence prefers an extended conformation as in PPII. Our results indicate that the depsipeptide is potentially useful in designing protein mimetics with controllable structure, function, and chemistry.

Molecular modeling of conformational properties of oligodepsipeptides. Publishing Authors By Initials

J Zhang,M King,L Suggs,P Ren,J Zhang,M King,L Suggs,P Ren,J Zhang,M King,L Suggs,P Ren,

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Molecular modeling of conformational properties of oligodepsipeptides. Journal Published:

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: Biomacromolecules

VOLUME: 8

Page Numbers: 3015-24

Journal Abbreviation: Biomacromolecules

ISSN: 1525-7797

DAY: 18

MONTH: 09

YEAR: 2007

Molecular modeling of conformational properties of oligodepsipeptides. Information

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LANGUAGE: eng

NlmUniqueID: 100892849

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Grant and Affiliation Information for Molecular modeling of conformational properties of oligodepsipeptides.

AFFILIATION: Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA.

Country: United States

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MEDLINETA: Biomacromolecules

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