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Evaluation of a cyclopentane-based ?-amino acid for the ability to promote ?/?-peptide secondary structure.

ABSTRACT: We report the asymmetric synthesis of the ?-amino acid (1R,2R)-2-aminomethyl-1-cyclopentane carboxylic acid (AMCP) and an evaluation of this residue's potential to promote secondary structure in ?/?-peptides. Simulated annealing calculations using NMR-derived distance restraints obtained for ?/?-peptides in chloroform reveal that AMCP-containing oligomers are conformationally flexible. However, additional evidence suggests that an internally hydrogen-bonded helical conformation is partially populated in solution. From these data, we propose characteristic NOE patterns for the formation of the ?/?-peptide 12/10-helix and discuss the apparent conformational frustration of AMCP-containing oligomers.

SUBMITTER: Giuliano MW

PROVIDER: S-EPMC4109159 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature

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Evaluation of a cyclopentane-based γ-amino acid for the ability to promote α/γ-peptide secondary structure.

Giuliano Michael W MW Maynard Stacy J SJ Almeida Aaron M AM Reidenbach Andrew G AG Guo Li L Ulrich Emily C EC Guzei Ilia A IA Gellman Samuel H SH

The Journal of organic chemistry 20131205 24

We report the asymmetric synthesis of the γ-amino acid (1R,2R)-2-aminomethyl-1-cyclopentane carboxylic acid (AMCP) and an evaluation of this residue's potential to promote secondary structure in α/γ-peptides. Simulated annealing calculations using NMR-derived distance restraints obtained for α/γ-peptides in chloroform reveal that AMCP-containing oligomers are conformationally flexible. However, additional evidence suggests that an internally hydrogen-bonded helical conformation is partially popu ...[more]

PMID: 24303945

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Project description:Prediction of protein secondary structure from FTIR spectra usually relies on the absorbance in the amide I-amide II region of the spectrum. It assumes that the absorbance in this spectral region, i.e., roughly 1700-1500 cm-1 is solely arising from amide contributions. Yet, it is accepted that, on the average, about 20% of the absorbance is due to amino acid side chains. The present paper evaluates the contribution of amino acid side chains in this spectral region and the potential to improve secondary structure prediction after correcting for their contribution. We show that the β-sheet content prediction is improved upon subtraction of amino acid side chain contributions in the amide I-amide II spectral range. Improvement is relatively important, for instance, the error of prediction of β-sheet content decreases from 5.42 to 4.97% when evaluated by ascending stepwise regression. Other methods tested such as partial least square regression and support vector machine have also improved accuracy for β-sheet content evaluation. The other structures such as α-helix do not significantly benefit from side chain contribution subtraction, in some cases prediction is even degraded. We show that co-linearity between secondary structure content and amino acid composition is not a main limitation for improving secondary structure prediction. We also show that, even though based on different criteria, secondary structures defined by DSSP and XTLSSTR both arrive at the same conclusion: only the β-sheet structure clearly benefits from side chain subtraction. It must be concluded that side chain contribution subtraction benefit for the evaluation of other secondary structure contents is limited by the very rough description of side chain absorbance which does not take into account the variations related to their environment. The study was performed on a large protein set. To deal with the large number of proteins present, we worked on protein microarrays deposited on BaF2 slides and FTIR spectra were acquired with an imaging system.

Dataset Information

Evaluation of a cyclopentane-based ?-amino acid for the ability to promote ?/?-peptide secondary structure.

Publications

Evaluation of a cyclopentane-based γ-amino acid for the ability to promote α/γ-peptide secondary structure.

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