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Populations of the three major backbone conformations in 19 amino acid dipeptides.

ABSTRACT: The amide III region of the peptide infrared and Raman spectra has been used to determine the relative populations of the three major backbone conformations (P(II), ?, and ?(R)) in 19 amino acid dipeptides. The results provide a benchmark for force field or other methods of predicting backbone conformations in flexible peptides. There are three resolvable backbone bands in the amide III region. The major population is either P(II) or ? for all dipeptides except Gly, whereas the ?(R) population is measurable but always minor (? 10%) for 18 dipeptides. (The Gly ?,? map is complex and so is the interpretation of the amide III bands of Gly.) There are substantial differences in the relative ? and P(II) populations among the 19 dipeptides. The band frequencies have been assigned as P(II), 1,317-1,306 cm(-1); ?(R), 1,304-1,294 cm(-1); and ?, 1,294-1,270 cm(-1). The three bands were measured by both attenuated total reflection spectroscopy and by Raman spectroscopy. Consistent results, both for band frequency and relative population, were obtained by both spectroscopic methods. The ? and P(II) bands were assigned from the dependence of the (3)J(H(N),H(?)) coupling constant (known for all 19 dipeptides) on the relative ? population. The P(II) band assignment agrees with one made earlier from Raman optical activity data. The temperature dependences of the relative ? and P(II) populations fit the standard model with Boltzmann-weighted energies for alanine and leucine between 30 and 60 °C.

SUBMITTER: Grdadolnik J

PROVIDER: S-EPMC3033284 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature

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Populations of the three major backbone conformations in 19 amino acid dipeptides.

Grdadolnik Joze J Mohacek-Grosev Vlasta V Baldwin Robert L RL Avbelj Franc F

Proceedings of the National Academy of Sciences of the United States of America 20110104 5

The amide III region of the peptide infrared and Raman spectra has been used to determine the relative populations of the three major backbone conformations (P(II), β, and α(R)) in 19 amino acid dipeptides. The results provide a benchmark for force field or other methods of predicting backbone conformations in flexible peptides. There are three resolvable backbone bands in the amide III region. The major population is either P(II) or β for all dipeptides except Gly, whereas the α(R) population i ...[more]

PMID: 21205907

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Project description:Recent papers have reported dipeptides containing d-amino acids to have novel effects that cannot be observed with ll-dipeptides, and such dipeptides are expected to be novel functional compounds for pharmaceuticals and food additives. Although the functions of d-amino acid-containing dipeptides are gaining more attention, there are few reports on the synthetic enzymes that can accept d-amino acids as substrates, and synthetic methods for d-amino acid-containing dipeptides have not yet been constructed. Previously, we developed a chemoenzymatic system for amide synthesis that comprised enzymatic activation and a subsequent nucleophilic substitution reaction. In this study, we demonstrated the application of the system for d-amino acid-containing-dipeptide synthesis. We chose six adenylation domains as targets according to our newly constructed hypothesis, i.e., an adenylation domain located upstream from the epimerization domain may activate d-amino acid as well as l-amino acid. We successfully synthesized over 40 kinds of d-amino acid-containing dipeptides, including ld-, dl-, and dd-dipeptides, using only two adenylation domains, TycA-A from tyrocidine synthetase and BacB2-A from bacitracin synthetase. Furthermore, this study offered the possibility that the epimerization domain could be a clue to the activity of the adenylation domains toward d-amino acid. This paper provides additional information regarding d-amino acid-containing-dipeptide synthesis through the combination of enzymatic adenylation and chemical nucleophilic reaction, and this system will be a useful tool for dipeptide synthesis.IMPORTANCE Because almost all amino acids in nature are l-amino acids, the functioning of d-amino acids has received little attention. Thus, there is little information available on the activity of enzymes toward d-amino acids or synthetic methods for d-amino acid-containing dipeptides. Recently, d-amino acids and d-amino acid-containing peptides have attracted attention as novel functional compounds, and d-amino acid-activating enzymes and synthetic methods are required for the development of the d-amino acid-containing-peptide industry. This study provides additional knowledge regarding d-amino acid-activating enzymes and proposes a unique synthetic method for d-amino acid-containing peptides, including ld-, dl-, and dd-dipeptides.

Dataset Information

Populations of the three major backbone conformations in 19 amino acid dipeptides.

Publications

Populations of the three major backbone conformations in 19 amino acid dipeptides.

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