Survey of conformational role of ester bonds in a cyclic depsipeptide. Study on cyclo(-L-Ala-L-Hmb-)2 by energy calculation and NMR spectroscopy.
The effect of ester bond on the conformation of peptide molecule was studied by designing and synthesizing a model tetradepsipeptide cyclo(-L-Ala-L-Hmb-)2 and by analyzing the conformation both theoretically and experimentally. Theoretical analysis showed that both ester and peptide bonds in the calculated low-energy conformations within 3 kcal/mol of the global minimum take a trans but distorted configuration. The distortion is larger in ester bonds than in peptide bonds. Further, the four carbonyls project from one side of the plane of the cyclic backbone, whereas the side chains project from the other side. These results are consistent with the experimental results obtained by NMR measurement; first, the coupling constant deduced from 1H-NMR species in DMSO-d6 is consistent with the dihedral angles of the calculated low-energy conformations; second, results of NOE measurement can reproduce the calculated configuration of the carbonyls and side chains. From the consistency between theoretical and experimental results, it is concluded that this model tetradepsipeptide takes an all-trans backbone conformation in solution and this backbone conformation is stabilized by large distortion in the ester bond, which compensates the strain resulted from the 12-membered cyclic backbone structure consisting only of L-residues.
Kato
T
T
Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka, Japan.
Mizuno
H
H
Lee
S
S
Aoyagi
H
H
Kodama
H
H
Go
N
N
Kato
T
T
D000595:Amino Acid Sequence; D002087:Butyrates / Q000737:chemistry*; D004952:Esters / Q000737:chemistry; D045782:Hemiterpenes; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D010421:Pentanoic Acids / Q000737:chemistry*; D010456:Peptides, Cyclic / Q000138:chemical synthesis / Q000737:chemistry*; D011487:Protein Conformation; D013057:Spectrum Analysis; D013816:Thermodynamics
D002087:Butyrates; D004952:Esters; D045782:Hemiterpenes; D010421:Pentanoic Acids; D010456:Peptides, Cyclic; C008216:isovaleric acid; C019475:2-methylbutanoic acid