Threonine6-bradykinin: Conformational study of a flexible peptide in dimethyl sulfoxide by NMR and ensemble calculations

Abstract

The conformation of the natural peptide threonine6 (Thr6)‐bradykinin, Arg1‐Pro2‐Pro3‐Gly4‐Phe5‐Thr6‐Pro7‐Phe8‐Arg9, was investigated in DMSO by nmr spectroscopy and computer simulations. The structural analysis of the Thr6‐peptide is made particularly interesting by the fact that despite the high sequence homology with native bradykinin (only one conservative substitution: Ser6/Thr6) there is a marked and significant difference in the biological profiles of the two peptides. The nmr spectra indicate a relatively flexible structure with the presence of an N‐terminal turn. Standard distance geometry calculations failed to produce structures in accord with the experimental observations; the resulting structures are indeed too rigid and conformationally restricted for the nmr data. The results of ensemble calculations reveal conformational changes occurring rapidly on the nmr time scale and allow for the establishment of a series of disordered conformations, prevalently extended with a partially populated turn in residues 2–5, which when considered together, as an average, fulfill the experimental restraints. The structural characterization of (Thr6)‐bradykinin supports the hypothesis of the significant role of the residue at position 6 on both conformation as well as biological activities and suggests a N‐terminal turn as a possible bioactive conformation. © 1997 John Wiley & Sons, Inc. Biopoly 40: 561–569, 1996

NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains

“…The application of the ROE distance restraints to each and every structure of an ensemble is not appropriate for cases in which conformational dynamics are taking place rapidly on the NMR time scale. One way to address this situation is by ensemble dynamics (20), in which the experimental observations are fulfilled by the average over the ensemble: each member of the ensemble must satisfy the constitutional constraints from the structural formula, whereas only the average over the ensemble must fulfill the experimental measurements. This method has been previously used to characterize equilibria between different conformations (20)(21)(22).…”

“…1D). By analogy to peptides (20), a molecule of such short length could be expected to populate multiple conformations in solution. Nevertheless, this length was sufficient to give rise to a strong double minimum CD signal (5), indicating that the backbone conformation of interest was significantly populated.…”

Cannabinoid receptor‐G protein interactions: Gαi1‐bound structures of IC3 and a mutant with altered G protein specificity

“…Pseudoatoms were used for methylene protons that could not be stereospecifically assigned. Distance geometry calculations were carried out employing the random metrization method of Havel (1991) to generate an ensemble of structures to be refined using IRMA (Boelens et al 1989; Bonvin et al 1993) following published procedures (Mierke et al 1994; Pellegrini et al 1996).…”

In silico folding of hydrophobic peptides that form β‐hairpin structures in solution

“…12 In fact, several peptides that are composed of hydrophobic amino acids do not adopt folded structures in DMSO. [13][14][15][16] In an effort to set insights into the conformational dynamics of model peptides that exhibit distinct conformations in solution, as indicated by 1D and 2D NMR spectroscopy and crystalline state, 2,3,11,17 we have carried out molecular dynamics simulations (MDS) of peptides whose structures have been characterised in detail in solution and in the crystalline state. The peptides studied (note: one-letter code has been used as follows: Leu, L; Val, V; D-Pro, p; Gly, G; Phe, F) were acetyl (Ac)-LVVpGLVV-NH 2 (1); Ac-LFVpGLFV-NH 2 (2); Ac-LFVpGLVLApGFVV-NH 2 (3); Ac-LFVpALFV-NH 2 (4).…”

“…This solvent is generally used to dissolve aggregating peptides such as amyloidogenic peptides to break up any secondary structures 12 . In fact, several peptides that are composed of hydrophobic amino acids do not adopt folded structures in DMSO 13–16 …”