A convenient method for determining cyclic peptide conformation from 1D 1H-NMR information.
A rapid and convenient method for determining the backbone conformation of cyclic peptides results from the combination of 1D 1H NMR information and molecular modeling. phi Angle torsional constraints calculated from 3JHN.H alpha coupling constants are used to determine the position of multiple-welled potential energy penalty functions that are imposed on the force field used in the structure refinement (Amber* with GB/SA solvation model). Monte Carlo searches and minimizations lead to a collection of structures that are clustered by backbone similarity and then filtered according to hydrogen-bonding constraints determined by the chemical shift temperature dependencies of the amide protons. This approach was applied to five cyclic peptides whose structures had been determined previously using more extensive 2D NMR techniques, and the importance of the torsional, H-bonding, and solvation restraints were assessed. For the four peptides that adopt a predominant conformation, this method reproduced the reported structures closely; lack of convergence for the fifth structure reflected the multiple backbone conformations that this macrocycle adopts.
Sefler
A M
AM
Department of Chemistry, University of California, Berkeley, USA.
Lauri
G
G
Bartlett
P A
PA
D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009010:Monte Carlo Method; D010456:Peptides, Cyclic / Q000737:chemistry*; D011487:Protein Conformation; D011522:Protons
D010456:Peptides, Cyclic; D011522:Protons