Solvent effects on the conformation of cyclo(-D-Trp-D-Asp-Pro-D-Val-Leu-). An NMR spectroscopy and molecular modeling study.
The conformations of cyclo(-D-Trp-D-Asp-Pro-D-Val-Leu-) in dimethyl sulfoxide-d6 (DMSO-d6) and water were determined using two-dimensional nuclear magnetic resonance spectroscopy and restrained molecular dynamics. Comparisons were made between conformations of the cyclic pentapeptide in both solvents. The NMR study revealed that, while the backbone remained relatively unchanged in both solvents, the side-chains adopted distinctly different orientations in DMSO-d6 vs. H2O. A modeling study, minus NOE constraints, produced a set of low-energy conformers possessing agreement in backbone conformation with the NMR-derived structures; however, lowest-energy conformers did not have this agreement. These results show that different solvents can significantly affect the preferred side-chain conformation of small cyclic peptides in solution. This finding will impact the selection of solvent when determining structures for use as templates in rational drug design.
Gonnella
N C
NC
Research Department, Ciba-Geigy Corporation, Summit, New Jersey.
Zhang
X
X
Jin
Y
Y
Prakash
O
O
Paris
C G
CG
Kolossváry
I
I
Guida
W C
WC
Bohacek
R S
RS
Vlattas
I
I
Sytwu
T
T
D000595:Amino Acid Sequence; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D004121:Dimethyl Sulfoxide / Q000737:chemistry*; D065128:Endothelin Receptor Antagonists; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010456:Peptides, Cyclic / Q000737:chemistry*; D011487:Protein Conformation; D012996:Solutions; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D065128:Endothelin Receptor Antagonists; D010456:Peptides, Cyclic; D012996:Solutions; D012997:Solvents; D014867:Water; C072247:cyclo(Trp-Asp-Pro-Val-Leu); D004121:Dimethyl Sulfoxide