Multi-conformational peptide dynamics derived from NMR data: a new search algorithm and its application to antamanide.
A search algorithm, called MEDUSA, is presented which allows the determination of multiple conformations of biomolecules in solution with exchange rate constants typically between 10(3) and 10(7) s-1 on the basis of experimental high-resolution NMR data. Multiples of structures are generated which are consistent as ensembles with NMR cross-relaxation rates (NOESY, ROESY), scalar J-coupling constants, and T1 rho measurements. The algorithm is applied to the cyclic decapeptide antamanide dissolved in chloroform. The characteristic radio-frequency field dependence of the T1 rho relaxation rates found for the NH protons of Val1 and Phe6 can be explained by a dynamical exchange between two structures.
Brüschweiler
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Laboratorium für Physikalische Chemie, Eidgenössische Technische Hochschule, Zürich, Switzerland.
Blackledge
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Ernst
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RR
D000465:Algorithms; D000595:Amino Acid Sequence; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D010456:Peptides, Cyclic / Q000737:chemistry
D010455:Peptides; D010456:Peptides, Cyclic; C100265:antamanide