Use of 13C(alpha) chemical shifts for accurate determination of beta-sheet structures in solution.
A physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13C(alpha) chemical shifts, is applied to determine the structure of a 20-residue all-beta peptide (BS2). The approach makes use of 13C(alpha) chemical shifts, computed at the density functional level of theory, to derive backbone and side-chain torsional constraints for all of the amino acid residues, without making use of information about residue occupancy in any region of the Ramachandran map. In addition, the torsional constraints are derived dynamically--i.e., they are redefined at each step of the algorithm. It is shown that, starting from randomly generated conformations, the final protein models are more accurate than existing NMR-derived models of the peptide, in terms of the agreement between predicted and observed 13C(beta) chemical shifts, and some stereochemical quality indicators. The accumulated evidence indicates that, for a highly flexible BS2 peptide in solution, it may not be possible to determine a single structure (or a small set of structures) that would satisfy all of the constraints exactly and simultaneously because the observed NOEs and 13C(alpha) chemical shifts correspond to a dynamic ensemble of conformations. Analysis of the structural flexibility, carried out by molecular dynamics simulations in explicit water, revealed that the whole peptide can be characterized as having liquid-like behavior, according to the Lindemann criterion. In summary, a beta-sheet structure of a highly flexible peptide in solution can be determined by a quantum-chemical-based procedure.
Vila
Jorge A
JA
Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
Arnautova
Yelena A
YA
Scheraga
Harold A
HA
D000595:Amino Acid Sequence; D002247:Carbon Isotopes / Q000737:chemistry*; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D017433:Protein Structure, Secondary; D012996:Solutions
D002247:Carbon Isotopes; D012996:Solutions