Sequential nearest-neighbor effects on computed 13Calpha chemical shifts.
To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of (13)C(alpha) chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue alpha/beta protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed (13)C(alpha) chemical shifts. A new ensemble of 20 conformers representing the NMR structure of the NAB, which was calculated with an input containing backbone torsion angle constraints derived from the theoretical (13)C(alpha) chemical shifts as supplementary data to the NOE distance constraints, exhibits very similar topology and comparable agreement with the NOE constraints as the published NMR structure. However, the two structures differ in the patterns of differences between observed and computed (13)C(alpha) chemical shifts, Delta(ca,i), for the individual residues along the sequence. This indicates that the Delta(ca,i)-values for the NAB protein are primarily a consequence of the limited sampling by the bundles of 20 conformers used, as in common practice, to represent the two NMR structures, rather than of local flaws in the structures.
Vila
Jorge A
JA
Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
Serrano
Pedro
P
Wüthrich
Kurt
K
Scheraga
Harold A
HA
D000465:Algorithms; D002247:Carbon Isotopes / Q000737:chemistry*; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D015203:Reproducibility of Results; D045473:Severe acute respiratory syndrome-related coronavirus / Q000737:chemistry; D014764:Viral Proteins / Q000737:chemistry
D002247:Carbon Isotopes; D014764:Viral Proteins