Sequential nearest-neighbor effects on computed 13Ca chemical shifts

VILA JA , SERRANO P , WUTHRICH K & SCHERAGA HA

JOURNAL OF BIOMOLECULAR NMR

SPRINGER

Año: 2010 vol. 48 p. 23 - 30

0925-2738

To evaluate sequential nearest-neighbor effectson quantum-chemical calculations of 13Ca chemical shifts,we selected the structure of the nucleic acid binding (NAB)protein from the SARS coronavirus determined by NMR insolution (PDB id 2K87). NAB is a 116-residue a/b protein,which contains 9 prolines and has 50% of its residueslocated in loops and turns. Overall, the results presentedhere show that sizeable nearest-neighbor effects are seenonly for residues preceding proline, where Pro introducesan overestimation, on average, of 1.73 ppm in the computed13Ca chemical shifts. A new ensemble of 20 conformersrepresenting the NMR structure of the NAB, whichwas calculated with an input containing backbone torsionangle constraints derived from the theoretical 13Ca chemicalshifts as supplementary data to the NOE distanceconstraints, exhibits very similar topology and comparableagreement with the NOE constraints as the published NMRstructure. However, the two structures differ in the patternsof differences between observed and computed 13Cachemical shifts, Dca,i, for the individual residues along thesequence. This indicates that the Dca,i -values for the NABprotein are primarily a consequence of the limited samplingby the bundles of 20 conformers used, as in commonpractice, to represent the two NMR structures, rather thanof local flaws in the structures