Rapid protein fold determination using unassigned NMR data.

Abstract

Experimental structure determination by x-ray crystallography and NMR spectroscopy is slow and time-consuming compared with the rate at which new protein sequences are being identified. NMR spectroscopy has the advantage of rapidly providing the structurally relevant information in the form of unassigned chemical shifts (CSs), intensities of NOESY crosspeaks [nuclear Overhauser effects (NOEs)], and residual dipolar couplings (RDCs), but use of these data are limited by the time and effort needed to assign individual resonances to specific atoms. Here, we develop a method for generating low-resolution protein structures by using unassigned NMR data that relies on the de novo protein structure prediction algorithm, rosetta [Simons, K. T., Kooperberg, C., Huang, E. & Baker, D. (1997) J. Mol. Biol. 268, 209-225] and a Monte Carlo procedure that searches for the assignment of resonances to atoms that produces the best fit of the experimental NMR data to a candidate 3D structure. A large ensemble of models is generated from sequence information alone by using rosetta, an optimal assignment is identified for each model, and the models are then ranked based on their fit with the NMR data assuming the identified assignments. The method was tested on nine protein sequences between 56 and 140 amino acids and published CS, NOE, and RDC data. The procedure yielded models with rms deviations between 3 and 6 A, and, in four of the nine cases, the partial assignments obtained by the method could be used to refine the structures to high resolution (0.6-1.8 A) by repeated cycles of structure generation guided by the partial assignments, followed by reassignment using the newly generated models.