Fully automated structure determinations of the Fes SH2 domain using different sets of NMR spectra

Abstract

The recently introduced fully automated protein NMR structure determination algorithm (FLYA) yields, without any human intervention, a three-dimensional (3D) protein structure starting from a set of two- and three-dimensional NMR spectra. This paper investigates the influence of reduced sets of experimental spectra on the quality of NMR structures obtained with FLYA. In a case study using the Src homology domain 2 from the human feline sarcoma oncogene Fes (Fes SH2), five reduced data sets selected from the full set of 13 three-dimensional spectra of the previously determined conventional structure were used to calculate the protein structure. Three reduced data sets utilized only CBCA(CO)NH and CBCANH for the backbone assignments and two data sets used only CBCA(CO)NH. All, some, or none of the five original side-chain assignment spectra were used. Results were compared with those of a FLYA calculation for the complete set of spectra and those of the conventionally determined structure. In four of the five cases tested, the three-dimensional structures deviated by less than 1.3 A in backbone RMSD from the conventionally determined Fes SH2 reference structure, showing that the FLYA algorithm is remarkably stable and accurate when used with reduced sets of input spectra.