PROTEIN 3-DIMENSIONAL STRUCTURE DETERMINATION AND SEQUENCE-SPECIFIC ASSIGNMENT OF C-13-SEPARATED AND N-15-SEPARATED NOE DATA - A NOVEL REAL-SPACE AB-INITIO APPROACH

The sequence-specific assignment of resonances is considered to be a requirement for the determination of the three-dimensional (3D) structure of a protein in solution by nuclear magnetic resonance methods. The main source of structural information is the nuclear Overhauser effect spectroscopy (NOESY) spectrum, which contains information about spatially close pairs of protons. Currently various J-correlated spectra must be recorded is order to obtain the sequence-specific assignments necessary to interpret the NOESY spectra. In this work, a novel procedure to determine the 3D structure and the sequence-specific assignments of a protein using only data from C-13 and N-15-separated multidimensional NOESY spectra is described. No information from J-correlated spectra is required. The algorithm is called ANSRS (Assignment of NOESY Spectra in Real Space) and is based on an inversion of the traditional strategy. A 3D real-space structure of detected, but unassigned, H-1 spins is calculated from the nuclear Overhauser effect (NOE) distance restraints using a dynamical simulated annealing procedure. The sequence-specific assignments are then deter mined by searching among the H-1 spins in the 3D real-space structure for plausible residue assignments. The search uses a Monte Carlo simulated annealing algorithm based on assignment probabilities derived from the H-1,N-15 and C-13 chemical shifts, various spatial constraints, and the known sequence of the protein. The procedure has been tested on semi-synthetic data sets comprising published experimental chemical shifts and NOE distance restraints derived from the known 3D structures of the two proteins GAL4 (residues 9 to 41) and bovine pancreatic trypsin inhibitor. The ANSRS procedure was able to determine the sequence-specific assignments for more than 95% of the spins, and was fairly robust with respect to missing NOE data. The potential of the ANSRS approach with respect to automated assignment, reduction of the number of NMR spectra required for a structure determination, assignment-of homologous and mutant proteins, and the possibility of analysing spectra recorded at high pH is discussed.