Protein three-dimensional structure determination and sequence-specific assignment of 13C and 15N-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 in 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 13C and 15N-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, 1H spins is calculated from the nuclear Overhauser effect (NOE) distance restraints using a dynamical simulated annealing procedure. The sequence-specific assignments are then determined by searching among the 1H 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 1H, 15N and 13C 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.
Kraulis
P J
PJ
Center for Structural Biochemistry, Karolinska Institutet, Huddinge, Sweden.
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D007611:Aprotinin / Q000737:chemistry*; D002250:Carbon Radioisotopes; D003198:Computer Simulation; D004268:DNA-Binding Proteins / Q000737:chemistry; D003627:Data Interpretation, Statistical; D016208:Databases, Factual; D005656:Fungal Proteins / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D009682:Magnetic Resonance Spectroscopy; D008667:Metalloproteins / Q000737:chemistry; D008970:Molecular Weight; D009010:Monte Carlo Method; D009590:Nitrogen Radioisotopes; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012015:Reference Standards; D029701:Saccharomyces cerevisiae Proteins; D013696:Temperature; D014157:Transcription Factors / Q000737:chemistry
D000596:Amino Acids; D002250:Carbon Radioisotopes; D004268:DNA-Binding Proteins; D005656:Fungal Proteins; C052130:GAL4 protein, S cerevisiae; D008667:Metalloproteins; D009590:Nitrogen Radioisotopes; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D007611:Aprotinin