ABSTRACT
The solution structure of the 56 amino acid residue turkey ovomucoid third domain was determined by n.m.r. methods. Of the 661 distance constraints used in the calculations, 120 were determined by quadratic approximation of the cross-relaxation rates. The remaining constraints were crudely estimated from a more standard analysis of NOESY spectra. Additionally, 29 torsion angle constraints, 17 hydrogen bonds, and three disulfide bridges were used in the structure calculations. Stereospecific assignments were accomplished for 24 beta-methylene groups and six isopropyl methyl groups (43% chiral assignments). The addition of more accurate distance constraints to the distance geometry/simulated annealing approach resulted in a significant reduction in the dispersion of calculated backbone torsion angles and root-mean-square deviations between structures. Detailed comparisons have been made between the n.m.r. structures of OMTKY3 and published X-ray structures of the same protein and of closely related avian ovomucoid third domains. The refinement with more accurate distance constraints reduced differences between families of the n.m.r. and the X-ray structures.
Subject(s)
Ovomucin/chemistry , Amino Acids/chemistry , Animals , Hydrogen Bonding , Magnetic Resonance Spectroscopy , Protein Conformation , Protein Structure, Tertiary , TurkeysABSTRACT
By applying a two-dimensional double-quantum carbon-13 nuclear magnetic resonance experiment to a protein uniformly enriched to 26 percent carbon-13, networks of directly bonded carbon atoms were identified by virtue of their one-bond spin-spin couplings and were classified by amino acid type according to their particular single- and double-quantum chemical shift patterns. Spin systems of 75 of the 98 amino acid residues in a protein, oxidized Anabaena 7120 ferredoxin (molecular weight 11,000), were identified by this approach, which represents a key step in an improved methodology for assigning protein nuclear magnetic resonance spectra. Missing spin systems corresponded primarily to residues located adjacent to the paramagnetic iron-sulfur cluster.
