Abstract We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and 13Cβ chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of beta-turns: I, II, I', II' and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and β-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7â??0.9 for the Matthews correlation coefficient of its predictions far exceed those attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures.
Content Type Journal Article
Category Article
Pages 1-22
DOI 10.1007/s10858-012-9602-0
Authors
Yang Shen, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 126, NIH, Bethesda, MD 20892-0520, USA
Ad Bax, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 126, NIH, Bethesda, MD 20892-0520, USA
Density functional calculations of backbone 15N shielding tensors in beta-sheet and turn residues of protein G
Density functional calculations of backbone 15N shielding tensors in beta-sheet and turn residues of protein G
Abstract We performed density functional calculations of backbone 15N shielding tensors in the regions of beta-sheet and turns of protein G. The calculations were carried out for all twenty-four beta-sheet residues and eight beta-turn residues in the protein GB3 and the results were compared with the available experimental data from solid-state and solution NMR measurements. Together with the alpha-helix data, our calculations cover 39 out of the 55 residues (or 71%) in GB3....
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BACKGROUND: Transmissible spongiform encephalopathies are a group of neurodegenerative disorders of man and animals...
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The beta-amyloid (Abeta) is the major peptide constituent of neuritic plaques in Alzheimer's disease, and its aggregation is believed to...
Identification of helix capping and beta-turn motifs from NMR chemical shifts
Linear Mode
