A tracked approach for automated NMR assignments in proteins (TATAPRO).
A novel automated approach for the sequence specific NMR assignments of 1HN, 13Calpha, 13Cbeta, 13C'/1Halpha and 15N spins in proteins, using triple resonance experimental data, is presented. The algorithm, TATAPRO (Tracked AuTomated Assignments in Proteins) utilizes the protein primary sequence and peak lists from a set of triple resonance spectra which correlate 1HN and 15N chemical shifts with those of 13Calpha, 13Cbeta and 13C'/1Halpha. The information derived from such correlations is used to create a 'master-_list' consisting of all possible sets of 1HN(i), 15N(i)13Calpha(i),13Cbeta(i) 13C'beta(i)/1Halpha(i), 13Calpha(i-1), 13Cbeta(i-1) and 13C'(i-1)/1Halpha(i-1) chemical shifts. On the basis of an extensive statistical analysis of 13Calpha and 13Cbeta chemical shift data of proteins derived from the BioMagResBank (BMRB), it is shown that the 20 amino acid residues can be grouped into eight distinct categories, each of which is assigned a unique two-digit code. Such a code is used to tag individual sets of chemical shifts in the master_list and also to translate the protein primary sequence into an array called pps_array. The program then uses the master_list to search for neighbouring partners of a given amino acid residue along the polypeptide chain and sequentially assigns a maximum possible stretch of residues on either side. While doing so. each assigned residue is tracked in an array called assig_array, with the two-digit code assigned earlier. The assig_array is then mapped onto the pps_array for sequence specific resonance assignment. The program has been tested using experimental data on a calcium binding protein from Entamoeba histolytica (Eh-CaBP, 15 kDa) having substantial internal sequence homology and using published data on four other proteins in the molecular weight range of 18-42 kDa. In all the cases, nearly complete sequence specific resonance assignments (> 95%) are obtained. Furthermore, the reliability of the program has been tested by deleting sets of chemical shifts randomly from the master_list created for the test proteins.
Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India.
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Atreya
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Sahu
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D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D000954:Antigens, Surface / Q000737:chemistry; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D001428:Bacterial Vaccines; D015748:Borrelia burgdorferi Group / Q000737:chemistry; D002135:Calcium-Binding Proteins / Q000737:chemistry; D002247:Carbon Isotopes; D002352:Carrier Proteins / Q000737:chemistry; D029721:Drosophila Proteins; D004748:Entamoeba histolytica / Q000737:chemistry; D007605:Juvenile Hormones / Q000737:chemistry; D008074:Lipoproteins; D022123:Lyme Disease Vaccines / Q000737:chemistry; D058619:Maltose-Binding Proteins; D020784:Matrix Metalloproteinase 8 / Q000737:chemistry; D008969:Molecular Sequence Data; D009587:Nitrogen Isotopes; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D015800:Protozoan Proteins / Q000737:chemistry; D017385:Sequence Homology
D000596:Amino Acids; D000954:Antigens, Surface; D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; D001428:Bacterial Vaccines; D002135:Calcium-Binding Proteins; D002247:Carbon Isotopes; D002352:Carrier Proteins; D029721:Drosophila Proteins; D007605:Juvenile Hormones; D008074:Lipoproteins; D022123:Lyme Disease Vaccines; D058619:Maltose-Binding Proteins; D009587:Nitrogen Isotopes; C072045:OspA protein; D011506:Proteins; D015800:Protozoan Proteins; C060606:numb protein, Drosophila; C075554:calcium-binding protein, Entamoeba histolytica; D020784:Matrix Metalloproteinase 8