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AbstractAbstract
[en] A novel automated approach for the sequence specific NMR assignments of 1HN, 13Cα, 13Cβ, 13C'/1Hα 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 13Cα, 13Cβ and 13C'/1Hα. The information derived from such correlations is used to create a 'masterlist' consisting of all possible sets of 1HNi, 15Ni, 13Cαi, 13Cβi, 13C'i/1Hαi, 13Cαi-1, 13Cβi-1 and 13C'i-1/ 1Hαi-1 chemical shifts. On the basis of an extensive statistical analysis of 13Cα and 13Cβ 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 masterlist and also to translate the protein primary sequence into an array called ppsarray. The program then uses the masterlist 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 assigarray, with the two-digit code assigned earlier. The assigarray is then mapped onto the ppsarray 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 masterlist created for the test proteins
Primary Subject
Source
Copyright (c) 2000 Kluwer Academic Publishers; Country of input: International Atomic Energy Agency (IAEA)
Record Type
Journal Article
Journal
Journal of Biomolecular NMR; ISSN 0925-2738;
; v. 17(2); p. 125-136

Country of publication
ALKALINE EARTH METALS, ANIMALS, CARBON ISOTOPES, CARBOXYLIC ACIDS, COMPUTER CODES, ELEMENTS, EVEN-ODD NUCLEI, INVERTEBRATES, ISOTOPES, LIGHT NUCLEI, MAGNETIC RESONANCE, MATHEMATICAL LOGIC, METALS, MICROORGANISMS, NITROGEN ISOTOPES, NUCLEI, ODD-EVEN NUCLEI, ORGANIC ACIDS, ORGANIC COMPOUNDS, PEPTIDES, PROTEINS, PROTOZOA, RESONANCE, SARCODINA, STABLE ISOTOPES
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