A tracked approach for automated NMR assignments in proteins (TATAPRO) View Full Text


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Article Info

DATE

2000-06

AUTHORS

H.S. Atreya, S.C. Sahu, K.V.R. Chary, Girjesh Govil

ABSTRACT

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 `master_list' 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 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. More... »

PAGES

125-136

References to SciGraph publications

  • 1994-05. Evaluation of an algorithm for the automated sequential assignment of protein backbone resonances: A demonstration of the connectivity tracing assignment tools (CONTRAST) software package in JOURNAL OF BIOMOLECULAR NMR
  • 1998-05. NMR studies of Borrelia burgdorferi OspA, a 28 kDa protein containing a single-layer β-sheet in JOURNAL OF BIOMOLECULAR NMR
  • 1999-05. Letter to the Editor: Sequence-specific 1H, 13C and 15N assignments of a calcium binding protein from Entamoeba histolytica in JOURNAL OF BIOMOLECULAR NMR
  • 1998-01. Automated backbone assignment of labeled proteins using the threshold accepting algorithm in JOURNAL OF BIOMOLECULAR NMR
  • 1998-12. Structure of a Numb PTB domain–peptide complex suggests a basis for diverse binding specificity in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 1991-09. A relational database for sequence-specific protein NMR data in JOURNAL OF BIOMOLECULAR NMR
  • 1994-09. An automated procedure for the assignment of protein 1HN, 15N, 13Cα, 1Hα, 13Cβ and 1Hβ resonances in JOURNAL OF BIOMOLECULAR NMR
  • 1997-07. Assignments, secondary structure and dynamics of the inhibitor-free catalytic fragment of human fibroblast collagenase in JOURNAL OF BIOMOLECULAR NMR
  • 1998-10. CAMRA: Chemical shift based computer aided protein NMR assignments in JOURNAL OF BIOMOLECULAR NMR
  • 1996-05. Automated sequence-specific NMR assignment of homologous proteins using the program GARANT in JOURNAL OF BIOMOLECULAR NMR
  • 1997-02. Automated probabilistic method for assigning backbone resonances of (13C,15N)-labeled proteins in JOURNAL OF BIOMOLECULAR NMR
  • 1994-01. A computer-based protocol for semiautomated assignments and 3D structure determination of proteins in JOURNAL OF BIOMOLECULAR NMR
  • 1994-01. Application of neural networks to automated assignment of NMR spectra of proteins in JOURNAL OF BIOMOLECULAR NMR
  • 1994-03. Automated sequencing of amino acid spin systems in proteins using multidimensional HCC(CO)NH-TOCSY spectroscopy and constraint propagation methods from artificial intelligence in JOURNAL OF BIOMOLECULAR NMR
  • 1992-03. A new 3D HN(CA)HA experiment for obtaining fingerprint HN-Hα cross peaks in15N- and13C-labeled proteins in JOURNAL OF BIOMOLECULAR NMR
  • 1993-03. Amino acid type determination in the sequential assignment procedure of uniformly 13C/15N-enriched proteins in JOURNAL OF BIOMOLECULAR NMR
  • 1992-07. A triple-resonance pulse scheme for selectively correlating amide1HN and15N nuclei with the1Hα proton of the preceding residue in JOURNAL OF BIOMOLECULAR NMR
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    http://scigraph.springernature.com/pub.10.1023/a:1008315111278

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    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/10921777


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    48 schema:description 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 `master_list' 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 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.
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