Automated Resonance Assignment of Proteins Using Heteronuclear 3D NMR. 2. Side Chain and Sequence-Specific Assignment

A sequential assignment protocol for proteins was developed using heteronuclear 3D NMR. The protocol consists of an amino acid type recognition algorithm and a primary sequence mapping algorithm. The former measures the similarity between each detected spin pattern and 20 standard amino acid couplin...

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Bibliographic Details
Published in:Journal of Chemical Information and Computer Sciences 1997-05, Vol.37 (3), p.467-477
Main Authors: Li, Kuo-Bin, Sanctuary, B. C
Format: Article
Language:English
Subjects:
Algorithms
Amino Acid Sequence
Animals
Chickens
Magnetic Resonance Spectroscopy - methods
Molecular Sequence Data
Molecular Structure
Peptide Fragments - chemistry
Peptide Fragments - genetics
Peptide Mapping
Proteins - chemistry
Proteins - genetics
Software
Troponin C - chemistry
Troponin C - genetics
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Summary:A sequential assignment protocol for proteins was developed using heteronuclear 3D NMR. The protocol consists of an amino acid type recognition algorithm and a primary sequence mapping algorithm. The former measures the similarity between each detected spin pattern and 20 standard amino acid coupling patterns. Both chemical shift and topologically likeness are considered. The mapping algorithm uses the amino acid type information to direct detected polypeptides to proper position onto protein primary sequence. The assignment protocol can be applied to spin systems generated by many different approaches. We designed a few computer programs to derive a protein's backbone and side chain spin systems using heteronuclear 3D NMR. The results was then input to the sequential assignment protocol. All of the algorithms were tested on NMR data of a 90-residue N-domain of chicken skeletal troponin-C.
ISSN:0095-2338
1549-960X
1520-5142
DOI:10.1021/ci960372k