Sequence-specific NMR assignment of proteins by global fragment mapping with the program MAPPER

A new program, MAPPER, for semiautomatic sequence-specific NMR assignment in proteins is introduced. The program uses an input of short fragments of sequentially neighboring residues, which have been assembled based on sequential NMR connectivities and for which either the 13C(alpha) and 13C(beta) c...

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Bibliographic Details
Published in:Journal of biomolecular NMR 2000-10, Vol.18 (2), p.129-137
Main Authors: Güntert, P, Salzmann, M, Braun, D, Wüthrich, K
Format: Article
Language:English
Subjects:
Aldehyde-Lyases - chemistry
Algorithms
Amino Acid Sequence
Amino acids
Binding Sites
Carbon Isotopes
Molecular Sequence Data
Nuclear Magnetic Resonance, Biomolecular - methods
Peptide Fragments - chemistry
Proteins
Proteins - chemistry
Software
Staphylococcus aureus - enzymology
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Summary:A new program, MAPPER, for semiautomatic sequence-specific NMR assignment in proteins is introduced. The program uses an input of short fragments of sequentially neighboring residues, which have been assembled based on sequential NMR connectivities and for which either the 13C(alpha) and 13C(beta) chemical shifts or data on the amino acid type from other sources are known. MAPPER then performs an exhaustive search for self-consistent simultaneous mappings of all these fragments onto the protein sequence. Compared to using only the individual mappings of the spectroscopically connected fragments, the global mapping adds a powerful new constraint, which results in resolving many otherwise intractable ambiguities. In an initial application, virtually complete sequence-specific assignments were obtained for a 110 kDa homooctameric protein, 7,8-dihydroneopterin aldolase from Staphylococcus aureus.
ISSN:0925-2738
1573-5001
DOI:10.1023/A:1008318805889