spacer Fully automated solution structure determination of the Fes SH2 domain
Primary citation
Title Automated protein structure determination from NMR spectra
Authors Lopez-Mendez, B.search; Guntert, P.search
Journal J.AM.CHEM.SOC.search vol:128, pag:13112-13122 (2006), Identifiers: PubMed ID (17017791)search DOI (10.1021/ja061136l)
Abstract Fully automated structure determination of proteins in solution (FLYA) yields, without human intervention, three-dimensional protein structures starting from a set of multidimensional NMR spectra. Integrating existing and new software, automated peak picking over all spectra is followed by peak list filtering, the generation of an ensemble of initial chemical shift assignments, the determination of consensus chemical shift assignments for all (1)H, (13)C, and (15)N nuclei, the assignment of NOESY cross-peaks, the generation of distance restraints, and the calculation of the three-dimensional structure by torsion angle dynamics. The resulting, preliminary structure serves as additional input to the second stage of the procedure, in which a new ensemble of chemical shift assignments and a refined structure are calculated. The three-dimensional structures of three 12-16 kDa proteins computed with the FLYA algorithm coincided closely with the conventionally determined structures. Deviations were below 0.95 A for the backbone atom positions, excluding the flexible chain termini. 96-97% of all backbone and side-chain chemical shifts in the structured regions were assigned to the correct residues. The purely computational FLYA method is suitable for substituting all manual spectra analysis and thus overcomes a main efficiency limitation of the NMR method for protein structure determination.
MeSH terms Algorithmssearch, Humanssearch, Modelssearch, Molecularsearch, Nuclear Magnetic Resonancesearch, Biomolecularsearch, Protein Structuresearch, Tertiarysearch, Proteinssearch, Reproducibility of Resultssearch
Other entries described in this publication 2dcq, 2dcp
Secondary citations
Title Solution structure of the Src homology 2 domain from the human feline sarcoma oncogene Fes
Authors Scott, A.search; Pantoja-Uceda, D.search; Koshiba, S.search; Inoue, M.search; Kigawa, T.search; Terada, T.search; Shirouzu, M.search; Tanaka, A.search; Sugano, S.search; Yokoyama, S.search; Guntert, P.search
Journal J.BIOMOL.NMRsearch vol:31, pag:357-361 (2005), Identifiers: PubMed ID (15929003)search DOI (10.1007/s10858-005-0946-6)
MeSH terms Genomicssearch, Humanssearch, Modelssearch, Molecularsearch, Nuclear Magnetic Resonancesearch, Biomolecularsearch, Peptidessearch, Phosphotyrosinesearch, Protein Conformationsearch, Protein Structuresearch, Tertiarysearch, Protein-Tyrosine Kinasessearch, Proto-Oncogene Proteinssearch, Proto-Oncogene Proteins c-fessearch, Static Electricitysearch, src Homology Domainssearch
Title NMR assignment of the SH2 domain from the human feline sarcoma oncogene FES
Authors Scott, A.search; Pantoja-Uceda, D.search; Koshiba, S.search; Inoue, M.search; Kigawa, T.search; Terada, T.search; Shirouzu, M.search; Tanaka, A.search; Sugano, S.search; Yokoyama, S.search
Journal J.BIOMOL.NMRsearch vol:30, pag:463-464 (2004), Identifiers: PubMed ID (15630569)search DOI (10.1007/s10858-004-5432-z)
MeSH terms Humanssearch, Nuclear Magnetic Resonancesearch, Biomolecularsearch, Protein-Tyrosine Kinasessearch, Proto-Oncogene Proteinssearch, Proto-Oncogene Proteins c-fessearch, src Homology Domainssearch
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