spacer Inferential Structure Determination of the Fyn SH3 domain using NOESY data from a 15N,H2 enriched protein
Primary citation
Title Inferential Structure Determination
Authors Rieping,; Habeck,; Nilges,
Journal SCIENCEsearch vol:309, pag:303-306 (2005), Identifiers: PubMed ID (16002620)search DOI (10.1126/science.1110428)
Abstract Macromolecular structures calculated from nuclear magnetic resonance data are not fully determined by experimental data but depend on subjective choices in data treatment and parameter settings. This makes it difficult to objectively judge the precision of the structures. We used Bayesian inference to derive a probability distribution that represents the unknown structure and its precision. This probability distribution also determines additional unknowns, such as theory parameters, that previously had to be chosen empirically. We implemented this approach by using Markov chain Monte Carlo techniques. Our method provides an objective figure of merit and improves structural quality.
MeSH terms Algorithmssearch, Bayes Theoremsearch, Crystallographysearch, X-Raysearch, Macromolecular Substancessearch, Markov Chainssearch, Modelssearch, Molecularsearch, Molecular Conformationsearch, Monte Carlo Methodsearch, Nuclear Magnetic Resonancesearch, Biomolecularsearch, Probabilitysearch, Protein Conformationsearch, Proto-Oncogene Proteinssearch, Proto-Oncogene Proteins c-fynsearch, Thermodynamicssearch, src Homology Domainssearch, src-Family Kinasessearch
Secondary citations
Title Some NMR Experiments and a Structure Determination Employing a [15N,2H] Enriched Protein
Authors Mal,; Matthews,; Kovacs,; Campbell,; Boyd,
Journal J.BIOMOL.NMRsearch vol:12, pag:259-276 (1998), Identifiers: PubMed ID (9751998)search DOI (10.1023/A:1008238009056)
Abstract We present the results of studies of an aqueous sample of a highly [15N,2H] enriched protein, the SH3 domain from Fyn. Measurements of 1H relaxation and interactions between H2O solvent and exchangeable protons are given, as well as a method for increasing the effective longitudinal relaxation of solvent exchangeable proton resonances. The long-range isotope shifts are measured, for 1H and 15N, which arise due to perdeuteration. Simulations, which employed a 7 or 8 spin relaxation matrix analysis, were compared to the experimental data from a time series of 2D NOESY datasets for some resonances. The agreement between experiment and simulation suggest that, with this 1H dilute sample, relatively long mixing times (up to 1.2 s) can be used to detect specific dipolar interactions between amide protons up to about 7A apart. A set of 155 inter-amide NOEs and 7 side chain NOEs were thus identified in a series of 3D HSQC-NOESY-HSQC experiments. These data, alone and in combination with previously collected restraints, were used to calculate sets of structures using X-PLOR. These results are compared to the available X-ray and NMR structures of the Fyn SH3 domain.
MeSH terms Amidessearch, Amino Acid Sequencesearch, Deuteriumsearch, Escherichia colisearch, Magnetic Resonance Spectroscopysearch, Molecular Sequence Datasearch, Nitrogen Isotopessearch, Protein Conformationsearch, Protein Structuresearch, Secondarysearch, Protein-Tyrosine Kinasessearch, Proto-Oncogene Proteinssearch, Proto-Oncogene Proteins c-fynsearch, Protonssearch, Recombinant Proteinssearch, Solventssearch, Watersearch, src Homology Domainssearch