Direct use of unassigned resonances in NMR structure calculations with proxy residues

dc.contributor.authorEiso, A B
dc.contributor.authorPugh, David J R
dc.contributor.authorKaptein, Robert
dc.contributor.authorBoelens, Rolf
dc.contributor.authorBonvin, Alexandre M J J
dc.date.accessioned2016-09-01T06:57:36Z
dc.date.available2016-09-01T06:57:36Z
dc.date.issued2006
dc.date.updated2016-08-30T12:05:06Z
dc.description.abstractWe present a method that significantly enhances the robustness of (automated) NMR structure determination by allowing the NOE data corresponding to unassigned NMR resonances to be used directly in the calculations. The unassigned resonances are represented by additional atoms or groups of atoms that have no interaction with the regular protein atoms except through distance restraints. These so-called “proxy” residues can be used to generate NOE-based distance restraints in a similar fashion as for the assigned part of the protein. If sufficient NOE information is available, the restraints are expected to place the proxies at positions close to the correct atoms for the unassigned resonance, which can facilitate subsequent assignment. Convergence can be further improved by supplying additional information about the possible identities of the unassigned resonances. We have implemented this approach in the widely used automated assignment and structure calculation protocols ARIA and CANDID. We find that it significantly increases the robustness of structure calculations with regard to missing assignments and yields structures of higher quality. Our approach is still able to find correctly folded structures with up to 30% randomly missing resonance assignments, and even when only backbone and β resonances are present! This should be of significant value to NMR-based structural proteomics initiatives.en_ZA
dc.identifierhttp://dx.doi.org/10.1021/ja058504q
dc.identifier.apacitationEiso, A. B., Pugh, D. J. R., Kaptein, R., Boelens, R., & Bonvin, A. M. J. J. (2006). Direct use of unassigned resonances in NMR structure calculations with proxy residues. <i>Journal of the American Chemical Society</i>, http://hdl.handle.net/11427/21609en_ZA
dc.identifier.chicagocitationEiso, A B, David J R Pugh, Robert Kaptein, Rolf Boelens, and Alexandre M J J Bonvin "Direct use of unassigned resonances in NMR structure calculations with proxy residues." <i>Journal of the American Chemical Society</i> (2006) http://hdl.handle.net/11427/21609en_ZA
dc.identifier.citationAb, E., Pugh, D. J., Kaptein, R., Boelens, R., & Bonvin, A. M. (2006). Direct use of unassigned resonances in NMR structure calculations with proxy residues. Journal of the American Chemical Society, 128(23), 7566-7571.en_ZA
dc.identifier.issn0002-7863en_ZA
dc.identifier.ris TY - Journal Article AU - Eiso, A B AU - Pugh, David J R AU - Kaptein, Robert AU - Boelens, Rolf AU - Bonvin, Alexandre M J J AB - We present a method that significantly enhances the robustness of (automated) NMR structure determination by allowing the NOE data corresponding to unassigned NMR resonances to be used directly in the calculations. The unassigned resonances are represented by additional atoms or groups of atoms that have no interaction with the regular protein atoms except through distance restraints. These so-called “proxy” residues can be used to generate NOE-based distance restraints in a similar fashion as for the assigned part of the protein. If sufficient NOE information is available, the restraints are expected to place the proxies at positions close to the correct atoms for the unassigned resonance, which can facilitate subsequent assignment. Convergence can be further improved by supplying additional information about the possible identities of the unassigned resonances. We have implemented this approach in the widely used automated assignment and structure calculation protocols ARIA and CANDID. We find that it significantly increases the robustness of structure calculations with regard to missing assignments and yields structures of higher quality. Our approach is still able to find correctly folded structures with up to 30% randomly missing resonance assignments, and even when only backbone and β resonances are present! This should be of significant value to NMR-based structural proteomics initiatives. DA - 2006 DB - OpenUCT DP - University of Cape Town J1 - Journal of the American Chemical Society LK - https://open.uct.ac.za PB - University of Cape Town PY - 2006 SM - 0002-7863 T1 - Direct use of unassigned resonances in NMR structure calculations with proxy residues TI - Direct use of unassigned resonances in NMR structure calculations with proxy residues UR - http://hdl.handle.net/11427/21609 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/21609
dc.identifier.vancouvercitationEiso AB, Pugh DJR, Kaptein R, Boelens R, Bonvin AMJJ. Direct use of unassigned resonances in NMR structure calculations with proxy residues. Journal of the American Chemical Society. 2006; http://hdl.handle.net/11427/21609.en_ZA
dc.languageengen_ZA
dc.publisherAmerican Chemical Societyen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.rightsCreative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)*
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/en_ZA
dc.sourceJournal of the American Chemical Societyen_ZA
dc.source.urihttp://pubs.acs.org/journal/jacsat/about.html
dc.titleDirect use of unassigned resonances in NMR structure calculations with proxy residuesen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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