An automated iterative approach for protein structure refinement using pseudocontact shifts

  • NMR structure calculation using NOE-derived distance restraints requires a considerable number of assignments of both backbone and sidechains resonances, often difficult or impossible to get for large or complex proteins. Pseudocontact shifts (PCSs) also play a well-established role in NMR protein structure calculation, usually to augment existing structural, mostly NOE-derived, information. Existing refinement protocols using PCSs usually either require a sizeable number of sidechain assignments or are complemented by other experimental restraints. Here, we present an automated iterative procedure to perform backbone protein structure refinements requiring only a limited amount of backbone amide PCSs. Already known structural features from a starting homology model, in this case modules of repeat proteins, are framed into a scaffold that is subsequently refined by experimental PCSs. The method produces reliable indicators that can be monitored to judge about the performance. We applied it to a system in which sidechain assignments are hardly possible, designed Armadillo repeat proteins (dArmRPs), and we calculated the solution NMR structure of YM4A, a dArmRP containing four sequence-identical internal modules, obtaining high convergence to a single structure. We suggest that this approach is particularly useful when approximate folds are known from other techniques, such as X-ray crystallography, while avoiding inherent artefacts due to, for instance, crystal packing.
Author:Stefano CucuzzaORCiDGND, Peter GüntertORCiDGND, Andreas PlückthunORCiDGND, Oliver ZerbeORCiDGND
Parent Title (English):Journal of biomolecular NMR
Publisher:Springer Science + Business Media B.V
Place of publication:Dordrecht [u.a.]
Document Type:Article
Date of Publication (online):2021/08/02
Date of first Publication:2021/08/02
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2023/02/08
Tag:Armadillo repeat protein; NMR; Pseudocontact shift; Structure refinement
Page Number:16
First Page:319
Last Page:334
A tutorial containing a protocol capture with the relevant Python scripts and Cyana macros is available on Github ( Further Python scripts and CYANA macros are available upon request.
Open Access funding provided by University of Zurich. This work was rooted in a project financed via a SINERGIA grant from the Swiss National Science Foundation (Funder id: 10.13039/501100001711, [Titel anhand dieser DOI in Citavi-Projekt übernehmen] Grant No. 122686).
Institutes:Biochemie, Chemie und Pharmazie
Wissenschaftliche Zentren und koordinierte Programme / Zentrum für Biomolekulare Magnetische Resonanz (BMRZ)
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Licence (German):License LogoCreative Commons - Namensnennung 4.0