TY  - JOUR
A1  - Cucuzza, Stefano
A1  - Güntert, Peter
A1  - Plückthun, Andreas
A1  - Zerbe, Oliver
T1  - An automated iterative approach for protein structure refinement using pseudocontact shifts
T2  - Journal of biomolecular NMR
N2  - 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.
KW  - Pseudocontact shift
KW  - NMR
KW  - Armadillo repeat protein
KW  - Structure refinement
Y1  - 2021
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/69441
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-694414
SN  - 1573-5001
N1  - A tutorial containing a protocol capture with the relevant Python scripts and Cyana macros is available on Github (https://github.com/Evets90/Iterative_PCS_refinement). Further Python scripts and CYANA macros are available upon request.
N1  - 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).
VL  - 75
IS  - 8-9
SP  - 319
EP  - 334
PB  - Springer Science + Business Media B.V
CY  - Dordrecht [u.a.]
ER  -