Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra

Thomas Evangelidis, Santrupti Nerli, Jiří Nováček, Andrew E. Brereton, P. Andrew Karplus, Rochelle R. Dotas, Vincenzo Venditti, Nikolaos G. Sgourakis () and Konstantinos Tripsianes ()
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Thomas Evangelidis: Masaryk University
Santrupti Nerli: University of California Santa Cruz
Jiří Nováček: Masaryk University
Andrew E. Brereton: Oregon State University
P. Andrew Karplus: Oregon State University
Rochelle R. Dotas: Iowa State University
Vincenzo Venditti: Iowa State University
Nikolaos G. Sgourakis: University of California Santa Cruz
Konstantinos Tripsianes: Masaryk University

Nature Communications, 2018, vol. 9, issue 1, 1-13

Abstract: Abstract Automated methods for NMR structure determination of proteins are continuously becoming more robust. However, current methods addressing larger, more complex targets rely on analyzing 6–10 complementary spectra, suggesting the need for alternative approaches. Here, we describe 4D-CHAINS/autoNOE-Rosetta, a complete pipeline for NOE-driven structure determination of medium- to larger-sized proteins. The 4D-CHAINS algorithm analyzes two 4D spectra recorded using a single, fully protonated protein sample in an iterative ansatz where common NOEs between different spin systems supplement conventional through-bond connectivities to establish assignments of sidechain and backbone resonances at high levels of completeness and with a minimum error rate. The 4D-CHAINS assignments are then used to guide automated assignment of long-range NOEs and structure refinement in autoNOE-Rosetta. Our results on four targets ranging in size from 15.5 to 27.3 kDa illustrate that the structures of proteins can be determined accurately and in an unsupervised manner in a matter of days.

Date: 2018
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DOI: 10.1038/s41467-017-02592-z

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