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

T. Evangelidis, S. Nerli, J. Nováček, AE. Brereton, PA. Karplus, RR. Dotas, V. Venditti, NG. Sgourakis, K. Tripsianes,

. 2018 ; 9 (1) : 384. [pub] 20180126

Language English Country Great Britain

Document type Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't

Persistent link   https://www.medvik.cz/link/bmc18010193

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.

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$a Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra / $c T. Evangelidis, S. Nerli, J. Nováček, AE. Brereton, PA. Karplus, RR. Dotas, V. Venditti, NG. Sgourakis, K. Tripsianes,
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$a Nerli, Santrupti $u Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA. Department of Computer Science, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
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$a Nováček, Jiří $u CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.
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$a Brereton, Andrew E $u Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Bldg, Oregon State University, Corvallis, OR, 97331, USA.
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$a Karplus, P Andrew $u Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Bldg, Oregon State University, Corvallis, OR, 97331, USA.
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$a Dotas, Rochelle R $u Department of Chemistry, Iowa State University, 2438 Pammel Drive, Ames, IA, 50011, USA.
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$a Venditti, Vincenzo $u Department of Chemistry, Iowa State University, 2438 Pammel Drive, Ames, IA, 50011, USA. Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
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$a Sgourakis, Nikolaos G $u Department of Computer Science, University of California Santa Cruz, Santa Cruz, CA, 95064, USA. nsgourak@ucsc.edu.
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$a Tripsianes, Konstantinos $u CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic. kostas.tripsianes@ceitec.muni.cz.
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