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

J 2018

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

EVANGELIDIS, Thomas, S. NERLI, Jiří NOVÁČEK, A.E. BRERETON, P.A. KARPLUS et. al.

Basic information

Original name

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

Authors

EVANGELIDIS, Thomas (300 Greece, belonging to the institution), S. NERLI (840 United States of America), Jiří NOVÁČEK (203 Czech Republic, belonging to the institution), A.E. BRERETON (840 United States of America), P.A. KARPLUS (840 United States of America), R.R. DOTAS (840 United States of America), V. VENDITTI (840 United States of America), N.G. SGOURAKIS (840 United States of America) and Konstantinos TRIPSIANES (300 Greece, guarantor, belonging to the institution)

Edition

Nature Communications, London, Nature Publishing Group, 2018, 2041-1723

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10402 Inorganic and nuclear chemistry

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 11.878

RIV identification code

RIV/00216224:14740/18:00101162

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1038/s41467-017-02592-z

UT WoS

000423430900004

Keywords in English

PROTEIN-STRUCTURE DETERMINATION; CHEMICAL-SHIFTS; DIPOLAR COUPLINGS; NOESY ASSIGNMENT; LARGER PROTEINS; SPECTROSCOPY; ROSETTA; ROBUST; ALGORITHM; HOMOLOGY

Abstract

V originále

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.

Links

GJ15-22380Y, research and development project

Name: Molekulární stavba protein-DNA komplexů zapojených v opravě nukleotidových sestřihů

Investor: Czech Science Foundation

LM2015043, research and development project

Name: Česká infrastruktura pro integrativní strukturní biologii (Acronym: CIISB)

Investor: Ministry of Education, Youth and Sports of the CR

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

MUNI/E/0086/2017, interní kód MU

Name: From protein sequence to NMR structure in a matter of days using CHAINS/Rosetta

Investor: Masaryk University, Promoting quality excellence

618223, interní kód MU

Name: Structural studies of Nucleotide Excision Repair for drug development targeting protein-DNA interactions (Acronym: NER)

Investor: European Union, People

Citovat

EVANGELIDIS, Thomas, S. NERLI, Jiří NOVÁČEK, A.E. BRERETON, P.A. KARPLUS, R.R. DOTAS, V. VENDITTI, N.G. SGOURAKIS and Konstantinos TRIPSIANES. Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra. Nature Communications. London: Nature Publishing Group, 2018, vol. 9, JAN, p. 384-396. ISSN 2041-1723. Available from: https://dx.doi.org/10.1038/s41467-017-02592-z.

@article{1435119,
   author = {Evangelidis, Thomas and Nerli, S. and Nováček, Jiří and Brereton, A.E. and Karplus, P.A. and Dotas, R.R. and Venditti, V. and Sgourakis, N.G. and Tripsianes, Konstantinos},
   article_location = {London},
   article_number = {JAN},
   doi = {http://dx.doi.org/10.1038/s41467-017-02592-z},
   keywords = {PROTEIN-STRUCTURE DETERMINATION; CHEMICAL-SHIFTS; DIPOLAR COUPLINGS; NOESY ASSIGNMENT; LARGER PROTEINS; SPECTROSCOPY; ROSETTA; ROBUST; ALGORITHM; HOMOLOGY},
   language = {eng},
   issn = {2041-1723},
   journal = {Nature Communications},
   title = {Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra},
   url = {https://www.nature.com/articles/s41467-017-02592-z.pdf},
   volume = {9},
   year = {2018}
}

TY  - JOUR
ID  - 1435119
AU  - Evangelidis, Thomas - Nerli, S. - Nováček, Jiří - Brereton, A.E. - Karplus, P.A. - Dotas, R.R. - Venditti, V. - Sgourakis, N.G. - Tripsianes, Konstantinos
PY  - 2018
TI  - Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra
JF  - Nature Communications
VL  - 9
IS  - JAN
SP  - 384
EP  - 384
PB  - Nature Publishing Group
SN  - 20411723
KW  - PROTEIN-STRUCTURE DETERMINATION
KW  - CHEMICAL-SHIFTS
KW  - DIPOLAR COUPLINGS
KW  - NOESY ASSIGNMENT
KW  - LARGER PROTEINS
KW  - SPECTROSCOPY
KW  - ROSETTA
KW  - ROBUST
KW  - ALGORITHM
KW  - HOMOLOGY
UR  - https://www.nature.com/articles/s41467-017-02592-z.pdf
N2  - 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.
ER  -

EVANGELIDIS, Thomas, S. NERLI, Jiří NOVÁČEK, A.E. BRERETON, P.A. KARPLUS, R.R. DOTAS, V. VENDITTI, N.G. SGOURAKIS and Konstantinos TRIPSIANES. Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra. \textit{Nature Communications}. London: Nature Publishing Group, 2018, vol.~9, JAN, p.~384-396. ISSN~2041-1723. Available from: https://dx.doi.org/10.1038/s41467-017-02592-z.

Detailed Information on Publication Record