Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings

By Nikolaos G. Sgourakis, Oliver F. Lange, Frank DiMaio, Ingemar André, Nicholas C. Fitzkee, P. Rossi, Gaetano T. Montelione, A. Bax, David Baker. 2011

66 citations recorded by the source corpus.

Symmetric protein dimers, trimers, and higher-order cyclic oligomers play key roles in many biological processes. However, structural studies of oligomeric systems by solution NMR can be difficult due to slow tumbling of the system and the difficulty in identifying NOE interactions across protein interfaces. Here, we present an automated method (RosettaOligomers) for determining the solution structures of oligomeric systems using only chemical shifts, sparse NOEs, and domain orientation restraints from residual dipolar couplings (RDCs) without a need for a previously determined structure of the monomeric subunit. The method integrates previously developed Rosetta protocols for solving the structures of monomeric proteins using sparse NMR data and for predicting the structures of both nonintertwined and intertwined symmetric oligomers. We illustrated the performance of the method using a benchmark set of nine protein dimers, one trimer, and one tetramer with available experimental data and various interface topologies. The final converged structures are found to be in good agreement with both experimental data and previously published high-resolution structures. The new approach is more readily applicable to large oligomeric systems than conventional structure-determination protocols, which often require a large number of NOEs, and will likely become increasingly relevant as more high-molecular weight systems are studied by NMR.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. David Baker
2. Santrupti Nerli
3. Nikolaos G. Sgourakis
4. Frank DiMaio
5. Jens Meiler
6. Julia Koehler Leman
7. Andrew C. McShan
8. Philip Bradley

In Molecular Biology

1. David Baker
2. Nikolaos G. Sgourakis
3. Santrupti Nerli
4. Jens Meiler
5. Frank DiMaio
6. Julia Koehler Leman
7. Andrew C. McShan
8. Jeffrey J. Gray

In Spectroscopy

1. Santrupti Nerli
2. Nikolaos G. Sgourakis
3. David Baker
4. Frank DiMaio
5. Julia Koehler Leman
6. Richard Bonneau
7. Jens Meiler
8. Georg Kuenze

Citations in the corpus

• Chemical shift-based methods in NMR structure determination (2018, background): “NMR has enabled structural studies of such systems in vitro [136]; however full structure elucidation is challenging due to their large size and the presence of dynamics as well as the effects that become more pronounced at the interface between different subunits, which ultimately lead to exchange-”
• Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints (2019, methodology): “Three targets were taken from an earlier CS-RDC-Rosetta study on symmetric proteins (Sgourakis et al., 2011).”
• Modeling Symmetric Macromolecular Structures in Rosetta3 (2011, background): “In addition, we have recently shown that the structure of large homomeric protein complexes can be determined by combining limited NMR data and symmetric modeling (ab initio structure prediction followed by symmetric docking, or fold-anddock) [12], which establishes that symmetrical modeling in Rose”
• The structure of mouse cytomegalovirus m04 protein determined from sparse NMR data reveals a new fold of the m02-m06 family of viral immune modulators (2014, unknown): “…and the use of transverse relaxation optimized spectroscopy (TROSY) at high magnetic fields to improve 15N and amide 1H relaxation (Pervushin et al., 1997), the structure of larger proteins and protein complexes can now be determined by solution NMR (Raman et al., 2010; Sgourakis et al., 2011).”
• Accurate protein structure modeling using sparse NMR data and homologous structure information (2012, background): “Accurate structures can be generated for small proteins (up to 100–120 residues) using chemical shift information to guide structure prediction calculations (15, 16), but additional NMR data, including backbone NOEs and residual dipolar coupling (RDC) data, are required to obtained converged structu”
• The Protein Structure Initiative: achievements and visions for the future (2012, background): “PSI Centers are also involved in collaborative projects aimed at accelerating the field of protein NMR structure analysis [22-28] and computational protein design [29-31].”
• CS-ROSETTA (2018, methodology): “One such approach is RosettaOligomers (Sgourakis et al., 2011).”