A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta
By P. Rossi, Lei Shi, Gaohua Liu, C. M. Barbieri, Hsiau-Wei Lee, T. Grant, J. Luft, R. Xiao, T. Acton, E. Snell and 4 more. 2014
34 citations recorded by the source corpus.
Oligomeric proteins are important targets for structure determination in solution. While in most cases the fold of individual subunits can be determined experimentally, or predicted by homology‐based methods, protein–protein interfaces are challenging to determine de novo using conventional NMR structure determination protocols. Here we focus on a member of the bet‐V1 superfamily, Aha1 from Colwellia psychrerythraea. This family displays a broad range of crystallographic interfaces none of which can be reconciled with the NMR and SAXS data collected for Aha1. Unlike conventional methods relying on a dense network of experimental restraints, the sparse data are used to limit conformational search during optimization of a physically realistic energy function. This work highlights a new approach for studying minor conformational changes due to structural plasticity within a single dimeric interface in solution. Proteins 2015; 83:309–317. © 2014 Wiley Periodicals, Inc.
Subfields: Materials Chemistry, Molecular Biology
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In Materials Chemistry
- Santrupti Nerli
- Nikolaos G. Sgourakis
- Julia Koehler Leman
- Andrew C. McShan
- Richard Bonneau
- Georg Kuenze
- Jens Meiler
- David Baker
In Molecular Biology
- Santrupti Nerli
- Nikolaos G. Sgourakis
- Andrew C. McShan
- Julia Koehler Leman
- Richard Bonneau
- Georg Kuenze
- Jens Meiler
- Jeffrey J. Gray
Citations in the corpus
- Chemical shift-based methods in NMR structure determination (2018, methodology): “A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript RNA ribonucleic acid RosettaCM rosetta comparative modeling RTT regulator of Ty1 transposition SANS small-angle neutron scattering SAXS small-angle X-ray scattering SCOP structural classification of proteins SH src homol”
- Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints (2019, background): “…with C2 symmetry (PDB 2JWK (Parsons et al., 2008), PDB 2L01, PDB 2LTD, PDB 2KOD (Byeon et al., 2009), PDB 1RJJ (Cornilescu et al., 2004), PDB 2M89 (Rossi et al., 2015)), one target with C3 symmetry (PDB 2KO8 (Sachleben et al., 2010)), and one target with D2 symmetry (PDB 2KBY (Coutandin et al.,…”