A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta.
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.
Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey, 08854.
Paolo
P
Rossi
Lei
L
Shi
Gaohua
G
Liu
Christopher M
CM
Barbieri
Hsiau-Wei
HW
Lee
Thomas D
TD
Grant
Joseph R
JR
Luft
Rong
R
Xiao
Thomas B
TB
Acton
Edward H
EH
Snell
Gaetano T
GT
Montelione
David
D
Baker
Oliver F
OF
Lange
Nikolaos G
NG
Sgourakis
D034241:Alteromonadaceae / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry*; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D053838:Scattering, Small Angle; D012996:Solutions; D014961:X-Ray Diffraction
D001426:Bacterial Proteins; D012996:Solutions
CS-Rosetta modeling; nuclear magnetic resonance spectroscopy; protein complex; residual dipolar coupling; small-angle X-ray scattering