Structure and Dynamics of Ribosomal Protein L12: An Ensemble Model Based on SAXS and NMR Relaxation.
Ribosomal protein L12 is a two-domain protein that forms dimers mediated by its N-terminal domains. A 20-residue linker separates the N- and C-terminal domains. This linker results in a three-lobe topology with significant flexibility, known to be critical for efficient translation. Here we present an ensemble model of spatial distributions and correlation times for the domain reorientations of L12 that reconciles experimental data from small-angle x-ray scattering and nuclear magnetic resonance. We generated an ensemble of L12 conformations in which the structure of each domain is fixed but the domain orientations are variable. The ensemble reproduces the small-angle x-ray scattering data and the optimized correlation times of its reorientational eigenmodes fit the (15)N relaxation data. The ensemble model reveals intrinsic conformational properties of L12 that help explain its function on the ribosome. The two C-terminal domains sample a large volume and extend further away from the ribosome anchor than expected for a random-chain linker, indicating that the flexible linker has residual order. Furthermore, the distances between each C-terminal domain and the anchor are anticorrelated, indicating that one of them is more retracted on average. We speculate that these properties promote the function of L12 to recruit translation factors and control their activity on the ribosome.
Bernadó
Pau
P
Institute for Research in Biomedicine, Barcelona, Spain. pau.bernado@irbbarcelona.org
Modig
Kristofer
K
Grela
Przemysław
P
Svergun
Dmitri I
DI
Tchorzewski
Marek
M
Pons
Miquel
M
Akke
Mikael
M
D029968:Escherichia coli Proteins / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy / Q000009:adverse effects*; D019906:Nuclear Magnetic Resonance, Biomolecular; D039881:Prokaryotic Initiation Factor-2; D011487:Protein Conformation / Q000528:radiation effects; D017510:Protein Folding / Q000528:radiation effects; D017434:Protein Structure, Tertiary; D012269:Ribosomal Proteins / Q000737:chemistry / Q000378:metabolism / Q000528:radiation effects*; D012270:Ribosomes / Q000378:metabolism / Q000528:radiation effects*; D053838:Scattering, Small Angle; D014965:X-Rays
D029968:Escherichia coli Proteins; D039881:Prokaryotic Initiation Factor-2; D012269:Ribosomal Proteins; C016700:ribosomal protein L7-L12