Ribosomal dynamics inferred from variations in experimental measurements.
The crystal structures of the ribosome reveal remarkable complexity and provide a starting set of snapshots with which to understand the dynamics of translation. To augment the static crystallographic models with dynamic information present in crosslink, footprint, and cleavage data, we examined 2691 proximity measurements and focused on the subset that was apparently incompatible with >40 published crystal structures. The measurements from this subset generally involve regions of the structure that are functionally conserved and structurally flexible. Local movements in the crystallographic states of the ribosome that would satisfy biochemical proximity measurements show coherent patterns suggesting alternative conformations of the ribosome. Three different types of data obtained for the two subunits display similar "mismatching" patterns, suggesting that the signals are robust and real. In particular, there is an indication of coherent motion in the decoding region within the 30S subunit and central protuberance and surrounding areas of the 50S subunit. Directions of rearrangements fluctuate around the proposed path of tRNA translocation and the plane parallel to the interface of the two subunits. Our results demonstrate that systematic combination and analysis of noisy, apparently incompatible data sources can provide biologically useful signals about structural dynamics.
Gabashvili
Irene S
IS
Department of Genetics and Section on Medical Informatics, Stanford University, Stanford, California 94305-5479, USA.
Whirl-Carrillo
Michelle
M
Bada
Michael
M
Banatao
D Rey
DR
Altman
Russ B
RB
D018360:Crystallography, X-Ray; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012335:RNA, Ribosomal / Q000737:chemistry*; D012270:Ribosomes / Q000737:chemistry*
D012335:RNA, Ribosomal