Characteristic Domain Motion in the Ribosome Recycling Factor Revealed by 15N NMR Relaxation Experiments and Molecular Dynamics Simulations

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Abstract
The backbone dynamics of ribosome recycling factor (RRF) from Escherichia coli in water were characterized by 15N NMR relaxation analysis and molecular dynamics (MD) simulation. RRF is composed of two domains connected by a joint region that consists of two peptide chains, such that the overall structure seems to mimic that of tRNA. MD trajectories indicated that the relative orientation of domains varies on the nanosecond time scale. We analyzed the observed 15N T1, T2, and NOE using an extended model-free spectral density function in which the domain motions with a nanosecond time scale were considered. At 30 °C, the order parameters of slow motion ( ) were determined to be approximately 0.9 for domain I and 0.7 for domain II, respectively. These values indicate that domain I is nearly fixed on the molecular diffusion frame, and domain II is wobbling in a cone for which the semi-angle is about 30°.