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The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering.

ABSTRACT: Conformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the 'lubricant' for the conformational fluctuations required for biological activity. The method was applied to compare water dynamics and conformational fluctuations in the 30?S and 50?S ribosomal subunits from Haloarcula marismortui, under high salt, stable conditions. Similar free and hydration water diffusion parameters are found for both subunits. With respect to the 50?S subunit, the 30?S is characterized by a softer force constant and larger mean square displacements (MSD), which would facilitate conformational adjustments required for messenger and transfer RNA binding. It has been shown previously that systems from mesophiles and extremophiles are adapted to have similar MSD under their respective physiological conditions. This suggests that the results presented are not specific to halophiles in high salt but a general property of ribosome dynamics under corresponding, active conditions. The current study opens new perspectives for neutron scattering characterization of component functional molecular dynamics within the ribosome.

SUBMITTER: Zaccai G

PROVIDER: S-EPMC5111069 | biostudies-other | 2016 Nov

REPOSITORIES: biostudies-other

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The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering.

Zaccai Giuseppe G Natali Francesca F Peters Judith J Řihová Martina M Zimmerman Ella E Ollivier J J Combet J J Maurel Marie-Christine MC Bashan Anat A Yonath Ada A

Scientific reports 20161116

Conformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the 'lubricant' for the conformational fluctuations required for biological activity. The method was applied to compare water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula m ...[more]

PMID: 27849042

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Project description:Zeolite ZSM-5 is a key catalyst in commercially relevant processes including the widely studied methanol to hydrocarbon reaction, and molecular diffusion in zeolite pores is known to be a crucial factor in controlling catalytic reactions. Here, we present critical analyses of recent quasi-elastic neutron scattering (QENS) data and complementary molecular dynamics (MD) simulations. The QENS experiments show that the nature of methanol diffusion dynamics in ZSM-5 pores is dependent both on the Si/Al ratio (11, 25, 36, 40 and 140), which determines the Brønsted acid site density of the zeolite, and that the nature of the type of motion observed may vary qualitatively over a relatively small temperature range. At 373 K, on increasing the ratio from 11 to 140, the observed mobile methanol fraction increases and the nature of methanol dynamics changes from rotational (in ZSM-5 with Si/Al of 11) to translational diffusion. The latter is either confined localized diffusion within a pore in zeolites with ratios up to 40 or non-localized, longer-range diffusion in zeolite samples with the ratio of 140. The complementary MD simulations conducted over long time scales (1 ns), which are longer than those measured in the present study by QENS (≈1-440 ps), at 373 K predict the occurrence of long-range translational diffusion of methanol in ZSM-5, independent of the Si/Al ratios (15, 47, 95, 191 and siliceous MFI). The rate of diffusion increases slightly by increasing the ratio from 15 to 95 and thereafter does not depend on zeolite composition. Discrepancies in the observed mobile methanol fraction between the MD simulations (100% methanol mobility in ZSM-5 pores across all Si/Al ratios) and QENS experiments (for example, ≈80% immobile methanol in ZSM-5 with Si/Al of 11) are attributed to the differences in time resolutions of the techniques. This perspective provides comprehensive information on the effect of acid site density on methanol dynamics in ZSM-5 pores and highlights the complementarity of QENS and MD, and their advantages and limitations. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 2)'.

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The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering.

Publications

The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering.

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