Dataset Information

Quasi-elastic Neutron Scattering Reveals Ligand-Induced Protein Dynamics of a G-Protein-Coupled Receptor.

ABSTRACT: Light activation of the visual G-protein-coupled receptor (GPCR) rhodopsin leads to significant structural fluctuations of the protein embedded within the membrane yielding the activation of cognate G-protein (transducin), which initiates biological signaling. Here, we report a quasi-elastic neutron scattering study of the activation of rhodopsin as a GPCR prototype. Our results reveal a broadly distributed relaxation of hydrogen atom dynamics of rhodopsin on a picosecond-nanosecond time scale, crucial for protein function, as only observed for globular proteins previously. Interestingly, the results suggest significant differences in the intrinsic protein dynamics of the dark-state rhodopsin versus the ligand-free apoprotein, opsin. These differences can be attributed to the influence of the covalently bound retinal ligand. Furthermore, an idea of the generic free-energy landscape is used to explain the GPCR dynamics of ligand-binding and ligand-free protein conformations, which can be further applied to other GPCR systems.

SUBMITTER: Shrestha UR

PROVIDER: S-EPMC5378701 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

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Quasi-elastic Neutron Scattering Reveals Ligand-Induced Protein Dynamics of a G-Protein-Coupled Receptor.

Shrestha Utsab R UR Perera Suchithranga M D C SMDC Bhowmik Debsindhu D Chawla Udeep U Mamontov Eugene E Brown Michael F MF Chu Xiang-Qiang XQ

The journal of physical chemistry letters 20161004 20

Light activation of the visual G-protein-coupled receptor (GPCR) rhodopsin leads to significant structural fluctuations of the protein embedded within the membrane yielding the activation of cognate G-protein (transducin), which initiates biological signaling. Here, we report a quasi-elastic neutron scattering study of the activation of rhodopsin as a GPCR prototype. Our results reveal a broadly distributed relaxation of hydrogen atom dynamics of rhodopsin on a picosecond-nanosecond time scale, ...[more]

PMID: 27628201

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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)'.

Dataset Information

Quasi-elastic Neutron Scattering Reveals Ligand-Induced Protein Dynamics of a G-Protein-Coupled Receptor.

Publications

Quasi-elastic Neutron Scattering Reveals Ligand-Induced Protein Dynamics of a G-Protein-Coupled Receptor.

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