Time-Resolved WAXS Reveals Accelerated Conformational Changes in Iodoretinal-Substituted Proteorhodopsin

Malmerberg, Erik; Omran, Ziad; Hub, Jochen S.; Li, Xuewen; Katona, Gergely; Westenhoff, Sebastian; Johansson, Linda C.; Andersson, Magnus; Cammarata, Marco; Wulff, Michaël; Spoel, David van der; Davidsson, Jan; Specht, Alexandre; Neutze, Richard

doi:10.1016/j.bpj.2011.07.050

Cited by 60 publications

(75 citation statements)

References 49 publications

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“…For modelling the ligand we used the Amber GAFF small molecule force field 47 . The parameters of covalently bound 11-cis-retinal were obtained from a previous report 48 . The ligand geometry was submitted to the GAUSSIAN 09 programme 49 for optimization at Hartree-Fock 6-31G* level, when generating force filed parameters.…”

Section: Methodsmentioning

confidence: 99%

Activation of G-protein-coupled receptors correlates with the formation of a continuous internal water pathway

et al. 2014

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Recent crystal structures of G-protein-coupled receptors (GPCRs) have revealed ordered internal water molecules, raising questions about the functional role of those waters for receptor activation that could not be answered by the static structures. Here, we used molecular dynamics simulations to monitor-at atomic and high temporal resolutionconformational changes of central importance for the activation of three prototypical GPCRs with known crystal structures: the adenosine A 2A receptor, the b 2 -adrenergic receptor and rhodopsin. Our simulations reveal that a hydrophobic layer of amino acid residues next to the characteristic NPxxY motif forms a gate that opens to form a continuous water channel only upon receptor activation. The highly conserved tyrosine residue Y 7.53 undergoes transitions between three distinct conformations representative of inactive, G-protein activated and GPCR metastates. Additional analysis of the available GPCR crystal structures reveals general principles governing the functional roles of internal waters in GPCRs.

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Section: Methodsmentioning

confidence: 99%

Activation of G-protein-coupled receptors correlates with the formation of a continuous internal water pathway

et al. 2014

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“…Several complementary approaches exist to refine structural changes against difference WAXS data (24,25,27,(29)(30)(31)(32)(33). Unlike x-ray crystallography, however, broadly accepted standards for structural refinement have not yet emerged.…”

Section: Structural Fitting To the Tr-waxs Difference Signalmentioning

confidence: 97%

Conformational activation of visual rhodopsin in native disc membranes

et al. 2015

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Rhodopsin is the G protein-coupled receptor (GPCR) that serves as a dim-light receptor for vision in vertebrates. We probed light-induced conformational changes in rhodopsin in its native membrane environment at room temperature using time-resolved wide-angle x-ray scattering. We observed a rapid conformational transition that is consistent with an outward tilt of the cytoplasmic portion of transmembrane helix 6 concomitant with an inward movement of the cytoplasmic portion of transmembrane helix 5. These movements were considerably larger than those reported from the basis of crystal structures of activated rhodopsin, implying that light activation of rhodopsin involves a more extended conformational change than was previously suggested.

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“…[2][3][4][5][6][7][8] More recently, TR-WAXS was applied to track the conformational transitions of photo-active globular proteins [9][10][11][12][13][14][15][16] and proton pumps. [17][18][19][20] The structural interpretation of such TR-WAXS signals is challenging since, due to the orientational average inherent to solution X-ray scattering, WAXS patterns contain typically only 10-20 independent data points, 21 whereas proteins contain many more degrees of freedom.…”

Section: Introductionmentioning

confidence: 99%

Anisotropic time-resolved solution X-ray scattering patterns from explicit-solvent molecular dynamics

Brinkmann

Hub

2015

The Journal of Chemical Physics

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Time-resolved wide-angle X-ray scattering (TR-WAXS) is an emerging experimental technique used to track chemical reactions and conformational transitions of proteins in real time. Thanks to increased time resolution of the method, anisotropic TR-WAXS patterns were recently reported, which contain more structural information than isotropic patterns. So far, however, no method has been available to compute anisotropic WAXS patterns of biomolecules, thus limiting the structural interpretation. Here, we present a method to compute anisotropic TR-WAXS patterns from molecular dynamics simulations. The calculations accurately account for scattering of the hydration layer and for thermal fluctuations. For many photo-excitable proteins, given a low intensity of the excitation laser, the anisotropic pattern is described by two independent components: (i) an isotropic component, corresponding to common isotropic WAXS experiments and (ii) an anisotropic component depending on the orientation of the excitation dipole of the solute. We present a set of relations for the calculation of these two components from experimental scattering patterns. Notably, the isotropic component is not obtained by a uniform azimuthal average on the detector. The calculations are illustrated and validated by computing anisotropic WAXS patterns of a spheroidal protein model and of photoactive yellow protein. Effects due to saturated excitation at high intensities of the excitation laser are discussed, including opportunities to extract additional structural information by modulating the laser intensity.

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Time-Resolved WAXS Reveals Accelerated Conformational Changes in Iodoretinal-Substituted Proteorhodopsin

Cited by 60 publications

References 49 publications

Activation of G-protein-coupled receptors correlates with the formation of a continuous internal water pathway

Activation of G-protein-coupled receptors correlates with the formation of a continuous internal water pathway

Conformational activation of visual rhodopsin in native disc membranes

Anisotropic time-resolved solution X-ray scattering patterns from explicit-solvent molecular dynamics

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