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Active state-like conformational elements in the beta2-AR and a photoactivated intermediate of rhodopsin identified by dynamic properties of GPCRs.

Han DS, Wang SX, Weinstein H - Biochemistry (2008)

Bottom Line: G-Protein-coupled receptors (GPCRs) adopt various functionally relevant conformational states in cell signaling processes.Recently determined crystal structures of rhodopsin and the beta 2-adrenergic receptor (beta 2-AR) offer insight into previously uncharacterized active conformations, but the molecular states of these GPCRs are likely to contain both inactive and active-like conformational elements.We have identified conformational rearrangements in the dynamics of the TM7-HX8 segment that relate to the properties of the conserved NPxxY(x)5,6F motif and show that they can be used to identify active state-like conformational elements in the corresponding regions of the new structures of rhodopsin and the beta 2-AR.

View Article: PubMed Central - PubMed

Affiliation: Department of Physiology and Biophysics, Weill Medical College, Cornell University, 1300 York Avenue, New York, New York 10021, USA.

ABSTRACT
G-Protein-coupled receptors (GPCRs) adopt various functionally relevant conformational states in cell signaling processes. Recently determined crystal structures of rhodopsin and the beta 2-adrenergic receptor (beta 2-AR) offer insight into previously uncharacterized active conformations, but the molecular states of these GPCRs are likely to contain both inactive and active-like conformational elements. We have identified conformational rearrangements in the dynamics of the TM7-HX8 segment that relate to the properties of the conserved NPxxY(x)5,6F motif and show that they can be used to identify active state-like conformational elements in the corresponding regions of the new structures of rhodopsin and the beta 2-AR.

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(A) Average structure of rhodopsin from the WT simulation (0−20 ns) with arrows indicating the positive direction of motion proportional to the mean square fluctuation of each Cα atom along the reference eigenvector (the first principal eigenvector derived from the WT simulation) for the TM7−HX8 segment. (B) TM7−HX8 segments from the photoactivated rhodopsin intermediate (yellow) and the β2-AR (red) fitted onto the average structure of inactive rhodopsin from the WT simulation (0−20 ns). Cα atoms for the sequence from position 7.50 to 7.57, and from position 2.40 to 2.43, were used to fit the structures onto each other. Note that these segments lie along the positive direction of the reference eigenvector. (C) Projections of the TM7–HX8 segment from each simulation onto the reference eigenvector, which is the first principal eigenvector derived from the WT simulation. The projections were measured and binned starting from t = 5 ns and represent the total distribution from all corresponding trajectories for each construct of rhodopsin (see Table 1). These distributions are plotted as the fold change relative to the mean square fluctuation of the WT simulation along the reference eigenvector.
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fig1: (A) Average structure of rhodopsin from the WT simulation (0−20 ns) with arrows indicating the positive direction of motion proportional to the mean square fluctuation of each Cα atom along the reference eigenvector (the first principal eigenvector derived from the WT simulation) for the TM7−HX8 segment. (B) TM7−HX8 segments from the photoactivated rhodopsin intermediate (yellow) and the β2-AR (red) fitted onto the average structure of inactive rhodopsin from the WT simulation (0−20 ns). Cα atoms for the sequence from position 7.50 to 7.57, and from position 2.40 to 2.43, were used to fit the structures onto each other. Note that these segments lie along the positive direction of the reference eigenvector. (C) Projections of the TM7–HX8 segment from each simulation onto the reference eigenvector, which is the first principal eigenvector derived from the WT simulation. The projections were measured and binned starting from t = 5 ns and represent the total distribution from all corresponding trajectories for each construct of rhodopsin (see Table 1). These distributions are plotted as the fold change relative to the mean square fluctuation of the WT simulation along the reference eigenvector.

Mentions: We first examined the conformations explored by the cytoplasmic end of TM7 and HX8 [from P303 (7.50) to C323 (7.70)], a segment termed TM7−HX8, using essential dynamics (ED) analysis. ED analysis of structures from the WT simulation (0−20 ns) produced eigenvectors describing the directions of correlated motion. The fraction of the total fluctuation during this initial time interval contributed by the eigenvector that had the highest corresponding eigenvalue describes up to 33% of the overall fluctuations for TM7−HX8, at least twice as much as any other eigenvector. The same analysis was conducted on structures taken from the last 20 ns of the simulation (25−45 ns) and compared with the eigenvectors derived from the 0−20 ns segment. A calculated inner product value of 0.91 indicated that the fluctuations described by the first eigenvector persist throughout the simulation, in contrast to motion described by other eigenvectors. Consequently, the first eigenvector was chosen as a reference vector in the conformational space against which the sampling from the simulations of the mutant constructs can be measured. The average structure of rhodopsin from the WT simulation (0−20 ns) is shown in Figure 1A with arrows assigned to each of the Cα atoms of the TM7−HX8 segment pointing in the positive direction of the reference eigenvector.


Active state-like conformational elements in the beta2-AR and a photoactivated intermediate of rhodopsin identified by dynamic properties of GPCRs.

Han DS, Wang SX, Weinstein H - Biochemistry (2008)

(A) Average structure of rhodopsin from the WT simulation (0−20 ns) with arrows indicating the positive direction of motion proportional to the mean square fluctuation of each Cα atom along the reference eigenvector (the first principal eigenvector derived from the WT simulation) for the TM7−HX8 segment. (B) TM7−HX8 segments from the photoactivated rhodopsin intermediate (yellow) and the β2-AR (red) fitted onto the average structure of inactive rhodopsin from the WT simulation (0−20 ns). Cα atoms for the sequence from position 7.50 to 7.57, and from position 2.40 to 2.43, were used to fit the structures onto each other. Note that these segments lie along the positive direction of the reference eigenvector. (C) Projections of the TM7–HX8 segment from each simulation onto the reference eigenvector, which is the first principal eigenvector derived from the WT simulation. The projections were measured and binned starting from t = 5 ns and represent the total distribution from all corresponding trajectories for each construct of rhodopsin (see Table 1). These distributions are plotted as the fold change relative to the mean square fluctuation of the WT simulation along the reference eigenvector.
© Copyright Policy - open-access - ccc-price
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2664832&req=5

fig1: (A) Average structure of rhodopsin from the WT simulation (0−20 ns) with arrows indicating the positive direction of motion proportional to the mean square fluctuation of each Cα atom along the reference eigenvector (the first principal eigenvector derived from the WT simulation) for the TM7−HX8 segment. (B) TM7−HX8 segments from the photoactivated rhodopsin intermediate (yellow) and the β2-AR (red) fitted onto the average structure of inactive rhodopsin from the WT simulation (0−20 ns). Cα atoms for the sequence from position 7.50 to 7.57, and from position 2.40 to 2.43, were used to fit the structures onto each other. Note that these segments lie along the positive direction of the reference eigenvector. (C) Projections of the TM7–HX8 segment from each simulation onto the reference eigenvector, which is the first principal eigenvector derived from the WT simulation. The projections were measured and binned starting from t = 5 ns and represent the total distribution from all corresponding trajectories for each construct of rhodopsin (see Table 1). These distributions are plotted as the fold change relative to the mean square fluctuation of the WT simulation along the reference eigenvector.
Mentions: We first examined the conformations explored by the cytoplasmic end of TM7 and HX8 [from P303 (7.50) to C323 (7.70)], a segment termed TM7−HX8, using essential dynamics (ED) analysis. ED analysis of structures from the WT simulation (0−20 ns) produced eigenvectors describing the directions of correlated motion. The fraction of the total fluctuation during this initial time interval contributed by the eigenvector that had the highest corresponding eigenvalue describes up to 33% of the overall fluctuations for TM7−HX8, at least twice as much as any other eigenvector. The same analysis was conducted on structures taken from the last 20 ns of the simulation (25−45 ns) and compared with the eigenvectors derived from the 0−20 ns segment. A calculated inner product value of 0.91 indicated that the fluctuations described by the first eigenvector persist throughout the simulation, in contrast to motion described by other eigenvectors. Consequently, the first eigenvector was chosen as a reference vector in the conformational space against which the sampling from the simulations of the mutant constructs can be measured. The average structure of rhodopsin from the WT simulation (0−20 ns) is shown in Figure 1A with arrows assigned to each of the Cα atoms of the TM7−HX8 segment pointing in the positive direction of the reference eigenvector.

Bottom Line: G-Protein-coupled receptors (GPCRs) adopt various functionally relevant conformational states in cell signaling processes.Recently determined crystal structures of rhodopsin and the beta 2-adrenergic receptor (beta 2-AR) offer insight into previously uncharacterized active conformations, but the molecular states of these GPCRs are likely to contain both inactive and active-like conformational elements.We have identified conformational rearrangements in the dynamics of the TM7-HX8 segment that relate to the properties of the conserved NPxxY(x)5,6F motif and show that they can be used to identify active state-like conformational elements in the corresponding regions of the new structures of rhodopsin and the beta 2-AR.

View Article: PubMed Central - PubMed

Affiliation: Department of Physiology and Biophysics, Weill Medical College, Cornell University, 1300 York Avenue, New York, New York 10021, USA.

ABSTRACT
G-Protein-coupled receptors (GPCRs) adopt various functionally relevant conformational states in cell signaling processes. Recently determined crystal structures of rhodopsin and the beta 2-adrenergic receptor (beta 2-AR) offer insight into previously uncharacterized active conformations, but the molecular states of these GPCRs are likely to contain both inactive and active-like conformational elements. We have identified conformational rearrangements in the dynamics of the TM7-HX8 segment that relate to the properties of the conserved NPxxY(x)5,6F motif and show that they can be used to identify active state-like conformational elements in the corresponding regions of the new structures of rhodopsin and the beta 2-AR.

Show MeSH
Related in: MedlinePlus