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RNA recognition and self-association of CPEB4 is mediated by its tandem RRM domains.

Schelhorn C, Gordon JM, Ruiz L, Alguacil J, Pedroso E, Macias MJ - Nucleic Acids Res. (2014)

Bottom Line: Self-association does not affect the proteins' ability to interact with RNA as demonstrated by ion mobility-mass spectrometry.Chemical shift effects measured by NMR of the apo forms of the RRM1-RRM2 samples indicate that the two domains are orientated toward each other.We propose a model of the CPEB4 RRM1-RRM2-CPE complex that illustrates the experimental data.

View Article: PubMed Central - PubMed

Affiliation: Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain.

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(A) Comparison of 1H, 15N-HSQC spectra of the apo RRM1 (orange) and apo RRM1–RRM2 (blue). Backbone assignment of both constructs allows us to identify the chemical shift of the residues in both samples. (B) Significant differences in chemical shifts are mapped onto the homology model for RRM1. As those differences are clustering on one surface of the model, we assume that this surface lies in proximity of the RRM2. Secondary 13C chemical shifts ΔCα – ΔCβ of CPEB4 RRM1–RRM2 (D) and comparison of the CSI of RRM1 single and in the RRM1–RRM2 tandem (C). Residues with negative CSI indicate β-strand conformation whereas positive values indicate turn or α-helix. (D) Secondary structure of RRM1 is not significantly altered due to the presence of RRM2.
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Figure 2: (A) Comparison of 1H, 15N-HSQC spectra of the apo RRM1 (orange) and apo RRM1–RRM2 (blue). Backbone assignment of both constructs allows us to identify the chemical shift of the residues in both samples. (B) Significant differences in chemical shifts are mapped onto the homology model for RRM1. As those differences are clustering on one surface of the model, we assume that this surface lies in proximity of the RRM2. Secondary 13C chemical shifts ΔCα – ΔCβ of CPEB4 RRM1–RRM2 (D) and comparison of the CSI of RRM1 single and in the RRM1–RRM2 tandem (C). Residues with negative CSI indicate β-strand conformation whereas positive values indicate turn or α-helix. (D) Secondary structure of RRM1 is not significantly altered due to the presence of RRM2.

Mentions: A comparison of the secondary 13C chemical shifts obtained for the samples to reference values indicate that both RRM1 and RRM2 in the tandem construct adopt the canonical αβ sandwich structure with a β1α1β2β3α2β4 topology with an additional β-strand β4 at the C-terminus of RRM1 (Figure 2A). Comparison of the 13C chemical shifts of RRM1, when assigned independently or in the RRM1–RRM2 construct, indicates that the secondary structure is not altered due to the presence of RRM2 (Figure 2B). For RRM1, a homology model was built using SWISS-MODEL (Template: PDB entry 2DNL, RRM1 of CPEB3, sequence identity 97%, http://swissmodel.expasy.org/; a quality report is shown in Supplementary Figure S1). The topology of the model obtained is consistent with the elements of secondary structure indicated by the analysis of the 13C chemical shifts. The spatial arrangement of the canonical four-stranded antiparallel β-sheet is β4β1β3β2. The homology model we obtained indicates that the additional β4 strand is arranged antiparallel to β4 resulting in the following order for the extended β-sheet: β4’β4β1β3β2.


RNA recognition and self-association of CPEB4 is mediated by its tandem RRM domains.

Schelhorn C, Gordon JM, Ruiz L, Alguacil J, Pedroso E, Macias MJ - Nucleic Acids Res. (2014)

(A) Comparison of 1H, 15N-HSQC spectra of the apo RRM1 (orange) and apo RRM1–RRM2 (blue). Backbone assignment of both constructs allows us to identify the chemical shift of the residues in both samples. (B) Significant differences in chemical shifts are mapped onto the homology model for RRM1. As those differences are clustering on one surface of the model, we assume that this surface lies in proximity of the RRM2. Secondary 13C chemical shifts ΔCα – ΔCβ of CPEB4 RRM1–RRM2 (D) and comparison of the CSI of RRM1 single and in the RRM1–RRM2 tandem (C). Residues with negative CSI indicate β-strand conformation whereas positive values indicate turn or α-helix. (D) Secondary structure of RRM1 is not significantly altered due to the presence of RRM2.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4150798&req=5

Figure 2: (A) Comparison of 1H, 15N-HSQC spectra of the apo RRM1 (orange) and apo RRM1–RRM2 (blue). Backbone assignment of both constructs allows us to identify the chemical shift of the residues in both samples. (B) Significant differences in chemical shifts are mapped onto the homology model for RRM1. As those differences are clustering on one surface of the model, we assume that this surface lies in proximity of the RRM2. Secondary 13C chemical shifts ΔCα – ΔCβ of CPEB4 RRM1–RRM2 (D) and comparison of the CSI of RRM1 single and in the RRM1–RRM2 tandem (C). Residues with negative CSI indicate β-strand conformation whereas positive values indicate turn or α-helix. (D) Secondary structure of RRM1 is not significantly altered due to the presence of RRM2.
Mentions: A comparison of the secondary 13C chemical shifts obtained for the samples to reference values indicate that both RRM1 and RRM2 in the tandem construct adopt the canonical αβ sandwich structure with a β1α1β2β3α2β4 topology with an additional β-strand β4 at the C-terminus of RRM1 (Figure 2A). Comparison of the 13C chemical shifts of RRM1, when assigned independently or in the RRM1–RRM2 construct, indicates that the secondary structure is not altered due to the presence of RRM2 (Figure 2B). For RRM1, a homology model was built using SWISS-MODEL (Template: PDB entry 2DNL, RRM1 of CPEB3, sequence identity 97%, http://swissmodel.expasy.org/; a quality report is shown in Supplementary Figure S1). The topology of the model obtained is consistent with the elements of secondary structure indicated by the analysis of the 13C chemical shifts. The spatial arrangement of the canonical four-stranded antiparallel β-sheet is β4β1β3β2. The homology model we obtained indicates that the additional β4 strand is arranged antiparallel to β4 resulting in the following order for the extended β-sheet: β4’β4β1β3β2.

Bottom Line: Self-association does not affect the proteins' ability to interact with RNA as demonstrated by ion mobility-mass spectrometry.Chemical shift effects measured by NMR of the apo forms of the RRM1-RRM2 samples indicate that the two domains are orientated toward each other.We propose a model of the CPEB4 RRM1-RRM2-CPE complex that illustrates the experimental data.

View Article: PubMed Central - PubMed

Affiliation: Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain.

Show MeSH
Related in: MedlinePlus