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Dynamic profiling of double-stranded RNA binding proteins.

Wang X, Vukovic L, Koh HR, Schulten K, Myong S - Nucleic Acids Res. (2015)

Bottom Line: Our results demonstrate that despite the highly conserved dsRNA binding domains, the dsRBPs exhibit diverse substrate specificities and dynamic properties when in contact with different RNA substrates.MD simulations provide a detailed atomic interaction map that is largely consistent with the affinity differences observed experimentally.Collectively, our study highlights the diverse nature of substrate specificity and mobility exhibited by dsRBPs that may be critical for their cellular function.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois, 1206 W. Gregory St,. Urbana, IL 61801, USA.

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Interactions between dsRNA and individual dsRBDs. (A) Canonical binding mode between dsRNA and one dsRBD. The binding mode is shown for TRBP dsRBD2 and dsRNA, based on the crystal structure (pdbID 3ADL). RNA is shown in gray and protein is colored according to secondary structure, where helices are shown in yellow, beta strands in blue, and coils/turns in green. The conserved amino acids (H, E, K) crucial for binding to dsRNA are shown in van der Waals representation, with atoms colored in gray (C), red (O) and blue (N). (B) Selected individual dsRBDs of the studied proteins. The structures shown are either crystal structures (labeled with pdbIDs) or homology models (described in ‘Materials and Methods’ section). The coloring scheme for proteins is as in (A). The conserved amino acids crucial for binding to dsRNA are here shown in vdW representation. (C) Average contact areas and interaction energies between dsRNA and four selected dsRBDs. The shown values were averaged over the last 35 ns (ADAD2, ADAR1–3) or 85 ns (TRBP dsRBDs) of trajectories, collected after the initial 15 ns-long relaxation.
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Figure 5: Interactions between dsRNA and individual dsRBDs. (A) Canonical binding mode between dsRNA and one dsRBD. The binding mode is shown for TRBP dsRBD2 and dsRNA, based on the crystal structure (pdbID 3ADL). RNA is shown in gray and protein is colored according to secondary structure, where helices are shown in yellow, beta strands in blue, and coils/turns in green. The conserved amino acids (H, E, K) crucial for binding to dsRNA are shown in van der Waals representation, with atoms colored in gray (C), red (O) and blue (N). (B) Selected individual dsRBDs of the studied proteins. The structures shown are either crystal structures (labeled with pdbIDs) or homology models (described in ‘Materials and Methods’ section). The coloring scheme for proteins is as in (A). The conserved amino acids crucial for binding to dsRNA are here shown in vdW representation. (C) Average contact areas and interaction energies between dsRNA and four selected dsRBDs. The shown values were averaged over the last 35 ns (ADAD2, ADAR1–3) or 85 ns (TRBP dsRBDs) of trajectories, collected after the initial 15 ns-long relaxation.

Mentions: The type-1 dsRBDs in all four proteins bear high similarity in both amino acid sequence and ‘α1-β1-β2-β3-α2’ subdomain arrangement (Figure 1B). In particular, the amino acid motifs known to bind to dsRNA are highly conserved across the listed dsRBDs. The three key regions that are critical for interacting with dsRNA are highlighted in the structural models of TRBP–dsRBD2 bound to dsRNA (Figure 5A) and of other dsRBDs bound to dsRNA (Figure 5B). First, there is a conserved E residue (red) in helix α1, which binds to the minor groove of dsRNA. This residue is present in all dsRBDs with the exception of Staufen1 dsRBD3, which nonetheless has a similar Q amino acid in the position. The second conserved dsRNA binding residue is an H residue (light blue) in the loop connecting β1 and β2 strands; this residue is present in all dsRBDs except in ADAD2 dsRBD and Staufen1 dsRBD2. The conserved H residue is known to form a hydrogen bond to the dsRNA minor groove. The third conserved dsRNA binding motif is the KKxxK motif (dark blue) on helix α2; this motif, which binds across dsRNA major groove, is present in all the dsRBDs except in ADAD2 dsRBD (Figure 5B).


Dynamic profiling of double-stranded RNA binding proteins.

Wang X, Vukovic L, Koh HR, Schulten K, Myong S - Nucleic Acids Res. (2015)

Interactions between dsRNA and individual dsRBDs. (A) Canonical binding mode between dsRNA and one dsRBD. The binding mode is shown for TRBP dsRBD2 and dsRNA, based on the crystal structure (pdbID 3ADL). RNA is shown in gray and protein is colored according to secondary structure, where helices are shown in yellow, beta strands in blue, and coils/turns in green. The conserved amino acids (H, E, K) crucial for binding to dsRNA are shown in van der Waals representation, with atoms colored in gray (C), red (O) and blue (N). (B) Selected individual dsRBDs of the studied proteins. The structures shown are either crystal structures (labeled with pdbIDs) or homology models (described in ‘Materials and Methods’ section). The coloring scheme for proteins is as in (A). The conserved amino acids crucial for binding to dsRNA are here shown in vdW representation. (C) Average contact areas and interaction energies between dsRNA and four selected dsRBDs. The shown values were averaged over the last 35 ns (ADAD2, ADAR1–3) or 85 ns (TRBP dsRBDs) of trajectories, collected after the initial 15 ns-long relaxation.
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Figure 5: Interactions between dsRNA and individual dsRBDs. (A) Canonical binding mode between dsRNA and one dsRBD. The binding mode is shown for TRBP dsRBD2 and dsRNA, based on the crystal structure (pdbID 3ADL). RNA is shown in gray and protein is colored according to secondary structure, where helices are shown in yellow, beta strands in blue, and coils/turns in green. The conserved amino acids (H, E, K) crucial for binding to dsRNA are shown in van der Waals representation, with atoms colored in gray (C), red (O) and blue (N). (B) Selected individual dsRBDs of the studied proteins. The structures shown are either crystal structures (labeled with pdbIDs) or homology models (described in ‘Materials and Methods’ section). The coloring scheme for proteins is as in (A). The conserved amino acids crucial for binding to dsRNA are here shown in vdW representation. (C) Average contact areas and interaction energies between dsRNA and four selected dsRBDs. The shown values were averaged over the last 35 ns (ADAD2, ADAR1–3) or 85 ns (TRBP dsRBDs) of trajectories, collected after the initial 15 ns-long relaxation.
Mentions: The type-1 dsRBDs in all four proteins bear high similarity in both amino acid sequence and ‘α1-β1-β2-β3-α2’ subdomain arrangement (Figure 1B). In particular, the amino acid motifs known to bind to dsRNA are highly conserved across the listed dsRBDs. The three key regions that are critical for interacting with dsRNA are highlighted in the structural models of TRBP–dsRBD2 bound to dsRNA (Figure 5A) and of other dsRBDs bound to dsRNA (Figure 5B). First, there is a conserved E residue (red) in helix α1, which binds to the minor groove of dsRNA. This residue is present in all dsRBDs with the exception of Staufen1 dsRBD3, which nonetheless has a similar Q amino acid in the position. The second conserved dsRNA binding residue is an H residue (light blue) in the loop connecting β1 and β2 strands; this residue is present in all dsRBDs except in ADAD2 dsRBD and Staufen1 dsRBD2. The conserved H residue is known to form a hydrogen bond to the dsRNA minor groove. The third conserved dsRNA binding motif is the KKxxK motif (dark blue) on helix α2; this motif, which binds across dsRNA major groove, is present in all the dsRBDs except in ADAD2 dsRBD (Figure 5B).

Bottom Line: Our results demonstrate that despite the highly conserved dsRNA binding domains, the dsRBPs exhibit diverse substrate specificities and dynamic properties when in contact with different RNA substrates.MD simulations provide a detailed atomic interaction map that is largely consistent with the affinity differences observed experimentally.Collectively, our study highlights the diverse nature of substrate specificity and mobility exhibited by dsRBPs that may be critical for their cellular function.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois, 1206 W. Gregory St,. Urbana, IL 61801, USA.

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