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Domain motions of Argonaute, the catalytic engine of RNA interference.

Ming D, Wall ME, Sanbonmatsu KY - BMC Bioinformatics (2007)

Bottom Line: Normal modes are then calculated using an all-atom molecular mechanics force field.The analysis reveals low-frequency vibrations that facilitate the accommodation of RNA duplexes - an essential step in target recognition.Overall, low-frequency vibrations of Argonaute are consistent with mechanisms within the current reaction cycle model for RNA interference.

View Article: PubMed Central - HTML - PubMed

Affiliation: Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, USA. dming@lanl.gov

ABSTRACT

Background: The Argonaute protein is the core component of the RNA-induced silencing complex, playing the central role of cleaving the mRNA target. Visual inspection of static crystal structures already has enabled researchers to suggest conformational changes of Argonaute that might occur during RNA interference. We have taken the next step by performing an all-atom normal mode analysis of the Pyrococcus furiosus and Aquifex aeolicus Argonaute crystal structures, allowing us to quantitatively assess the feasibility of these conformational changes. To perform the analysis, we begin with the energy-minimized X-ray structures. Normal modes are then calculated using an all-atom molecular mechanics force field.

Results: The analysis reveals low-frequency vibrations that facilitate the accommodation of RNA duplexes - an essential step in target recognition. The Pyrococcus furiosus and Aquifex aeolicus Argonaute proteins both exhibit low-frequency torsion and hinge motions; however, differences in the overall architecture of the proteins cause the detailed dynamics to be significantly different.

Conclusion: Overall, low-frequency vibrations of Argonaute are consistent with mechanisms within the current reaction cycle model for RNA interference.

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Related in: MedlinePlus

a) A model of Aa-Ago bound to guide DNA-mRNA. The hybrid duplex is colored in green, with the central red bar as its axis. As a comparison, the protein structure in its apo-form conformation is colored in light gray, and the one containing the hybrid duplex (model) is colored yellow. The yellow structure has an orientation similar to that in Figure 4b). b) The normal mode representation of the Cα conformational changes of Aa-Ago in adopting DNA-mRNA duplex. The coefficient was calculated using Equation (5). The inset shows the cumulative contribution to the Cα conformation change by each mode. c) The radius change of the imaginary cylinder, which encloses Cα atoms located within 5 Å of the DNA-RNA duplex in panel a).
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Figure 7: a) A model of Aa-Ago bound to guide DNA-mRNA. The hybrid duplex is colored in green, with the central red bar as its axis. As a comparison, the protein structure in its apo-form conformation is colored in light gray, and the one containing the hybrid duplex (model) is colored yellow. The yellow structure has an orientation similar to that in Figure 4b). b) The normal mode representation of the Cα conformational changes of Aa-Ago in adopting DNA-mRNA duplex. The coefficient was calculated using Equation (5). The inset shows the cumulative contribution to the Cα conformation change by each mode. c) The radius change of the imaginary cylinder, which encloses Cα atoms located within 5 Å of the DNA-RNA duplex in panel a).

Mentions: Similar to Pf -Ago, the second-lowest frequency mode (1.61 cm-1) in Aa-Ago involves a major torsion between the PIWI-containing lobe and the N-terminal domain (Figure 6e). The torsional axis extends from the N-terminal domain to the Mid domain (Figure 7a). In contrast with the torsional motion in Pf-Ago, the Aa-Ago PAZ domain does not involve a major rotation, but adopts an additional torsion motion with respect to the N-terminal domain. This secondary movement has a rotational axis extending from the PAZ domain to the N-terminal domain. Superposition of the two torsional modes produces a conformational change that allows the protein to change between "locked" and "unlocked" states. In the "locking" process, the PAZ domain rotates outwards, while the N-terminal domain and linker regions move towards the PIWI-containing lobe. In the "unlocking" process, the PAZ domain moves inwards and the N-terminal domain and the linker region moves away from the PIWI domain. Of the four domains in Aa-Ago, the PIWI domain has the smallest displacement.


Domain motions of Argonaute, the catalytic engine of RNA interference.

Ming D, Wall ME, Sanbonmatsu KY - BMC Bioinformatics (2007)

a) A model of Aa-Ago bound to guide DNA-mRNA. The hybrid duplex is colored in green, with the central red bar as its axis. As a comparison, the protein structure in its apo-form conformation is colored in light gray, and the one containing the hybrid duplex (model) is colored yellow. The yellow structure has an orientation similar to that in Figure 4b). b) The normal mode representation of the Cα conformational changes of Aa-Ago in adopting DNA-mRNA duplex. The coefficient was calculated using Equation (5). The inset shows the cumulative contribution to the Cα conformation change by each mode. c) The radius change of the imaginary cylinder, which encloses Cα atoms located within 5 Å of the DNA-RNA duplex in panel a).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238725&req=5

Figure 7: a) A model of Aa-Ago bound to guide DNA-mRNA. The hybrid duplex is colored in green, with the central red bar as its axis. As a comparison, the protein structure in its apo-form conformation is colored in light gray, and the one containing the hybrid duplex (model) is colored yellow. The yellow structure has an orientation similar to that in Figure 4b). b) The normal mode representation of the Cα conformational changes of Aa-Ago in adopting DNA-mRNA duplex. The coefficient was calculated using Equation (5). The inset shows the cumulative contribution to the Cα conformation change by each mode. c) The radius change of the imaginary cylinder, which encloses Cα atoms located within 5 Å of the DNA-RNA duplex in panel a).
Mentions: Similar to Pf -Ago, the second-lowest frequency mode (1.61 cm-1) in Aa-Ago involves a major torsion between the PIWI-containing lobe and the N-terminal domain (Figure 6e). The torsional axis extends from the N-terminal domain to the Mid domain (Figure 7a). In contrast with the torsional motion in Pf-Ago, the Aa-Ago PAZ domain does not involve a major rotation, but adopts an additional torsion motion with respect to the N-terminal domain. This secondary movement has a rotational axis extending from the PAZ domain to the N-terminal domain. Superposition of the two torsional modes produces a conformational change that allows the protein to change between "locked" and "unlocked" states. In the "locking" process, the PAZ domain rotates outwards, while the N-terminal domain and linker regions move towards the PIWI-containing lobe. In the "unlocking" process, the PAZ domain moves inwards and the N-terminal domain and the linker region moves away from the PIWI domain. Of the four domains in Aa-Ago, the PIWI domain has the smallest displacement.

Bottom Line: Normal modes are then calculated using an all-atom molecular mechanics force field.The analysis reveals low-frequency vibrations that facilitate the accommodation of RNA duplexes - an essential step in target recognition.Overall, low-frequency vibrations of Argonaute are consistent with mechanisms within the current reaction cycle model for RNA interference.

View Article: PubMed Central - HTML - PubMed

Affiliation: Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, USA. dming@lanl.gov

ABSTRACT

Background: The Argonaute protein is the core component of the RNA-induced silencing complex, playing the central role of cleaving the mRNA target. Visual inspection of static crystal structures already has enabled researchers to suggest conformational changes of Argonaute that might occur during RNA interference. We have taken the next step by performing an all-atom normal mode analysis of the Pyrococcus furiosus and Aquifex aeolicus Argonaute crystal structures, allowing us to quantitatively assess the feasibility of these conformational changes. To perform the analysis, we begin with the energy-minimized X-ray structures. Normal modes are then calculated using an all-atom molecular mechanics force field.

Results: The analysis reveals low-frequency vibrations that facilitate the accommodation of RNA duplexes - an essential step in target recognition. The Pyrococcus furiosus and Aquifex aeolicus Argonaute proteins both exhibit low-frequency torsion and hinge motions; however, differences in the overall architecture of the proteins cause the detailed dynamics to be significantly different.

Conclusion: Overall, low-frequency vibrations of Argonaute are consistent with mechanisms within the current reaction cycle model for RNA interference.

Show MeSH
Related in: MedlinePlus