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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

The root-mean-square fluctuations of Cα atoms at T = 300 K calculated using normal mode analysis for (A) Pf-Ago and (B) Aa-Ago.
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Figure 3: The root-mean-square fluctuations of Cα atoms at T = 300 K calculated using normal mode analysis for (A) Pf-Ago and (B) Aa-Ago.

Mentions: Figure 3 shows the root-mean-squared fluctuations (RMSFs) of Cα atoms vs. residue number for the Aa-Ago and the Pf-Ago proteins. RMSFs were calculated with Equation (4) at the ambient temperature of T = 300 K using the first 500 modes. The correlation between the above RMSFs with that calculated using only the first 15 modes is 0.85 for Aa-Ago and 0.93 for Pf-Ago, demonstrating that in this case, the low-frequency modes dominate the fluctuation spectrum, as found in normal-mode analyses of other proteins [17-19,22,23]. For Pf-Ago, the range of fluctuations is wider in the N-terminal and PAZ domains than in the Mid and PIWI domains. The mean value of Cα-RMSFs in the N-terminal and PAZ domains is 0.54 Å, which is larger than the mean value of 0.33 Å in the Mid and PIWI domains. By contrast, for Aa-Ago, the Cα RMSFs are more evenly distributed, and the mean value varies from 0.34 Å in the PIWI domain to 0.44 Å in the PAZ domain. The RMSF plots for both proteins are strongly peaked – Figure 4 shows that the peaks tend to reside in unstructured surface regions connecting secondary structures, with the exception of one peak which spans the α5 and α6 helices of the PAZ domain of Pf-Ago (residues E219 to Q237).


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

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

The root-mean-square fluctuations of Cα atoms at T = 300 K calculated using normal mode analysis for (A) Pf-Ago and (B) Aa-Ago.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: The root-mean-square fluctuations of Cα atoms at T = 300 K calculated using normal mode analysis for (A) Pf-Ago and (B) Aa-Ago.
Mentions: Figure 3 shows the root-mean-squared fluctuations (RMSFs) of Cα atoms vs. residue number for the Aa-Ago and the Pf-Ago proteins. RMSFs were calculated with Equation (4) at the ambient temperature of T = 300 K using the first 500 modes. The correlation between the above RMSFs with that calculated using only the first 15 modes is 0.85 for Aa-Ago and 0.93 for Pf-Ago, demonstrating that in this case, the low-frequency modes dominate the fluctuation spectrum, as found in normal-mode analyses of other proteins [17-19,22,23]. For Pf-Ago, the range of fluctuations is wider in the N-terminal and PAZ domains than in the Mid and PIWI domains. The mean value of Cα-RMSFs in the N-terminal and PAZ domains is 0.54 Å, which is larger than the mean value of 0.33 Å in the Mid and PIWI domains. By contrast, for Aa-Ago, the Cα RMSFs are more evenly distributed, and the mean value varies from 0.34 Å in the PIWI domain to 0.44 Å in the PAZ domain. The RMSF plots for both proteins are strongly peaked – Figure 4 shows that the peaks tend to reside in unstructured surface regions connecting secondary structures, with the exception of one peak which spans the α5 and α6 helices of the PAZ domain of Pf-Ago (residues E219 to Q237).

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