Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding.
The influenza viruses contain a segmented, negative stranded RNA genome. Each RNA segment is covered by multiple copies of the nucleoprotein (NP). X-ray structures have shown that NP contains well-structured domains juxtaposed with regions of missing electron densities corresponding to loops. In thi...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2012-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3260217?pdf=render |
| _version_ | 1819237089284194304 |
|---|---|
| author | Bogdan Tarus Christophe Chevalier Charles-Adrien Richard Bernard Delmas Carmelo Di Primo Anny Slama-Schwok |
| author_facet | Bogdan Tarus Christophe Chevalier Charles-Adrien Richard Bernard Delmas Carmelo Di Primo Anny Slama-Schwok |
| author_sort | Bogdan Tarus |
| collection | DOAJ |
| description | The influenza viruses contain a segmented, negative stranded RNA genome. Each RNA segment is covered by multiple copies of the nucleoprotein (NP). X-ray structures have shown that NP contains well-structured domains juxtaposed with regions of missing electron densities corresponding to loops. In this study, we tested if these flexible loops gated or promoted RNA binding and RNA-induced oligomerization of NP. We first performed molecular dynamics simulations of wt NP monomer and trimer in comparison with the R361A protein mutated in the RNA binding groove, using the H1N1 NP as the initial structure. Calculation of the root-mean-square fluctuations highlighted the presence of two flexible loops in NP trimer: loop 1 (73-90), loop 2 (200-214). In NP, loops 1 and 2 formed a 10-15 Å-wide pinch giving access to the RNA binding groove. Loop 1 was stabilized by interactions with K113 of the adjacent β-sheet 1 (91-112) that interacted with the RNA grove (linker 360-373) via multiple hydrophobic contacts. In R361A, a salt bridge formed between E80 of loop 1 and R208 of loop 2 driven by hydrophobic contacts between L79 and W207, due to a decreased flexibility of loop 2 and loop 1 unfolding. Thus, RNA could not access its binding groove in R361A; accordingly, R361A had a much lower affinity for RNA than NP. Disruption of the E80-R208 interaction in the triple mutant R361A-E80A-E81A increased its RNA binding affinity and restored its oligomerization back to wt levels in contrast with impaired levels of R361A. Our data suggest that the flexibility of loops 1 and 2 is required for RNA sampling and binding which likely involve conformational change(s) of the nucleoprotein. |
| first_indexed | 2024-12-23T13:14:47Z |
| format | Article |
| id | doaj.art-69ab5dbd69f0404186bcb50ff480abb8 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-23T13:14:47Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-69ab5dbd69f0404186bcb50ff480abb82022-12-21T17:45:38ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0171e3003810.1371/journal.pone.0030038Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding.Bogdan TarusChristophe ChevalierCharles-Adrien RichardBernard DelmasCarmelo Di PrimoAnny Slama-SchwokThe influenza viruses contain a segmented, negative stranded RNA genome. Each RNA segment is covered by multiple copies of the nucleoprotein (NP). X-ray structures have shown that NP contains well-structured domains juxtaposed with regions of missing electron densities corresponding to loops. In this study, we tested if these flexible loops gated or promoted RNA binding and RNA-induced oligomerization of NP. We first performed molecular dynamics simulations of wt NP monomer and trimer in comparison with the R361A protein mutated in the RNA binding groove, using the H1N1 NP as the initial structure. Calculation of the root-mean-square fluctuations highlighted the presence of two flexible loops in NP trimer: loop 1 (73-90), loop 2 (200-214). In NP, loops 1 and 2 formed a 10-15 Å-wide pinch giving access to the RNA binding groove. Loop 1 was stabilized by interactions with K113 of the adjacent β-sheet 1 (91-112) that interacted with the RNA grove (linker 360-373) via multiple hydrophobic contacts. In R361A, a salt bridge formed between E80 of loop 1 and R208 of loop 2 driven by hydrophobic contacts between L79 and W207, due to a decreased flexibility of loop 2 and loop 1 unfolding. Thus, RNA could not access its binding groove in R361A; accordingly, R361A had a much lower affinity for RNA than NP. Disruption of the E80-R208 interaction in the triple mutant R361A-E80A-E81A increased its RNA binding affinity and restored its oligomerization back to wt levels in contrast with impaired levels of R361A. Our data suggest that the flexibility of loops 1 and 2 is required for RNA sampling and binding which likely involve conformational change(s) of the nucleoprotein.http://europepmc.org/articles/PMC3260217?pdf=render |
| spellingShingle | Bogdan Tarus Christophe Chevalier Charles-Adrien Richard Bernard Delmas Carmelo Di Primo Anny Slama-Schwok Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. PLoS ONE |
| title | Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. |
| title_full | Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. |
| title_fullStr | Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. |
| title_full_unstemmed | Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. |
| title_short | Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. |
| title_sort | molecular dynamics studies of the nucleoprotein of influenza a virus role of the protein flexibility in rna binding |
| url | http://europepmc.org/articles/PMC3260217?pdf=render |
| work_keys_str_mv | AT bogdantarus moleculardynamicsstudiesofthenucleoproteinofinfluenzaavirusroleoftheproteinflexibilityinrnabinding AT christophechevalier moleculardynamicsstudiesofthenucleoproteinofinfluenzaavirusroleoftheproteinflexibilityinrnabinding AT charlesadrienrichard moleculardynamicsstudiesofthenucleoproteinofinfluenzaavirusroleoftheproteinflexibilityinrnabinding AT bernarddelmas moleculardynamicsstudiesofthenucleoproteinofinfluenzaavirusroleoftheproteinflexibilityinrnabinding AT carmelodiprimo moleculardynamicsstudiesofthenucleoproteinofinfluenzaavirusroleoftheproteinflexibilityinrnabinding AT annyslamaschwok moleculardynamicsstudiesofthenucleoproteinofinfluenzaavirusroleoftheproteinflexibilityinrnabinding |