Template-Based Modeling of Protein-RNA Interactions.
Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2016-09-01
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| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC5035060?pdf=render |
| _version_ | 1818024213654536192 |
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| author | Jinfang Zheng Petras J Kundrotas Ilya A Vakser Shiyong Liu |
| author_facet | Jinfang Zheng Petras J Kundrotas Ilya A Vakser Shiyong Liu |
| author_sort | Jinfang Zheng |
| collection | DOAJ |
| description | Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes. |
| first_indexed | 2024-12-10T03:56:39Z |
| format | Article |
| id | doaj.art-363fd47820c94116be42228bdbac87a2 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-10T03:56:39Z |
| publishDate | 2016-09-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-363fd47820c94116be42228bdbac87a22022-12-22T02:03:06ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582016-09-01129e100512010.1371/journal.pcbi.1005120Template-Based Modeling of Protein-RNA Interactions.Jinfang ZhengPetras J KundrotasIlya A VakserShiyong LiuProtein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes.http://europepmc.org/articles/PMC5035060?pdf=render |
| spellingShingle | Jinfang Zheng Petras J Kundrotas Ilya A Vakser Shiyong Liu Template-Based Modeling of Protein-RNA Interactions. PLoS Computational Biology |
| title | Template-Based Modeling of Protein-RNA Interactions. |
| title_full | Template-Based Modeling of Protein-RNA Interactions. |
| title_fullStr | Template-Based Modeling of Protein-RNA Interactions. |
| title_full_unstemmed | Template-Based Modeling of Protein-RNA Interactions. |
| title_short | Template-Based Modeling of Protein-RNA Interactions. |
| title_sort | template based modeling of protein rna interactions |
| url | http://europepmc.org/articles/PMC5035060?pdf=render |
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