Understanding disorder-to-order transitions in protein-RNA complexes using molecular dynamics simulations
Intrinsically disordered regions (IDRs) in proteins are characterized by their flexibilities and low complexity regions, which lack unique 3 D structures in solution. IDRs play a significant role in signaling, regulation, and binding multiple partners, including DNA, RNA, and proteins. Although various experiments have shown the role of disordered regions in binding with RNA, a detailed computational analysis is required to understand their binding and recognition mechanism. In this work, we performed molecular dynamics simulations of 10 protein-RNA complexes to understand the binding governed by intrinsically disordered regions. The simulation results show that most of the disordered regions are important for RNA-binding and have a transition from disordered-to-ordered conformation upon binding, which often contribute significantly towards the binding affinity. Interestingly, most of the disordered residues are present at the interface or located as a linker between two regions having similar movements. The DOT regions are overlaped or flanked with experimentally reported functionally important residues in the recognition of protein-RNA complexes. This study provides additional insights for understanding the role and recognition mechanism of disordered regions in protein-RNA complexes.Communicated by Ramaswamy H. Sarma.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2022 |
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| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:40 |
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| Enthalten in: |
Journal of biomolecular structure & dynamics - 40(2022), 17 vom: 04. Okt., Seite 7915-7925 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Srivastava, Ambuj [VerfasserIn] |
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| Links: |
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| Anmerkungen: |
Date Completed 28.09.2022 Date Revised 13.10.2022 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1080/07391102.2021.1904005 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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NLM323353371 |
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| 245 | 1 | 0 | |a Understanding disorder-to-order transitions in protein-RNA complexes using molecular dynamics simulations |
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| 520 | |a Intrinsically disordered regions (IDRs) in proteins are characterized by their flexibilities and low complexity regions, which lack unique 3 D structures in solution. IDRs play a significant role in signaling, regulation, and binding multiple partners, including DNA, RNA, and proteins. Although various experiments have shown the role of disordered regions in binding with RNA, a detailed computational analysis is required to understand their binding and recognition mechanism. In this work, we performed molecular dynamics simulations of 10 protein-RNA complexes to understand the binding governed by intrinsically disordered regions. The simulation results show that most of the disordered regions are important for RNA-binding and have a transition from disordered-to-ordered conformation upon binding, which often contribute significantly towards the binding affinity. Interestingly, most of the disordered residues are present at the interface or located as a linker between two regions having similar movements. The DOT regions are overlaped or flanked with experimentally reported functionally important residues in the recognition of protein-RNA complexes. This study provides additional insights for understanding the role and recognition mechanism of disordered regions in protein-RNA complexes.Communicated by Ramaswamy H. Sarma | ||
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| 700 | 1 | |a Yesudhas, Dhanusha |e verfasserin |4 aut | |
| 700 | 1 | |a Ahmad, Shandar |e verfasserin |4 aut | |
| 700 | 1 | |a Gromiha, M Michael |e verfasserin |4 aut | |
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