Differential conformational dynamics in two type-A RNA-binding domains drive the double-stranded RNA recognition and binding.
E. coli
MD simulation
RNA recognition
conformational heterogeneity
molecular biophysics
protein dynamics
structural biology
Journal
eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614
Informations de publication
Date de publication:
08 Aug 2024
08 Aug 2024
Historique:
medline:
8
8
2024
pubmed:
8
8
2024
entrez:
8
8
2024
Statut:
epublish
Résumé
Trans-activation response (TAR) RNA-binding protein (TRBP) has emerged as a key player in the RNA interference pathway, wherein it binds to different pre-microRNAs (miRNAs) and small interfering RNAs (siRNAs), each varying in sequence and/or structure. We hypothesize that TRBP displays dynamic adaptability to accommodate heterogeneity in target RNA structures. Thus, it is crucial to ascertain the role of intrinsic and RNA-induced protein dynamics in RNA recognition and binding. We have previously elucidated the role of intrinsic and RNA-induced conformational exchange in the double-stranded RNA-binding domain 1 (dsRBD1) of TRBP in shape-dependent RNA recognition. The current study delves into the intrinsic and RNA-induced conformational dynamics of the TRBP-dsRBD2 and then compares it with the dsRBD1 study carried out previously. Remarkably, the two domains exhibit differential binding affinity to a 12-bp dsRNA owing to the presence of critical residues and structural plasticity. Furthermore, we report that dsRBD2 depicts constrained conformational plasticity when compared to dsRBD1. Although, in the presence of RNA, dsRBD2 undergoes induced conformational exchange within the designated RNA-binding regions and other residues, the amplitude of the motions remains modest when compared to those observed in dsRBD1. We propose a dynamics-driven model of the two tandem domains of TRBP, substantiating their contributions to the versatility of dsRNA recognition and binding.
Identifiants
pubmed: 39116184
doi: 10.7554/eLife.94842
pii: 94842
doi:
pii:
Substances chimiques
RNA-Binding Proteins
0
RNA, Double-Stranded
0
trans-activation responsive RNA-binding protein
136628-24-5
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Science and Engineering Research Board
ID : EMR/2015/001966
Organisme : Department of Biotechnology, Ministry of Science and Technology, India
ID : BT/PR24185/BRB/10/1605/2017
Informations de copyright
© 2024, Parvez et al.
Déclaration de conflit d'intérêts
FP, DS, HP, ZA, JC No competing interests declared
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