Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual...

Area of Science:

• Structural biology
• Molecular biology
• Biochemistry

Background:

• RNA-binding proteins (RBPs) regulate gene expression through interactions with RNA.
• Many RBPs contain intrinsically disordered regions, complicating structural determination.
• Ribonucleoprotein (RNP) complexes often lack a single stable state, requiring integrative approaches.

Purpose of the Study:

• To determine the solution structure of polypyrimidine-tract binding protein 1 (PTBP1/hnRNP I) complexed with an encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES) RNA fragment.
• To characterize the structural consequences of PTBP1 binding to IRES RNA.
• To understand the role of PTBP1 as an RNA chaperone in viral translation.

Main Methods:

• Integrative structural modeling combining magnetic resonance, mass spectrometry, and small-angle scattering data.
• Solution-state structural analysis of RNP complexes.
• Characterization of protein-RNA interactions and conformational dynamics.

Main Results:

• The PTBP1-EMCV IRES RNA complex exhibits both compaction and significant conformational flexibility.
• PTBP1 acts as an RNA chaperone, organizing the IRES RNA into distinct conformations with exposed stems.
• Atomic-level structural details of a heterogeneous RNP complex were achieved.

Conclusions:

• PTBP1 binding to IRES RNA induces a dynamic, yet organized, RNP structure crucial for viral translation.
• Conformational diversity in RNP complexes is likely a common feature with functional importance.
• Integrative structural modeling is a powerful approach for characterizing complex, flexible RNP structures.