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Updated: Aug 30, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Cryptic binding properties of a transient folding intermediate in a PDZ tandem repeat
Francesca Malagrinò1, Giuliana Fusco2, Valeria Pennacchietti1
1Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy.
This study reveals that a misfolded intermediate of sPDZD2 protein binds its ligand with higher affinity than the native state, suggesting a cryptic function for this folding intermediate.
Area of Science:
- Protein structure and function
- Molecular biology
- Biochemistry
Background:
- PDZ domains are prevalent protein-protein interaction modules in the human proteome.
- PDZD2 protein contains six PDZ domains and is proteolytically cleaved into sPDZD2 (PDZ5-PDZ6 tandem).
- The physiological ligand interactions of sPDZD2 are not well understood.
Purpose of the Study:
- To investigate the folding pathway of sPDZD2 to understand its stability and function.
- To characterize the interaction of sPDZD2 with its endogenous ligand.
Main Methods:
- Differential scanning fluorimetry and circular dichroism spectroscopy were used to study protein folding.
- Double jump kinetic experiments were employed to analyze ligand binding to folding intermediates.
Main Results:
- The folding of sPDZD2 involves a complex pathway with a transiently populated intermediate.
- This intermediate, formed by concurrent denaturation of PDZ5 and PDZ6 domains, binds the physiological ligand with higher affinity than the native state.
Conclusions:
- sPDZD2 folding intermediates can exhibit enhanced ligand binding affinity.
- Misfolded protein intermediates may possess cryptic functions not apparent in the native state.
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