The PCNA interaction motifs revisited: thinking outside the PIP-box

Area of Science:

• Molecular Biology
• Biochemistry
• Structural Biology

Background:

• Proliferating cell nuclear antigen (PCNA) is crucial for DNA metabolism and a target for drug development.
• PCNA-binding proteins utilize a short linear motif (SLiM) called the PCNA-interacting protein-box (PIP-box).
• Sequence-divergent motifs binding to PCNA suggest a complex interaction mechanism.

Purpose of the Study:

• To investigate how PCNA accommodates diverse binding motifs.
• To analyze features governing the binding affinity of PCNA-binding proteins.
• To understand the role of flanking regions in PCNA-motif interactions.

Main Methods:

• Analysis of 77 experimentally confirmed PCNA-binding proteins.
• Nuclear Magnetic Resonance (NMR) spectroscopy.
• Affinity measurements and computational analyses.

Main Results:

• Most PCNA-binding motifs are located in intrinsically disordered regions.
• Structure preformation does not correlate with binding affinity.
• Binding affinity is encoded by sequence patterns extending beyond the canonical PIP-box.
• Positive charges in flanking regions modulate PIP-box affinity across four orders of magnitude.

Conclusions:

• PCNA binding is more complex than previously thought, involving flanking sequences.
• Understanding these extended motifs is vital for interpreting disease-related mutations.
• This knowledge can guide the rational design of drugs targeting DNA replication and repair.