How Does the Proliferating Cell Nuclear Antigen Modulate Binding Specificity to Multiple Partner Proteins?

Area of Science:

• Molecular Biology
• Biophysics
• Structural Biology

Background:

• Proliferating cell nuclear antigen (PCNA) is a crucial sliding clamp protein involved in DNA repair and replication.
• PCNA functions as a homotrimer, interacting with various proteins via its intrinsically disordered interdomain connecting loop.
• This loop adopts different conformations upon binding to distinct partner proteins, influencing binding affinities.

Purpose of the Study:

• To investigate whether unbound PCNA samples conformations similar to those observed when bound to partner proteins.
• To identify key interactions and dynamics governing PCNA-partner protein complex formation.
• To elucidate the role of intrinsically disordered regions in PCNA's multifunctional nature.

Main Methods:

• All-atom molecular dynamics simulations of PCNA in various states: unbound, bound to peptides, and bound to the Fen 1 protein.
• Analysis of sampled PCNA conformations and comparison between unbound and bound states.
• Calculation of binding energies and correlation with experimentally measured affinities.

Main Results:

• PCNA samples many peptide-bound conformations even in its unbound state.
• PCNA selects specific conformations upon binding to partner proteins.
• Identified crucial PCNA-peptide interactions and proposed a recruitment mechanism.
• Calculated binding energies accurately reflect experimental binding affinities.

Conclusions:

• The intrinsically disordered interdomain connecting loop of PCNA allows it to sample diverse conformations, facilitating interactions with multiple partners.
• PCNA's conformational flexibility is essential for its role in DNA repair, replication, and other cellular processes.
• This study provides insights into the dynamic mechanisms underlying protein-protein interactions involving intrinsically disordered regions.