Sliding, Fast and Slow: Distinct Diffusion Mechanisms of Eukaryotic and Prokaryotic DNA Clamps

Abstract

Various proteins diffuse along millions to billions of base pairs (bp) long linear genome to replicate, repair, and transcribe DNA. Among those proteins, an outstanding example is the DNA clamp—proliferating cell nuclear antigen (PCNA) in eukaryotes and β in prokaryotes. Despite the low sequence homology between β and PCNA, they form a highly similar closed ring structure that encircles double-stranded DNA (dsDNA). Because the primary role of the clamp is facilitating the replication and repair processes by controlling the diffusion mechanism, revealing the diffusion mechanism has been at the core of the biophysical studies of the clamps. Importantly, single-molecule experiments revealed that PCNA diffuses an order of magnitude faster than β does. However, no existing model can explain how the structurally similar clamps show such a dramatic difference in the diffusion speed. Here, we use the molecular dynamics (MD) simulation technique to answer the question. For each of β and PCNA systems, we generated tens of microsecond-long continuous trajectory, in which the computed diffusion coefficients matched the experimental measurements. The MD trajectories revealed that the difference in the binding mode between DNA and clamps could explain the difference in the diffusion speed. For β, arginine residue 24 (R24) spontaneously bound to the minor groove of A:T base pairs, providing a braking mechanism that slows down the diffusion by friction. For PCNA, conversely, no basic residues were found to bind to the minor groove, resulting in a fast diffusion without a braking mechanism. Further, using the MD trajectories, we could validate the diffusion modes proposed based on the experiments. While the diffusion of PCNA stochastically switches between the translational and cogwheel modes, that of β is mostly the cogwheel mode with a high rotation-translation coupling.