Single-Trajectory Bayesian Modeling Reveals Multi-State Diffusion of the MSH Sliding Clamp

Abstract

DNA mismatch repair (MMR) is the essential mechanism for preserving genomic integrity in various living organisms. In this process, MutS homologs (MSH) play crucial roles in identifying mismatched basepairs and recruiting downstream MMR proteins. The MSH protein exhibits distinct functions and diffusion dynamics before and after the recognition of mismatches while traversing along DNA. An ADP-bound MSH, known as the MSH searching clamp, scans DNA sequences via rotational diffusion along the DNA backbone. Upon recognizing a mismatch, the MSH combines with ATP molecules, forming a stable sliding clamp. Recent experimental evidence challenges the conventional view that the sliding clamp performs a simple Brownian motion. In this study, we explore the diffusion dynamics of the ATP-bound MSH sliding clamp through single-particle tracking experiments and introduce a Bayesian single-trajectory modeling framework to analyze its motion. Our quantitative analysis reveals that the diffusion characteristics defy explanation by a single-state diffusion mechanism. Instead, our in-depth model inference uncovers three distinct diffusion states, each characterized by specific diffusion coefficients. These states alternate over time, with cross-state transitions predominantly involving one intermediate state, and direct transitions between the slowest and the fastest states being scarce. We propose that these multi-state dynamics reflect underlying conformational changes in the MSH sliding clamp, highlighting a more intricate diffusion mechanism than previously appreciated.