Diffusion state identification of XPC proteins: single-trajectory analysis
ABSTRACT
The XPC protein, a crucial component of nucleotide excision repair, is one of the proteins that identify DNA damage during global genomic repair. Understanding the diffusion dynamics of XPC while searching for damaged DNA is fundamental in studying diseases resulting from DNA damage, such as cancer. In this study, we explore the diffusion dynamics of XPC proteins traversing along DNA. For this purpose, we utilize the single-particle tracking data of XPCs on $\lambda$-DNA using the single-molecule DNA curtain assay. Employing sliding-window trajectory slice (STS) techniques, we observe that the dynamics of XPC diffusion exhibit temporal heterogeneity, revealing multiple dynamic states. Through a detailed examination of each dynamic state's diffusion characteristics, such as mean-squared displacement, diffusivity, and van-Hove correlation functions, among others, we discern three distinct types of diffusion states: fast diffusion, slow diffusion, and immobile states. Furthermore, we identify the stochastic model that best describes each dynamic state. Additionally, we briefly discuss the transitions observed between these dynamic states.