Analysis of single-molecule diffusion movement in cell membrance based on unsupervised learning methods: Different effects of cholesterol on flowability of model membrane and living cell membrane

Abstract

<sec>Single molecular tracking is a valuable approach to investigating the dynamic processes and molecular interactions in soft matter systems, particularly in biological systems. However, understanding the complexity of single molecule motion behaviors in biological systems remains a significant challenge. To address this issue, we propose a two-step classification method based on unsupervised learning to efficiently identify and classify single molecule trajectories. Firstly, we employ an entropy-constrained least square method to distinguish between confined diffusion trajectory (e.g., immobile) and unconfined diffusion trajectory. Subsequently, statistical tests are utilized to categorize the unconfined trajectories into different diffusion modes such as sub-diffusion, normal diffusion, and super-diffusion.</sec><sec>By applying this method, we analyze the diffusion motion of single molecules in both DOPC model cell membranes and living cell membranes while uncovering their distinct responses to cholesterol composition. Our findings demonstrate that both model membranes and living cell membranes exhibit diverse molecular diffusion modes. Specifically, in the DOPC model membrane system, the presence of cholesterol components impedes lipid diffusion within the membrane. The degree of inhibition is positively correlated with the amount of cholesterol present. For instance, as the cholesterol content in the membrane increases from 0 to 20% (DOPC:Chol = 4:1) and 50% (DOPC:Chol = 1:1), there is an increase in the proportion of molecules, exhibiting confined diffusion and sub-diffusion (from 55% to 45%), while there is a decrease in the proportion of molecules, displaying normal diffusion and super-diffusion (from 45% to 35%). The ensemble diffusion coefficient of molecules in the membrane significantly decreases, which can be attributed to both a decrease in velocity among fast-moving molecules. Interestingly, after using MeβCD to remove cholesterol, the single-molecule mobility within the DOPC/Chol composite membrane system is restored to a level similar to that of the pure DOPC membrane.</sec><sec>Conversely, in the living cell membrane system, the diffusion coefficient values of molecules are significantly lower than those observed in the model membrane system; furthermore, the removal of cholesterol further slows down the molecular diffusion rate. This study contributes to understanding the intricacies of biomolecular motility and its dependence on environmental factors from a perspective of single molecular motion.</sec>