Modeling pathogen AMP evasion

In this project, an antimicrobial peptide (AMP) evasion mechanism is modeled and simulated. This mechanism, which we refer to as spatial distancing, consists of a pathogen cell secreting defense molecules that can bind to AMP and form complexes with the highest concentration close to the cell surface that diffuse away from the pathogen. As a result, AMP are transported away from the pathogen’s surface, effectively protecting it from the immune attack by AMP.

The modeling of spatial distancing, where pathogens secrete defense molecules that bind AMPs to diffuse them away is important to understand the meachnism.

Visualization of the system. The model is simulated as a three-dimensional cube, with the pathogen cell (yellow) modeled as a sphere centered in the environment. AMP (blue), defense molecule (red), and complexes (purple) molecules diffuse and interact with each other as well as with the pathogen cell in the extracellular space.

To gain a comprehensive understanding of spatial distancing, we simulate a pathogenic cell in a three-dimensional environment with molecule concentrations modeled by partial differential equations. Two different scenarios are simulated, respectively, representing AMPs secreted by immune cells and AMPs administered for medical treatment. Spatial distancing was then applied and studied in the case of the human-pathogenic fungus Candida albicans.

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