Modelling antibody orientation at bacterial surfaces

Abstract: Bacteria and humans have co-evolved since their common existence. They have thereby developed very specific defence and target mechanisms against one another. Understanding the complex biomolecular processes behind these interactions can be of great use for developing treatments against bacterial diseases. The aim of this thesis project was to verify, and introduce a model for understanding, the implications of previous findings regarding the binding tendencies of antibodies to bacterial surface proteins. Antibodies typically bind to substances foreign to the host via regions referred to as Fab, exposing the Fc region that can then be recognized by the immune system. However, certain bacterial proteins express a so called IgGFc-binding region enabling additional binding via Fc. This can prevent these bacteria from being recognized and eliminated from the host organism. The goal of this model was to calculate the binding orientation probability of antibodies at bacterial surfaces. The binding probability was calculated for S types of antibodies characterized by their concentration c and binding constant K to a specific site i on the bacterial protein of length N . Transfer matrices, describing the probability of site i being in a certain state m, provided site i + 1 is in state m0 , were generated. Each antibody was ascribed a binding constant from a gaussian distribution of standard deviation σ and mean value KD . Additional experiments were performed in order to confirm whether or not the previous experimental findings were reproducible. The model was found to best fit the experimental values for the parameters σ = 45 (µg/ml)−1 and mean KD = 140 (µg/ml)−1 . The dissociation constant for the Fc binding region was determined to be 1500 (µg/ml)−1 Both our experimental and theoretical results imply that bacterial proteins with a IgGFc-binding region effectively reduce the amount of Fab-binding. The theoretically obtained values were consistent with the measured experimental values. This model incorporated many important aspects of the antibody-bacterial protein binding system and was an improvement from the previous model. However, in order to draw any general conclusions about the model it is necessary to perform additional experiments with a higher level of precision.