Atherosclerosis is the primary trigger for severe pathologies. The atherosclerotic inflammatory process is well known after low-density lipoprotein (LDL) adhesion in blood vessel walls, however, limited information exists regarding LDL penetration into subendothelial layers. Here, we propose for the first time, to the best of our knowledge, the pathway for the initial trajectory of the lipid molecules internalization into the arterial endothelial tissue. The investigation shows a computational model analyzing molecules involved in the atherosclerotic process, specifically LDL and molecules of the vascular endothelium. The theoretical model was experimentally tested using carrageenan to simulate the anionic counterparts of vascular tissue and amino acids from apolipoprotein B-100. The molecular interactions were analyzed by conductimetric titration, FTIR, and rheology. The computational model identified potential amino acids involved in the process, and the experimental results demonstrated the interaction between lysine and polymer, as the mechanism of adhesion, confirming the model.