Effect of a nonuniform external mechanical load on high density lipoprotein (HDL) in aqueous medium was investigated using course-grained molecular dynamics simulations. The nonuniform load was achieved by a few layer graphene on one side and closed single-walled carbon nanotube (SWNT) (7, 7) on the opposite side of lipoprotein. The tube had a diameter of 1 nm and was oriented perpendicularly to the graphene. HDL was located between them. The tube was approaching to HDL on graphene deforming it. We considered two cases of the tube movement with velocities of 20 and 5 m/s. Coarse-grained (CG) molecular dynamics with application of the MARTINI force field for HDL and coarse-grained model with an all-atom (AA)/CG mapping ratio of 1.5 for carbon nanotube (CNT) (each CG bead was modeled by the 4-site CG benzene) were used. Coarse-grained model of HDL was received by method of self-assembly. HDL was static but not fixed that gave the possibility to compensate its external influence in some way. It was established that in water medium HDL interacted with graphene substrate. It was established that in water HDL interacts with graphene substrate, slightly flattening but retaining its shape of the whole. It was also observed that during the calculations HDL partially dodged nanotube. Lipoprotein belts unfolded on the graphene substrate in the way of the best compensation for the impact of nanotubes. Finally, we observed that the approaching tube has passed through the less dense medium of dipalmitoylphosphatidylcholine (DPPC) and its pressure on the macromolecule decreased. Inhomogeneity of the external exposure deformed HDL at approximately 10-50%. The character of deformation demonstrated that lipoprotein has viscoelastic properties similar to a fluid. The discovered ability of lipoprotein may help to establish mechanism of interaction of lipoproteins with arterial walls and dynamic behavior of lipoproteins in arterial intima.