In this thesis, Martini coarse-grained simulations were performed to investigate the dynamic behavior of lipids and proteins in two different membrane-protein systems. In the first study, I simulated a chromatophore membrane. The model consists of the cytochrome-bc1 from Rhodobacter sphaeroides embedded in an asymmetric distribution of three lipid species. Analyses of a simulation carried out over 40 microseconds highlight specific lipid-protein interactions that are of biological relevance for ongoing research. The second study works towards the modeling of biological membranes at a larger scale. We developed a protocol to build and simulate complex models more representative of physiological membranes, in terms of crowdedness of proteins and lipid diversity. Several eukaryotic plasma membrane models were generated. Analyses of a system consisting of 150 proteins with more than 60 lipid species and simulated for 6 microseconds are discussed.