I work on a membrane protein that dimerizes in the presence of certain lipids. We know this from cryoEM structure. I run clear native and BN-PAGE with and without lipids. Some lipids including the one structurally confirmed make the dimer, but dimer runs below the monomer of on both gels. I understand that in clear native PAGE dimer might have different charges and lipid influence the mobility too but in BN-PAGE charges are shielded by Coomassie G250. BN-PAGE should run based on relative molecular weight. Can someone explain why still the apparent dimer runs lower?