Packing of apolar amino acids is not a strong stabilizing force in transmembrane helix dimerization

Abstract The factors that stabilize the folding and oligomerization of membrane proteins are still not well understood. In particular, it remains unclear how the tight and complementary packing between apolar side chains observed in the core of membrane proteins contributes to their stability. Complementary packing is a necessary feature since packing defects are generally destabilizing for membrane proteins. The question is the extent by which packing of apolar side chains – and the resulting van der Waals interactions – are a sufficient driving force for stabilizing the interaction between transmembrane helices in the absence of hydrogen bonding and polar interactions. We addressed this question with an approach based on high-throughout protein design and the homodimerization of single-pass helices as the model system. We designed hundreds of transmembrane helix dimers mediated by apolar packing in the backbone configurations that are most commonly found in membrane proteins. We assessed the association propensity of the designs in the membrane of Escherichia coli and found that they were most often monomeric or, at best, weakly dimeric. Conversely, a set of controls designed in the backbone configuration of the GAS right motif, which is mediated by weak hydrogen bonds, displayed significantly higher dimerization propensity. The data suggest that packing of apolar side chains and van der Waals interactions may be a relatively weak force in driving transmembrane helix dimerization, unless highly optimized. It also confirms that GAS right is a special configuration for achieving stability in membrane proteins. Statement of Significance The proteins that insert into the cellular membranes provide the cell with essential functionalities. However, how nature designed these proteins to fold into a precise conformation and become active is still poorly understood. In this article we investigate the role of one of the most important factors for protein folding, the van der Waals forces that produce favorable interactions when atoms are in close contact. We know that the formation of extensive van der Waals interactions through contacts are critical for proteins to be stable but we do not know if they are a strong driving force for folding a membrane protein. We addressed this question by designing hundreds of new membrane proteins design based on the optimization of these interatomic contacts and measuring if the resulting proteins come together to form stable pairs. The data suggest that the packing of apolar side chains and the resulting van der Waals interactions are not a strong force for supporting folding in the membrane.