Specificity in transmembrane helix–helix interactions can define a hierarchy of stability for sequence variants

Abstract

The folding, stability, and oligomerization of helical membrane proteins depend in part on a precise set of packing interactions between transmembrane helices. To understand the energetic principles of these helix-helix interactions, we have used alaninescanning mutagenesis and sedimentation equilibrium analytical ultracentrifugation to quantitatively examine the sequence dependence of the glycophorin A transmembrane helix dimerization. In all cases, we found that mutations to alanine at interface positions cost free energy of association. In contrast, mutations to alanine away from the dimer interface showed free energies of association that are insignificantly different from wild-type or are slightly stabilizing. Our study further revealed that the energy of association is not evenly distributed across the interface, but that there are several ''hot spots'' for interaction including both glycines participating in a GxxxG motif. Inspection of the NMR structure indicates that simple principles of protein-protein interactions can explain the changes in energy that are observed. A comparison of the dimer stability between different hydrophobic environments suggested that the hierarchy of stability for sequence variants is conserved. Together, these findings imply that the protein-protein interaction portion of the overall association energy may be separable from the contributions arising from protein-lipid and lipid-lipid energy terms. This idea is a conceptual simplification of the membrane protein folding problem and has implications for prediction and design. G enome sequencing efforts reveal that approximately 20% of ORFs in complex organisms may encode proteins containing at least one helical transmembrane segment (1). Despite these numbers, as well as the fact that membrane proteins carry out many essential cell functions, our understanding of the sequence-structure-function relationships for this class of proteins lags far behind that of soluble proteins. These realities underscore the importance of biophysical and structural work aimed toward understanding chemical principles of helical membrane protein structural stability.Because the phospholipid bilayer places structural constraints on a helical membrane protein, the folding of a polypeptide sequence into a helical membrane protein can be considered, experimentally and theoretically, in separable thermodynamic steps (2, 3). The usefulness of this framework arises from the fact that individual energetic processes can be independently studied. The principal features of a polypeptide sequence that will give rise to the formation of an independently stable transmembrane ␣-helix are generally known (3). This information has been used extensively in computational search algorithms with reasonable accuracy rates to identify potential helical transmembrane proteins (reviewed in ref.3). Once this is accomplished, however, the helical membrane protein folding problem then becomes focused on understanding and predicting the side-to-side associations in which these...

The Affinity of GXXXG Motifs in Transmembrane Helix-Helix Interactions Is Modulated by Long-range Communication

“…The solution NMR structure of GpA further confirmed how the presence of the two Gly residues in the interface can facilitate the close approach of helices, thereby allowing extensive backbone-backbone and side chain-side chain interactions to occur (12). Analytical ultracentrifugation experiments have shown that mutation of any interfacial position along the GpA-TM to Ala is energetically costly (42). This is most significantly pronounced with Gly 79 and Gly 83 , where the dimer is destabilized by 1.7 and 3.2 Kcal/mol, respectively.…”

The Mitochondrial Citrate Transport Protein

“…Interestingly, with the exception of Arg 110 , each of these charged residues is conserved among CTPs of widely divergent origin (11). Second, the amino-terminal segment of TMDIII contains the dimerization consensus sequence 115 GXXXG 119 , which is thought to be involved in formation of a high affinity association between transmembrane domains (15)(16)(17)(18)(19) and is conserved among CTPs (11). Importantly, we have demonstrated by two different approaches that the CTP exists as a homodimer in solution (13).…”

Structural differences between thermophilic and mesophilic membrane proteins

“…[8][9][10][11][12] Although most hydrogen-bonded sidechain interactions that have been experimentally measured in membrane proteins appear to make relatively modest contributions, [21][22][23][24][25][26][27] some have been measured as high as 1.8 kcal/mol and in theory it is possible that they could be made even stronger. 26,28 Thus, it seems reasonable to expect that the number of transmembrane interhelical hydrogen bonds might increase in thermophiles.…”