The importance of the membrane interface as the reference state for membrane protein stability

Abstract

The insertion of nascent polypeptide chains into lipid bilayer membranes and the stability of membrane proteins crucially depend on the equilibrium partitioning of polypeptides. For this, the transfer of full sequences of amino-acid residues into the bilayer, rather than individual amino acids, must be understood. Earlier studies have revealed that the most likely reference state for partitioning very hydrophobic sequences is the membrane interface. We have used µs-scale simulations to calculate the interface-to-transmembrane partitioning free energies ΔGS→TM for two hydrophobic carrier sequences in order to estimate the insertion free energy for all 20 amino acid residues when bonded to the center of a partitioning hydrophobic peptide. Our results show that prior single-residue scales likely overestimate the partitioning free energies of polypeptides. The correlation of ΔGS→TM with experimental full-peptide translocon insertion data is high, suggesting an important role for the membrane interface in translocon-based insertion. The choice of carrier sequence greatly modulates the contribution of each single-residue mutation to the overall partitioning free energy. Our results demonstrate the importance of quantifying the observed full-peptide partitioning equilibrium, which is between membrane interface and transmembrane inserted, rather than combining individual water-to-membrane amino acid transfer free energies.

Cotranslational recruitment of ribosomes in protocells recreates a translocon-independent mechanism of proteorhodopsin biogenesis

“…Our experiments with TM1 suggest that this N-terminal interaction also guides the insertion of the downstream helices of PR, which would otherwise tend to aggregate in the aqueous interior of GUVs. Previous studies have implicated the bilayer interface as an important chemical environment that facilitates the adoption of a-helical structure and subsequent partitioning of hydrophobic peptides into the bilayer interior (Ulmschneider et al, 2011(Ulmschneider et al, , 2018White et al, 2001). It is an intriguing possibility that the N-terminal hydrophobic regions of other membrane proteins beyond the rhodopsins also have a high affinity for ll OPEN…”

Rational tuning of a membrane-perforating antimicrobial peptide to selectively target membranes of different lipid composition

“…This is consistent to the experimental findings, and it demonstrates the extreme effect even tiny sequence changes can have on the pore forming equilibrium. Anionic sidechains are known for their steep insertion penalties, 88 so the reason for the lack of TM insertion likely is the shift of the 2 Asp residues one position towards the center of the peptide. The propensity of a peptide sequence to aggregate and assemble in a given environment depends in a highly complex and non-linear way on the its sequence.…”

How lipids affect the energetics of co-translational alpha helical membrane protein folding

“…For a range of peptides, transfer free energies for the spontaneous transition from interfacially bound to transmembrane state have been shown to be quantitatively similar to those measured for translocon-assisted peptide insertion [ 77 ]. This suggests that for both spontaneous and translocon-assisted insertion, the peptide transitions from an interfacially bound to transmembrane state — although presumably via different pathways [ 78 ]. It is therefore reasonable to hypothesise that the properties of the bilayer interface may affect both translocon-assisted and spontaneous insertion through similar mechanisms, and thus measurements on spontaneous insertion in vitro may give clues to the effects of lipids on membrane protein insertion in vivo .…”