If a protein folds in a hydrophobic environment such as the lipid bilayer of a cellular membrane, the folding process and driving forces differ significantly from those in aqueous environments due to the absence of bulk water and the distinct physical properties of the membrane.

Expected Effects on Protein Folding in a Hydrophobic Membrane Environment

• Reduced Role of the Hydrophobic Effect:
  In aqueous solution, the hydrophobic effect drives folding by causing hydrophobic amino acid side chains to cluster away from water, typically forming the protein's interior. In the lipid bilayer, which is itself hydrophobic, this driving force is largely absent because the hydrophobic side chains are already in a nonpolar environment and do not need to avoid water

• Formation of Stable Transmembrane Helices:
  The first stage of membrane protein folding involves insertion of polypeptide segments as transmembrane helices (TMHs) into the lipid bilayer. This insertion is driven primarily by the hydrophobic nature of the TMH amino acids and the energetic cost of exposing backbone hydrogen bonds in the membrane's nonpolar core

• Secondary Stage Driven by Van der Waals and Polar Interactions:
  After insertion, TMHs associate into a compact native structure mainly through van der Waals packing and polar interactions rather than the classical hydrophobic effect, since water is scarce in the bilayer core. This stage replaces the hydrophobic collapse seen in soluble proteins with different molecular forces

• Potential "Lipophobic Effect":
  Analogous to the hydrophobic effect in water, a "lipophobic effect" may promote coalescence of TM helices by driving them to associate and exclude lipids. However, this can also increase the risk of nonspecific aggregation and misfolding within the membrane, necessitating cellular quality control mechanisms such as chaperones and proteases

• Hydrophobic Matching and Membrane Thickness:
  The folding and packing of TM helices are influenced by hydrophobic matching- the alignment between the hydrophobic length of TM segments and the lipid bilayer thickness. Mismatches can affect helix packing and protein stability

• Reduced Side-Chain Entropic Cost:
  Membrane proteins may exhibit more dynamic side-chain motions in the bilayer interior, potentially lowering the entropic cost of folding compared to globular proteins in water

Summary

In a hydrophobic membrane environment, proteins do not fold by burying hydrophobic residues away from water but rather by inserting hydrophobic segments into the bilayer and then assembling via van der Waals and polar interactions. The lipid bilayer stabilizes the folded state differently than water, and folding efficiency is often lower with a higher risk of misfolding, necessitating cellular folding assistance

. Thus, the hydrophobic effect that drives folding in aqueous solution is replaced by membrane-specific forces, and the protein's hydrophobic side chains interact favorably with the lipid environment rather than being sequestered from it.