Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.

Broadly, these modifications can be categorized into four main categories — glycosylation, formation of disulfide bonds, assembly of protein subunits, and specific proteolytic cleavages like removal of signal sequences.

N-linked glycosylation of proteins

Almost half of the membrane and soluble proteins that transit via the rough ER are converted to a glycoprotein by the covalent addition of carbohydrate moieties, making it the most common ER modification. The oligosaccharide is attached to the asparagine residues of the tripeptide sequences Asn-X-Ser and Asn-X-Thr, where X can be any amino acid, except proline. The oligosaccharyltransferase membrane complex can catalyze glycosylation during cotranslational as well as post-translational protein translocation.

Glycosylation alters inherent physical properties of the protein. For instance, N-linked glycoproteins have improved thermodynamic kinetics and fold better as compared to their non-glycosylated counterparts. Glycosylation also increases protein stability by masking cleavage sites and hydrophobic stretches. Additionally, resident ER chaperones like BiP and lectins use the polypeptide glycosylation status to assess the correctness of protein folding before clearing it for exit from the ER.

Disulfide bonding of polypeptide chains

Disulfide bond formation is favored in an oxidizing environment and is formed predominantly in the rough ER lumen. However, a small fraction of disulfide bonds can form in the mitochondrial intermembrane space.

Protein disulfide isomerase (PDI) is the most abundant and best characterized oxidoreductase in the ER lumen. While the oxidized PDI forms disulfide linkage between cysteine residues, the reduced PDI acts as a proofreader, correcting inappropriately paired cysteine residues by rearranging the disulfide linkage. ER oxidoreductase 1, or Ero1, utilizes a significant fraction of molecular oxygen available in the cell to recycle oxidized PDI and generate hydrogen peroxide. Both PDI and Ero1 are responsible for the oxidative folding of proteins and maintaining redox homeostasis inside the ER.