The endoplasmic reticulum (ER) is a major protein folding compartment for s
ecreted, plasma membrane and organelle proteins. Each of these newly-synthe
sized polypeptides folds in a deterministic process, affected Ey the unique
conditions that exist in the ER. An understanding of protein folding in th
e ER is a fundamental biomolecular challenge at two levels. The first level
addresses how the amino acid sequence programs that polypeptide to efficie
ntly arrive at a particular fold Out Of a multitude of alternatives, and ho
w different sequences obtain similar folds. At the second level are the iss
ues introduced by folding not in the cytosol, but in the ER, including the
risk of aggregation in a molecularly crowded environment, accommodation of
post-translational modifications and the compatibility with subsequent intr
acellular trafficking. This review discusses both the physicochemical and c
ell biological constraints of folding, which are the challenges that the ER
molecular chaperones help overcome.