Protein folding in a cell is a highly complex process that involves transport of the newly synthesized proteins to appropriate cellular compartments through targeting, permanent misfolding, temporarily unfolded states, post-translational modifications, quality control, and formation of protein complexes facilitated by chaperones.   
Some proteins need the assistance of chaperone proteins to fold properly. It has been suggested that this disproves Anfinsen's dogma. However, the chaperones do not appear to affect the final state of the protein; they seem to work primarily by preventing aggregation of several protein molecules prior to the final folded state of the protein. However, at least some chaperones are required for the proper folding of their subject proteins.
Many proteins can also undergo aggregation and misfolding. For example, prions are stable conformations of proteins which differ from the native folding state. In bovine spongiform encephalopathy, native proteins re-fold into a different stable conformation, which causes fatal amyloid buildup. Other amyloid diseases, including Alzheimers disease and Parkinsons disease, are also exceptions to Anfinsen's dogma.
Some proteins have multiple native structures, and change their fold based on some external factors. For example, the KaiB protein complex switches fold throughout the day, acting as a clock for cyanobacteria. It has been estimated that around 0.5&ndash;4% of PDB proteins switch folds. The switching between alternative structures is driven by interactions of the protein with small ligands or other proteins, by chemical modifications (such as phosphorylation) or by changed environmental conditions, such as temperature, pH or membrane potential. Each alternative structure may either correspond to the global minimum of free energy of the protein at the given conditions or be kinetically trapped in a higher local minimum of free energy.