Voortgezette Celbiologie Evelien Floor
Protein folding in the
endoplasmic reticulum
Proteins
The amino acid sequence of a protein’s polypeptide chain is called its primary structure. Different
regions of the sequence form local regular secondary structures, such as alpha helices or beta
strands. The tertiary structure is formed by packing such structural elements into one or several
compact globular units called domains. The final proteins may contain several polypeptide chains
arranged in a quaternary structure. By formation of such tertiary and quaternary structure, amino
acids far apart in the sequence are brought close together in three dimensions to form a functional
region, an active site. There is not a single protein that works alone in the cell.
Protein synthesis starts in the endoplasmic reticulum. The C=O bonds are
essential for the secondary structure. They can form antiparallel or parallel
beta-sheets. An antiparallel beta-sheets bonds are straight and thus the beta
sheet is tighter than the parallel beta-sheet. Formation of an alpha-helix can
happen much quicker than the formation of a beta-sheet.
Interactions needed for protein folding:
Van der Waals interactions
Electrostatic interactions
H-bonds
Hydrophilic and hydrophobic side chains interact with each other in a way that
the hydrophobic chains are on the inside and the hydrophilic on the outside.
Globular proteins are usually soluble proteins. There are plenty of H-bonds in a
single protein. H-bonds are stronger than Van der Waals interactions. An
unfolded protein is not necessarily unstable, it can also interact with water.
Protein folding
Proteins are folding all the time, but they
should not be folding. A protein of 101
amino acids contains of 100 bonds. There
are 3 conformations possible per bond. A
protein of 101 amino acids has 3100
conformations. This led to the conclusion
that protein folding has to be directed, it
can never be through random sampling:
folding pathways. Folding would
otherwise need many years longer than
the universe exists.
A newly synthesized protein will fold
multiple times until its native state.
Chaperones help the protein fold
afterwards, but they also prevent
unwanted interactions between unfolded
proteins. Amyloids are super stable beta
sheets, it is impossible to unfold this kind
of proteins.
1
, Voortgezette Celbiologie Evelien Floor
The difference of in vitro refolding and in vivo folding is that in vitro
refolding does not form disulfide bonds. In vivo folding happens co-
translationally, during synthesis. In vitro folding happens when the
whole protein is already synthesized. The in vitro refolding studies
work with low temperatures and diluted conditions. This is very
different than the conditions in vivo.
Proteins have a high chance of aggregation with other molecules
because they have a large interaction surface. Domain swapping: the swapping of mature structure
between two molecules. A cell is very crowded with a lot of proteins. Therefore, it is impossible to
make the same conditions in a test tube as it is in vivo. However, when you limit the amount of space
around a newly synthesized protein you limit the chance of aggregation and you help the protein
folding. With little space a protein will fold faster. The information of a protein how to fold is in the
sequence. It’s like the second genetic code.
Protein folding diseases
Disease Protein involved Molecular phenotype
Loss of function folding diseases (misfolding, with consequences for localization)
Scurvy (vitamin C deficiency) Collagen Misfolding and wrong localization
Cystic fibrosis CFTR
Familial hypercholesterolemia LDL receptor
Alpha-1-antitrypsin deficiency alpha-1-antitrypsin
Tay-Sachs disease beta-hexosaminidase
Gaucher disease glucocerebrosidase
Osteogenesis imperfecta Type I procollagen
Retinitis pigmentosa Rhodopsin
Marfan syndrome Fibrillin Misfolding
Cancer p53
Amyotrophic lateral sclerosis Superoxide dismutase
Gain of function folding diseases (toxic folds) this are diseases that are caused by the formation
of fibrils and amyloids
Scrapie/Creutzfeld-Jakob/BSE Prion protein Fibrils/amyloid
Alzheimer’s disease beta-amyloid
Huntington’s disease Huntingtin
Parkinson’s disease alpha-synuclein
Familial amyloidosis Transthyretin/lysozyme
Cataracts Crystallins
Amyotrophic lateral sclerosis Superoxide dismutase
The ER as protein folding factory
Almost all protein synthesis is co-translational and happens in the ER. The ER is completely filled with
chaperones, so the newly synthesized protein is welcomed by a lot of other proteins. Because of the
surrounding the chance of aggregation is limited. Besides that, there is quality control in the ER,
chaperones hold proteins that are not folded properly yet. Unfolded proteins are transported back
from the Golgi to the ER with retrograde transport. The unfolded protein response (UPR) in the ER is
causing degradation of those proteins.
The formation of glycoproteins starts in the ER, once the first sugar groups are added the protein
travels to the Golgi. In the Golgi the sugar groups are glycosylated by N-glycan modifying enzymes. N-
linked glycosylation is very important for protein folding because chaperones bind to the sugar
group. A mutated protein to which no sugar groups can be added will not move to the Golgi.
2
Protein folding in the
endoplasmic reticulum
Proteins
The amino acid sequence of a protein’s polypeptide chain is called its primary structure. Different
regions of the sequence form local regular secondary structures, such as alpha helices or beta
strands. The tertiary structure is formed by packing such structural elements into one or several
compact globular units called domains. The final proteins may contain several polypeptide chains
arranged in a quaternary structure. By formation of such tertiary and quaternary structure, amino
acids far apart in the sequence are brought close together in three dimensions to form a functional
region, an active site. There is not a single protein that works alone in the cell.
Protein synthesis starts in the endoplasmic reticulum. The C=O bonds are
essential for the secondary structure. They can form antiparallel or parallel
beta-sheets. An antiparallel beta-sheets bonds are straight and thus the beta
sheet is tighter than the parallel beta-sheet. Formation of an alpha-helix can
happen much quicker than the formation of a beta-sheet.
Interactions needed for protein folding:
Van der Waals interactions
Electrostatic interactions
H-bonds
Hydrophilic and hydrophobic side chains interact with each other in a way that
the hydrophobic chains are on the inside and the hydrophilic on the outside.
Globular proteins are usually soluble proteins. There are plenty of H-bonds in a
single protein. H-bonds are stronger than Van der Waals interactions. An
unfolded protein is not necessarily unstable, it can also interact with water.
Protein folding
Proteins are folding all the time, but they
should not be folding. A protein of 101
amino acids contains of 100 bonds. There
are 3 conformations possible per bond. A
protein of 101 amino acids has 3100
conformations. This led to the conclusion
that protein folding has to be directed, it
can never be through random sampling:
folding pathways. Folding would
otherwise need many years longer than
the universe exists.
A newly synthesized protein will fold
multiple times until its native state.
Chaperones help the protein fold
afterwards, but they also prevent
unwanted interactions between unfolded
proteins. Amyloids are super stable beta
sheets, it is impossible to unfold this kind
of proteins.
1
, Voortgezette Celbiologie Evelien Floor
The difference of in vitro refolding and in vivo folding is that in vitro
refolding does not form disulfide bonds. In vivo folding happens co-
translationally, during synthesis. In vitro folding happens when the
whole protein is already synthesized. The in vitro refolding studies
work with low temperatures and diluted conditions. This is very
different than the conditions in vivo.
Proteins have a high chance of aggregation with other molecules
because they have a large interaction surface. Domain swapping: the swapping of mature structure
between two molecules. A cell is very crowded with a lot of proteins. Therefore, it is impossible to
make the same conditions in a test tube as it is in vivo. However, when you limit the amount of space
around a newly synthesized protein you limit the chance of aggregation and you help the protein
folding. With little space a protein will fold faster. The information of a protein how to fold is in the
sequence. It’s like the second genetic code.
Protein folding diseases
Disease Protein involved Molecular phenotype
Loss of function folding diseases (misfolding, with consequences for localization)
Scurvy (vitamin C deficiency) Collagen Misfolding and wrong localization
Cystic fibrosis CFTR
Familial hypercholesterolemia LDL receptor
Alpha-1-antitrypsin deficiency alpha-1-antitrypsin
Tay-Sachs disease beta-hexosaminidase
Gaucher disease glucocerebrosidase
Osteogenesis imperfecta Type I procollagen
Retinitis pigmentosa Rhodopsin
Marfan syndrome Fibrillin Misfolding
Cancer p53
Amyotrophic lateral sclerosis Superoxide dismutase
Gain of function folding diseases (toxic folds) this are diseases that are caused by the formation
of fibrils and amyloids
Scrapie/Creutzfeld-Jakob/BSE Prion protein Fibrils/amyloid
Alzheimer’s disease beta-amyloid
Huntington’s disease Huntingtin
Parkinson’s disease alpha-synuclein
Familial amyloidosis Transthyretin/lysozyme
Cataracts Crystallins
Amyotrophic lateral sclerosis Superoxide dismutase
The ER as protein folding factory
Almost all protein synthesis is co-translational and happens in the ER. The ER is completely filled with
chaperones, so the newly synthesized protein is welcomed by a lot of other proteins. Because of the
surrounding the chance of aggregation is limited. Besides that, there is quality control in the ER,
chaperones hold proteins that are not folded properly yet. Unfolded proteins are transported back
from the Golgi to the ER with retrograde transport. The unfolded protein response (UPR) in the ER is
causing degradation of those proteins.
The formation of glycoproteins starts in the ER, once the first sugar groups are added the protein
travels to the Golgi. In the Golgi the sugar groups are glycosylated by N-glycan modifying enzymes. N-
linked glycosylation is very important for protein folding because chaperones bind to the sugar
group. A mutated protein to which no sugar groups can be added will not move to the Golgi.
2
