In this blog post, we will take a closer look at the protein folding process, the occurrence of denatured proteins, and their effects on cells.
When multiple amino acid molecules are connected in succession, they form a long, string-like chain structure. We call these chains polypeptides. These polypeptides do not simply exist in a straight line, but rather fold, bend, and roll up like paper or string to form a three-dimensional structure. This structuring process is called protein folding, and polypeptides with three-dimensional structures completed through folding are finally called “proteins.”
Proteins are extremely important biological macromolecules that are responsible for the structure and function of living organisms. Each protein must form its own precise and complex three-dimensional structure in order to perform its unique biological role, and only when this structure is properly formed can it function properly. If the structure is formed incorrectly, the protein will not only fail to perform its original function, but may even have a harmful effect on the cell.
The process of protein production is one of the complex life activities within cells, involving the organic interaction of various cell organelles and proteins. Among these, proteins called ribosomes and chaperones play particularly important roles. Ribosomes connect amino acids in sequence according to the base sequence of mRNA transcribed from DNA, which is genetic information transmitted from the cell nucleus.
In this way, a polypeptide is synthesized, and this process takes place actively in the cytoplasm or endoplasmic reticulum. Thus, ribosomes are the starting point of protein synthesis and can be considered important protein factories that produce the basic units of life. However, proteins are not completed simply by ribosomes connecting amino acids in series.
The polypeptides just synthesized in the ribosome are not yet capable of performing their functions and must undergo a folding process to form the appropriate three-dimensional structure before they can function as true proteins. Some polypeptides fold naturally on their own, but many are difficult to fold spontaneously or are likely to fail, so the help of chaperones is essential.
Chaperones are “molecular assistants” that help polypeptides form complex and accurate three-dimensional structures, acting like skilled folding experts. They prevent incorrect folding, prevent structures from becoming unstable during intermediate stages, and ultimately help them acquire structures that function properly. There are many types of chaperones in cells, and each chaperone specializes in a specific polypeptide. This specificity and diversity enable precise quality control for each of the many types of proteins produced by cells.
However, folding is not always perfect. In some cases, polypeptides fail to fold normally and become entangled, forming aggregates. These aggregates not only interfere with protein function but can also cause toxicity to cells. In particular, when cells are subjected to external stresses such as heat shock, heavy metal ions, or toxic chemicals, abnormalities are likely to occur in the folding process of proteins or in the structure of proteins that have already been folded.
Under such stressful conditions, proteins may undergo misfolding, in which they fold into abnormal structures, or unfolding, in which their already formed three-dimensional structures are completely unraveled. Proteins with such structural abnormalities are called denatured proteins, which means that they can no longer perform their functions.
Denatured proteins often change into a form in which the hydrophobic amino acids inside are exposed to the outside. These hydrophobic parts have low affinity for water and tend to bind strongly to other protein molecules in their vicinity.
As a result, multiple denatured proteins interact and aggregate to form protein clumps that are poorly soluble in water, called aggregates. These aggregates can act like toxic substances within cells and are often associated with degenerative diseases and cellular dysfunction. Furthermore, once formed, aggregates are mostly irreversible and cannot be easily restored to their original state.
However, if appropriate measures are taken before aggregation occurs completely, it is possible for denatured proteins to return to their original structure. This recovery process is called refolding, and is usually aided by chaperones. However, it is known that some refolding is possible without chaperones under laboratory conditions, and this is being used to conduct various studies on protein structure and stability.
Cells do not leave misfolded or denatured proteins unattended, but manage them through a thorough quality control system. Cells have a complex and sophisticated system that is responsible for everything from protein production to folding, recovery, and final degradation, and this system plays an essential role in maintaining cell survival and health.
Among them, the endoplasmic reticulum is the central organ that performs protein folding and quality control functions. However, excessive accumulation of denatured proteins inside the endoplasmic reticulum places a heavy burden on the endoplasmic reticulum, causing endoplasmic reticulum stress. This stress can have serious effects on cells, so cells try to resolve it through various mechanisms.
First, when endoplasmic reticulum stress is detected, a protein called ATF6 is activated to promote the production of chaperones. This enhances refolding activity to restore denatured proteins to normal proteins. However, proteins that fail to refold or cannot be restored to their original structure are degraded by the activation of IRE1 and XBP-1. In this process, the problematic proteins are transported back to the cytoplasm and then degraded through the ubiquitin-proteasome pathway. This pathway is the intracellular protein disposal system, which marks defective proteins with a tag called ubiquitin and then degrades them to maintain intracellular homeostasis.
If the endoplasmic reticulum stress persists even after this refolding and degradation system has been activated, the cell will initiate a more powerful defense mechanism. This involves the activation of a protein called PERK, which phosphorylates and inactivates eIF2α, a protein synthesis initiation factor. As a result, protein synthesis in the ribosome is suspended, and the production of new proteins is reduced. This can be seen as a kind of “emergency brake” that prevents the accumulation of additional denatured proteins by stopping the cell from producing new proteins.
In this way, cells monitor and manage protein quality in various ways and constantly strive to maintain balance. However, if the accumulation of denatured proteins does not stop and the refolding and degradation mechanisms are ineffective, the cells make their final choice. This is the activation of a biological program called apoptosis, or cell suicide. Apoptosis is a self-protective mechanism of living organisms in which damaged cells choose to die on their own to prevent further damage to surrounding cells and tissues.
