Structural Biochemistry/Proteostasis

Is the term referring to "protein homeostasis" where a system of biological pathways leads to proper protein function. The system is called a proteostasis network, which will be responsible for successful protein transport, proper folding of proteins, and elimination of misfolded proteins. The factors responsible for in improper protein function are genetic diseases and environmental stress. More knowledge of the proteostasis network is still in need for development but researchers have studied some of the pathways to create pharmaceutical agents and provide therapy for such protein abnormalities. The pharmaceutical agents used to modify the network pathways are called protein regulators which affect a pathway in a specific manner. For example, the antibiotic geldanamycin is known to act as an inhibitor for the chaperone protein HSP90. The HSP90 chaperone is involved in network pathways for protein folding, the success of HSP90 in assisting protein folding results in cell proliferation. Cancer cells are more sensitive to HSP90 inhibitors, consequently, by using geldanamycin as a protein regulator to inhibit HSP90 function will lead to cancer cell death. More research on the effects of HSP90 inhibitors is still done to propose a therapeutic treatment for cancer. Although the number of pathways involved in protein regulation is great, detailed study of these pathways will result in a successful treatment to ensure proteostasis.

Some diseases that can be caused by protein homeostasis are Parkinson’s, Alzheimer’s and cystic fibrosis. These diseases can occur as the results of the proteostasis network’s decreased ability to cope with misfolding prone proteins, aging, or environmental stress.

The protein homeostasis network and its networks are also controlled by integrated signaling pathways. These signaling pathways have the ability to maximize the capacity of the network in order to ensure consistent and correct protein function. Some examples of signal pathways include those that regulate protein synthesis, aggregation, as well as the degradative pathways of proteostasis.

Managing Proteostasis
For the proteostasis network to function correctly and in a stable condition, there are many interactions that help monitor and facilitate the process of successful protein folding.

1.	The proteostasis network is made up of ribosomes, chaperons, aggregases, and disaggregases that control protein folding. There are also special pathways like the ubiquitin-proteasome system, endoplasmic reticulum-associated degradation systems, proteases, autophagic pathways, etc. that deal with the degradation of proteins.

2.	There are the signaling pathways like mitochondria, aging, heat shock response, and unfolding protein response that affect the process of protein folding within the proteostasis network. This is perhaps the most direct influence that can alter the folding and stability of the proteins.

3.	Outside influences include metabolities, physiological stress, genetics, and epigenetics that affect the overall activity of the proteostasis network. These influences can also alter the process of protein folding but some, like metabolites and physiological stress, can be prevented by the use of pharmacological chaperones and proteostasis regulators.

Within the cell the surroundings are compacted with many compartments and the lack of space triggers aggregation. Aggregation is related to the levels of toxicity and has to be balanced most importantly when the cell deals with stresses that are chemical, physical and metabolically related.

The overall energy of a protein is impacted by the folding aspect of the proteostasis network. The energy level of a protein achieves a good distribution by utilizing folding enzymes and chaperones to decrease the aggregation and improve folding. Chaperones and enzymes that help fold attach to the intermediate molecules and transition state.

The state and functionality of the proteostasis network directly influences the protein’s functional performance and proteins usually acquire intracellular help for protein folding.

Pharmacologic Chaperones and Proteostasis Regulators
The proteostasis, as the “protein homeostasis”, must maintain a stable level of activity in order to function correctly within a cell. The proteostasis boundary refers to the folding energies that the protein must have in order to achieve some level of functionality in a given proteostasis network. This proteostasis boundary can be regulated by both pharmacologic chaperones and proteostasis regulators. By regulation, the proteostasis boundary can be expanded to envelop destabilized protein (known as the node) by proteostasis regulators or pharmacologic chaperones can move the node from outside of the proteostasis boundary to the inside in order to stabilize the node. If the proteostasis boundary is not regulated, there will be loss-of-function misfolding diseases, which could create potential life-threatening diseases.

The pharmacologic chaperones (otherwise known as the PCs) perform its regulation by binding to the outside destabilized node in order to stabilize it. After binding to the node, the PCs can move the now stabilized protein inside the proteostasis boundary, which then increases the function within the proteostasis, maintaining a stable level of activity. This stability then translates to less misfolding diseases. The PCs can correct a misfolding disease in three ways:

1.	The destabilized node can be thermodynamically stabilized

2.	The folding rate of the node can be increased in order to stabilize the transition state of folding

3.	Decrease the misfolding rate by stabilizing the native state

On the other hand, the use of proteostasis regulators (known as PRs) allow for an expansion of the proteostasis boundary for a number of destabilized nodes (as long as the nodes all share the same proteostasis network). By expanding the proteostasis boundary, the PRs can favor folding of the proteins by adjusting composition, concentration, and capacity of the proteostasis network. Besides promoting a stable proteostasis for proteins to fold correctly, PRs can also prepare the proteostasis network to handle metabolic stress and aging. The expansion of the proteostasis boundary helps increase the protective capacity of the proteostasis, hence expanding helps prepare for future abuse.

The overall energy of a protein is impacted by the folding aspect of the proteostasis network. The energy level of a protein achieves a good distribution by utilizing folding enzymes and chaperones to decrease the aggregation and improve folding. Chaperones and enzymes that help fold attach to the intermediate molecules and transition state. Binding to the transition state helps stabilize the protein so that there is a decrease in wrong folding and aggregation.

Chaperones help encourage more folding and also plays a role of preservation in the cell due to increasing correct folding and decreasing aggregation and wrong folding. Chaperones are understood as a large molecule that attaches to exterior hydrophobic areas during aggregated mode. Chaperones are specific and different for different compartments.

In all, the use of pharmacologic chaperones and proteostasis regulators both aid the proteostasis network in preventing numerous loss-of-function misfolding diseases. However, the advantages of using either lies in whether it is to bring in one destabilized protein (via pharmacologic chaperones) or to bring in a collection of similar destabilized proteins by expanding the proteostasis boundary (via proteostasis regulators).

Models for the Proteostasis Network
FoldEX and FoldFX are both models representing the proteostasis boundaries. FoldEX is a model that shows when a protein would get exported from the endoplastic reticulum, whereas the FoldFX model shows when proteins would have its function, hence where proteostasis working. FoldFX stands for Folding for the Function of Protein X. The models have three dimensions and they include the folding rate, the misfolding rate, and the stability of the protein.

The FoldEX model is important because it establishes a threshold for protein export. This boundary is characterized by the protein’s correct and wrong folding rate and its stability. Proteins will be exported if their energy level matches the energy level of the threshold.

In a healthy cell, all the proteins would be situated usually well within the boundaries of the FoldFX model and all the enzymes would be working. However, when there is a disease that affects protein folding or if proteostasis is not quite working well, there could be proteins represented that fall outside the boundaries, which would mean that the proteins are not functioning properly.

In conservative mutation the substitution that occurs does not have a heavy impact on the kinetics or thermodynamics of folding. It does not really affect the functional aspects that much because the replacement of a similar amino acid is not too different from the amino acid that was changed. In a slightly conservative missense mutation and elimination of an amino acid does affect the thermodynamics and kinetics of protein folding because the change of a base in the genetic sequence does not alter the functional aspect.

However, there are ways to correct this. One way is with the application of PC’s, or pharmacologic chaperones. Pharmacologic chaperones specifically target proteins that fall outside of the proteostasis boundary and push it within the boundaries giving it the ability to fold properly and function. It does so by either increasing the folding rate, decreasing the misfolding rate or stabilizing the structure of the protein. Another way to correct this is by way of PR’s, or proteostasis regulators. Proteostasis regulators can either expand or retract the proteostasis barrier allowing more or less proteins to be correctly folded.