Protein folding diseases and mitochondrial dysfunction in Parkinson's disease

Mitochondrial Diseases

A gene is basically a one dimension sequence of nucleotides that signals for the production of a protein. (Reynaud, 2010) The protein itself is merely a sequence of amino acids arranged in a specific manner. The sequence of the gene is linear and so is the sequence of the protein. DNA, which is a common term heard now and then is merely a collective term for all the genes of the body. The mechanism by which genes on the DNA work its action and are expressed in the body is known as translation. (Reynaud, 2010) Through translation, the genes come out as proteins and thus do specific actions in the body. The amino acid sequence mentioned earlier basically is a blue print that tells how the protein is going to be made and what specific function it will do.

The genetic material that we have is present in every single cell of the body. Regardless of which cell it is, the DNA and the genes are always present t in it. The proteins that the gens make carry out the required acts that a person needs to do in order to live and grow. Along with the bodily functions and actions, it is genes that that determine how we look, the way we act and how are body functions two. Even a little kid knows that he got half his genes from the mother and half from the father. However, it is not only looks that our mother and father decide. Their genes and consequently our genes also decide whether all the functions in our body will be normal or not. Some errors or defects in a genetic sequence can carry on for generations and thus give rise to inherited diseases. A mutation in the simplest forms is an n error or a defect in the genetic sequence of a person. Some mutations may go unnoticed and not produce any harmful effects. On the other hand, mutations may alter the production of certain proteins that go on to affect our body negatively. These negative effects then cumulate and present in the form of inherited disorders that are so common.

Thesis

Age and Age related diseases have been linked to the declining function of the mitochondria of cells in the body. Aging is a natural process and the senescence has been linked to processes like DNA methylation, telomerase shortening and the lastly the damage done by reactive oxygen species made by the mitochondria. (Schapira, 2012) The mitochondrial dysfunction can lead to production of ROS that damages cells like the neurons in Substantia Niagara in the brain and lead to diseases like Parkinson's. Also, the mitochondrial dysfunction causes the production and further accumulation of abnormally folded proteins that causes more degeneration. These effects are observed in other organs and systems and cause disease like Alzheimer's and diabetes as well. With the ongoing research on the link between mitochondrial DNA mutations and degenerative disorders, much is being done to figure out diagnosis, treatment and prevention of disorders like Parkinson's disease.

Protein Folding Diseases

The information required for proteins to fold correctly resides in the amino acid sequence. According to Levinthals Paradox, the proteins fold very fast into their most stable form because all the amino acids interact locally. (Reynaud, 2010) These interactions and the limited space thus make the proteins fold into the proper format. The proteins that have a difficult time folding into their native state, take help from chaperone molecules that make sure that the proper format is achieved. Ron Lackey mentioned the term chaperone when he found out that nucleoplasmin is bale to bind to histones and thus ensure the interaction between histones and DNA doesn't go haywire. That is to say that nuceloplasmin functioned as a chaperone and thus ensures that no inappropriate interactions take place. (Reynaud, 2010) The chaperones are necessary in some instances so the proteins don't go away from their native state and thus alter their own three dimensional structure. The three dimensional structure is crucial in determining how a protein will at in the body.

For most of the proteins, the most apparent structural motif is the structural confirmation that is popular as alpha helix. Whenever a protein misfolds or in simpler terms becomes toxic, it takes on the beta form. Misfolding basically occurs when a protein goes about a different pathway for folding or it follows an energy minimizing funnel. (Reynaud 2010) The toxic or the misfiled form of the protein then goes on to interact with the normal proteins and make them turn into a toxic state. That is when the proteins become infectious and are known as a prion. These prions are known as infectious because neither are they detected by the cells protective mechanisms nor removed by ultra violet radiation.

Protein misfolding and the way it is incorporated into membranes is an important factor in causing diseases. There are many diseases that are due to mutation in the a1 anti-trypsin and neuroserpin that give rise to protein misfolding. (Appella & Johansson, 2011) So why exactly is protein folding a bad thing? Surely proteins go on to carry important functions and one might say that if they're misfiled, they just won't do the function. The deposition of proteins in abnormal places can give rise to derangements in the normal functioning of the body. A common type of prion is one that is filled with beta pleated sheets and can give rise to amyloids that can be very harmful for the body. (Norrby 2011) Prion related disorders were proven when a prion infected protein rich food was used to feed the cattle. This led to a pandemic of bovine spongiform brain disorder which was acquired when anyone consumed the infected meat. (Norrby 2011) The amyloid formation that is created by protein misfolding gives rise to many diseases like type 2 diabetes and Alzheimer's disease. (Appella & Johansson, 2011) Many studies and reviews have been done to highlight how the protein aggregation and deposition is all because of misfolding. T The deposition is harmful and so is the interaction that the misfiled proteins go on to have with the membrane of different cells in the body. (Appella & Johansson, 2011)

A lot of the neurodegenerative diseases known are known to be because of abnormal accumulation of portion aggregates. It is seen that when these proteins deposits, brain function gets damaged at a cellular and at the synapse level as well. A suggestion that is sent forward is that increased stress on the endoplasmic reticulum of a cell is a leading cause of dysfunction in the long run. (Matus, Glimcher & Hetz, 2011)

There is still a lot of uncertainty in determining what the reason for protein misfolding is. One speculation is that sometimes same sort of protein chains known as homologous proteins are present in the body with a set blueprint on how exactly they will fold. When one of the protein folds, the other proteins similar to it fold in the same manner and thus make aggregates that have detrimental effects. (Norrby 2011) The aforementioned mechanism has thought to be one of the leading causes of degenerative disorders. A second speculation could be that certain amino acids are prone to being pathogenic. The amino acids are present in a sequence that can lead to them misfolding and thus producing diseases.

How exactly did the idea about protein causes diseases come out forward? The Creutzfeldt-Jakob disease was discovered by two German neurpathologists in 1920s. (Norrby 2011) This disease is characterized by slow destruction of the neural tissue known as spongiform encephalopathy. The incidence of this disease kept increasing yet no one knows what exactly caused the disease. More than 80% of the cases of this disease were sporadic and only ten percent were familial. (Norrby 2011)

There were many links seen between CJD, scrapies in sheep and Kuru in the Stone Age Fore people. Kuru was a serious neurological disease that was said to be caused by an infectious agent. A major route of infection of this disease was due to the ritual of cannibalism that was taken by the Fore people. When someone died, their body would be taken for the funeral meal and the women and children for the brain. The central nervous system had the biggest concentration of this disease thus it spread to women and children. CJD was a more established and reformed form of Kuru but the cause still could not be found. In the 1970s when Gajdusek examined the brain tissue of infected hamster, he tried to isolate what the causing mechanism was. The scientist initially thought it to be virus yet the results revealed something more pure. (Norrby 2011) Since he could not discover any nucleic acid, he went on to name it a prion. This word was an amalgamation of both an infectious and a protein like agent. Further studies into the agent gave the discovery that this protein was created by a gene inside the person's own body. This explains why there went any inflammatory response to the infection. Since the body's genes itself made the disease, there was no host response present. (Norrby 2011)

The misfolded proteins once made should be destroyed by the detective machinery inside the cell, however when these proteins increase in number, the cell cannot work out its investigative functions anymore. Protein misfolding can either occur spontaneously or by a mutation in the gene. Sickle cell anemia is a disorder that is inherited and leads to the improper folding of the proteins that make up hemoglobin. (Botelho & Lupi, 2008)

The amyloid diseases consist of Parkinson's, Alzheimer, type II and other cutaneous or systemic amyloidosis. The diseases that are caused because of the prions are not considered amyloid disease in the general term because they only represent a certain category of protein misfolding disorders. Some forms of amyloidosis are the ones that are transmitted from generation to generation. The mutation in the genetic code leads to abnormal proteins that lead to their aggregation and thus amyloid pathologies in the long run. The amyloidosis problems can further be divided into systemic and cutaneous diseases depending on which of the proteins become amyloid-genic. (Botelho & Lupi, 2008) Prion diseases differ from amyloidic because of them being localized to the central nervous system and also because of the way they are transmitted. When talking about amyloidosis, usually one protein becomes the causative factor and then goes to deposit in certain tissues. IT is the mere deposition there that causes disorders then. For instance, the B. amyloid protein goes on to collect in the CNS and leads to Alzheimer. Similarly, the a-synuclein protein collects in the CNS and the dopaminergic centers and goes to cause Parkinson's. (Botelho & Lupi, 2008)

Parkinson's disease

Parkinson's disease is one of the most common neurodegenerative disorder that affects about 2% of the above 60 population all over the world.(Licker et al., 2009) The current epidemiological research has stated that the prevalence of this disease is expected to increase and double in the coming twenty years. Seeing how this is a burden on the new world and a challenge that is expected, a lot of research is being done to figure what exactly causes Parkinson's disease. Surely, if we know the cause, the therapeutic techniques will be better understood as well.

Parkinson's disease has been a subject of research since a long time. There have been attempts to see who is susceptible to the disease, how it progresses and what the etiologic factors behind it are. The common cause of the Parkinson's disease is said to be an amalgamation of environmental and genetic factors. The mechanisms that are involved in this are mitochondrial dysfunction, oxidative stress, iron deposition, and inflammation. (Licker, Kovari, Hochstrasser & Burkhard, 2009) A lot data is pointing toward the aggregation of an abnormal form of neuronal protein a-synuclein that leads to degeneration in the long run. (Licker et al., 2009)

Parkinson's disease is a disease that produces a distinct and asymmetric combination of resting tremors and rigidity of the body. The person affected has difficulty initiating and stopping movement and isn't able to carry out simple tasks like writing or sketching. The person also experiences postural instability and since the disease is of a progressive nature, it keeps getting worse as it proceeds. (Licker et al., 2009)

The simplest pathology discovered about PD is that there is a loss of dopamine secreting Substantia Niagara neurons in the pons and midbrain (Licker et al., 2009) It was revealed that the neurons that did stay showed inclusions that are known as Lewy bodies or pale bodies. The Lewy bodies (Lbs) or the Lewy neuritis (Lns) when contained in the neuronal process is seen to consist of a-synuclein. The aggregation of these proteins continues to increase in a caudal-rostral manner as the disease progresses in its course. (Licker et al., 2009) The inclusions start of from the dorsal motor nucleus of the vagus nerve in the brainstem then keep going anteriorly towards the olfactory bulb and the anterior olfactory nucleus. (Licker et al., 2009)

The argument for this is that the a-SYN inclusions are also present in other neurological conditions as well. These conditions are collectively known as "alpha-synucleinopathies" which also have disease multiple system atrophy, Alzheimer's disease and with brain iron accumulation type 1. (Licker et al., 2009)

The protein folding that does occur is not a random but seems to occur very specifically. There are certain homologous proteins that seem to clump thus leading to abnormalities. Normally the ubiquitin-proteasome system (UPS) and peptidases go on to destroy the abnormal proteins. When the amount of aggregated proteins outruns the capacity of UPS, there is formation of soluble monomers and oligomers and eventually the formation of Lewis bodies in PD. (Licker et al., 2009) The collection of Lbs and LNs then lead to disrupt the normal cellular processes like synaptic plasticity, transmission from neuron to neuron and axonal transport. The dysfunction of the UPS has been proposed to be a major factor in causing the pathogenesis of PD disease. (Licker et al., 2009)

Mitochondrial Diseases

We have covered why protein misfolding can lead to disorders all over the body and especially in the brain. Our attention is now turned to Mitochondria and the important role they have in cellular energy and cell death. PD along with many other diseases is an example when certain cells lose their function. In the simplest terms, if mitochondria provides the energy for cells and controls their death, then surely it has a link to the many degenerative disorders known today. Mitochondrial diseases that are carried from generations could be due to DNA in the mitochondria or genes that code for the mitochondrial proteins. (Schapira, 2012) Optic neuropathy and type 2 diabetes are examples of tissue specific mitochondrial disorders.

As mentioned earlier mitochondrial diseases can result from point mutations to the DNA, alterations in the cellular DNA and free radical mediated destruction. (Schapira, 2012) Mitochondrial fission and fusion is an important mechanism by which the organelle is transported to do its many functions. Inhibition of the fission by destruction of dynamin-1-like protein can cause an augmentation in the amount of mutant mitochondrial DNA (mtDNA). The mtDNA can then be further linked to lactic acidosis, encephalomyopathy and stroke like symptoms. (Schapira, 2012) PTEN induced putative kinase 1 (PINK 1) and Parkin has a crucial role in the mitophagy pathway. (Schapira, 2012) Parkin is an enzyme that helps in the movement of products from the cytoplasm to the mitochondria. Pink1 phosphorylates the aforementioned molecule and gets the job done. Mutations in the gens for these two proteins are prominent in causing PD as discussed later in the paper.

Along with mutations and oxidative damage, the functions of mitochondria are known to decrease since age as well. This could be due to the accumulation of ROS in the body that keeps on affecting the mitochondria. Deletions and mutations are seen normally in mtDNA as a person ages. (Schapira, 2012)

Single Deletions

Single deletions of mtDNA were the first genetic defects to be linked with human mitochondrial disorders. (Pitceathly, Rahman & Hanna, 2012) It was revealed that out of the patients diagnosed with mtDNA linked disease, single deletions were the causative agent behind 25% of all the diseases. Single deletions are considered sporadic and thus have no link of inheritance or the defected gene being transferred over many generations. (Pitceathly et al., 2012) The exact mechanism of the replication of mtDNA is not known yet most of the single cell deletions do take place while the DNA is replicating. (Pitceathly et al., 2012) Most of the genetic defects linked to the mitochondria are the ones that results in the loss of any one of the respiratory chain agent. Some of the clinical disorders associated with single deletions are Kearns-Sayre syndrome, Pearson marrow-pancreas syndrome, myopathies, deafness and diabetes. (Pitceathly et al., 2012)

Parkinson's disease (PD)

When a person has been diagnosed with Parkinson's disease, it is observed that there is impairment of both mitochondrial respirations. There has been sound evidence of mitochondrial protein imbalance and disrupted mitophagy established in PD.(Santos&Cardoso 2012) 90-95% of the cases of PD are present without a genetic linkage and thus mitochondrial damage is one of the causative factors of the disease.

This was discovered when exposure to MPTP which is a selective inhibitor of mitochondrial complex I, led to the development of irreversible and progressive Parkinsonism. (Santos&Cardoso 2012) CXI was also an important protein component that was seen missing in the post mortem brains of people have PD. The decreased levels of CXI were seen all throughout the body but mostly affected the Substantia Niagara. The Substantia Niagara is most vulnerable to this is due to the increased production of ROS from dopamine metabolism and because of the increased amount of iron in dopamine containing neurons. (Santos&Cardoso 2012) The mitochondria are one of the endogenous creators of ROS in the body. Consequently, decreased CXI and increased ROS have been correlated with PD. (Santos&Cardoso 2012)

Mitochondria have its own DNA and oxidation also occurs readily in this organelle because it is the powerhouse of the cell. The fact that the DNA resides so close to reactive oxygen species makes it more prone to be being mutated. A CXI defect in a brain affected with PD and an increase in more oxidative species causes the DNA to be more susceptible.

There have been studies that stated that mitochondrial DNA abnormality leads to Parkinson's disease. A mitochondrial 12 SrRna was the point mutation that was seen in the PD pedigree. (Santos & Cardoso 2012) The removal of the transcription factor a gene from the mitochondria of dopaminergic neurons caused them to degenerate. This degeneration is similar to the one that is caused in the PD disease. (Santos & Cardoso 2012) When this gene was taken out, the respiratory chain in the mitochondria was affected and the death of the neuron eventually ensued. Subsequent to this study, it was uncovered that mitochondrial DNA does have a link in causing PD. (Santos & Cardoso 2012)

To see if PD is in part caused by the mitochondrial gene, a study was conducted to look at mitochondrial DNA more closely. Seven of the mitochondrial genes that code for complex I were studied in patients with PD and patients who were just aging. The amino acid changing mutations that were revealed at the frequency of 59.3 per million in both the control patients and the PD patients.(Smigrodzki, Parks & Parker, 2004) It was revealed that on average, at least one of the genome that codes for the Complex I has a mutation in it. The loss of complex I lead to actions such as increased ROS, change in calcium metabolism, inclusion bodies as mentioned earlier and Lewy bodies as well. (Smigrodzki et al., 2004) Even though there are studies done on high frequency heteroplasmic mtDNa and homoplasic mutations, these include single nucleotide alterations and deletions as well. Still, no bold and solid correlation with PD and these mutations have been uncovered. (Smigrodzki et al., 2004) After the study was carried out, it was revealed that the difference in number of mutations in the old aged and the patients with PD was not significant. (Smigrodzki et al., 2004)

Even though the studies did not support the belief that patients with PD would have increased mutations, it is revealed that the Complex I damage is caused by mitochondrial DNA. (Smigrodzki et al., 2004) The study if done on selective cells or a small group of neurons could have yielded distinct results and gone to prove the hypothesis. Still, on the basis of this study, it cannot be ruled out that there is no link with PD and mutations in mitochondrial DNA. (Smigrodzki et al., 2004)

Mutations in the Parkin gene were said to be a cause of juvenile and early form of Parkinsonism. Loss of Parkin led to more and more defects being created in proteins and in mitochondrial quality control. These further led to protein inclusions and defective mitochondria. The protein inclusions and faulty mitochondria eventually led to neurodegenerative symptoms as the ones seen in PD. Further mutations in the PINK1 are linked to early onset Parkinson's disease. If PINK1 was lacking or deficient led to fault transport to and from the mitochondria and toxic accumulation of proteins inside the mitochondria. The mitophagy that removed and destroyed nonfunctional mitochondria s is also linked to Parkin and PINK1. Parkin plays a crucial role in not letting damaged mitochondria stay in the body and cause further damage. Thus it is clear how if these two proteins were deficient it would lead to increased degenerative symptoms throughout the body. (Santos & Cardoso, 2012)

Mitochondrial DNA & (tRNA & mRNA) Mutations

Even though it a challenge to diagnose and establish a disease belong to mitochondrial origin, there should be work on treating the disease as well. The satellite cells are present between the basal lamina and the muscle fiber. These are important in diagnosing a disease of this origin. Other ways of figuring out if someone has this disease is amniocentesis, chronic villus biopsy and polar body. (Taylor & Turnbull, 2005)

When it comes to mitochondrial DNA, there is homoplasmy which means all the copies of the mitochondrial genome are the same. On the other hand, there is heteroplasmy in which there are two or three forms of the mitochondrial mutations. There are mutations that affect all the copies of the genome and are obviously more severe. In the case of heteroplasmy mutations, there is a threshold level of mutation that has to be present in order for the symptoms to appear. (Taylor & Turnbull, 2005) Mitochondrial mutations are transmitted from mothers to their offspring thus fathers don't have to fret that they can infect their child. (Taylor & Turnbull, 2005)

The 16.6 kb worth of human mitochondrial genomic has a total of thirty seven genes. Out of all the 37, only 13 code for structural proteins. (Dunn, Cannon, Irwin & Carl, 2012) Most of the proteins that are coded for are actually complexes essential to the oxidative function in the mitochondria. There are 22 Trnas and 2 Rrnas that are coded by the mitochondrial DNA. (Dunn et al., 2012) Out of the many studies done on mutations of the mitochondria, it was revealed that they are crucial in causing neurological and myopathy diseases, (Dunn et al., 2012)

Since a person cannot phenotypically discern that a mutation is of mitochondrial origin, animals were used to see how alteration in genes led to mutations. Methods used to test mitochondrial DNA, RNA and MRNA mutation were Somatic cell nuclear transfer, allotropic expression, Polymerase gamma mutations, Direct injection of mitochondria into embryos, Cytoplasmic hybrids, Rho-zero cells, trans mitochondrial mice, and Xenomitochondrial modeling. (Dunn et al., 2012)

Mitochondrial Medicine

Aging is a natural phenomenon yet there is been a close correlation of aging, age related diseases and mitochondrial dysfunction. Mitochondrial dysfunction has been linked to severe diseases like Alzheimer, Diabetes, PD and many others. Out of all the theories presented about mitochondria, the fact that is linked to aging and death is a one that is accepted till now. (Mao et al., 2012) It was mentioned earlier that most of the e single deletions mutations occurred during replication. Another theory proposed is that the mutations occur during the repairing of damaged manna. (Mao et al., 2012) The study conducted on the rhesus monkey was to figure out the link between mtDNA and effects of aging on monkeys. The blood, brain and the buffy coat of the monkeys was analyzed via using amplification and PCR techniques. These results revealed that mutated DNA was increased till a significant amount in aged monkeys as opposed to young monkeys. (Mao et al., 2012) The age dependent changes in the DNA in mitochondria can be utilized to target beneficial therapeutics against diseases caused by mitochondrial damage. It was proposed that this increase in mutated DNA could be due to declining mitochondrial function as the monkey ages. (Mao et al., 2012)This study thus builds up on the previous one discussed in the paper that increased oxidative stress as the person ages leads to more mitochondrial damage