Structural Biochemistry, TDP-43

What is TDP-43?

TDP-43 is a binding protein of approximately 43 kildodaltons that has come under the scientific light for its potential neurodegeneration in humans. More specifically, TDP-43 aggregation is at the center of an extensive network of neuronal diseases that are collectively referred to as TDP-43 proteinopathies. In order to understand TDP-43 and its function in neurodegeneration, two biochemical properties were studied—it’s ability to bind RNA and its protein-protein interactions. Establishing direct links between TDP-43 and disease is not easy and may not get any easier in the near future due to the number of processes that can be aberrantly affected by TDP-43 aggregations in neurons and glia, and by nuclear depletion of TDP-43.

TDP-43 Protein (Image: Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute, Public domain)

Biochemical basis of the aggregation properties of TDP-43

It is now widely accepted that the C-terminal tail of TDP-43 is responsible for most of its tendency to aggregate, even in the absence of cofactors. The hypothesis is that there is a region that contains an infectious ‘prion domain’ from residues 277-414. This hypothesis has been supported by experimental evidence that in vitro prepared TDP-43 fibrils can be taken up by cultured cells and function to trigger aggregation in the cell. In recent times, experimental evidence has shown that either changes in the protein architecture itself or the surrounding protein environment can affect TDP 43 aggregation. C-terminal fragment expression in TDP-43 proteins in neurons was shown to promote aggregation in a considerable number of cells. Another important note is that TDP-43 aggregates have also been observed following knockdown of nuclear transport proteins such as karyopherin beta or the cellular apoptosis susceptibility proteins (CAS), which results in increased cytoplasmic localization of TDP-43.

TDP-43: Biochemical marker of neurodegenerative diseases

Due to the fact that TDP-43 is extremely prevalent in many areas of the body (muscle, skin, etc.), it is important to determine various thresholds of optimal TDP protein levels. There has been an increase in the effort of identifying biomarkers so that disease onset can be diagnosed in patients before neuronal damage becomes too severe, leaving time for scientists and doctors to attempt therapies that can slow down or even prevent the disease. Biomarkers can also help in evaluating the beneficial and harmful effects of novel therapeutic strategies. Several tissue samples from controls and patients have been analyzed to determine what level of TDP-43 expression might be used as a biomarker for disease diagnosis or prognosis. The tissues have been tested for the presence of abnormal levels of TDP-43. However, unfortunately, there is still limited specificity between patients and controls when it comes to TDP-43 expression levels in CSF (cerebrospinal fluid) & plasma.

Therefore, in addition to determining specific biomarkers for the disease, scientists are beginning to use common molecular biology techniques including western and northern blots, PCR, and SDS-PAGE analyses. The hope is that these techniques will not require an excessive amount of effort and training to be set up efficiently in a clinical setting. Through these techniques scintists can look at several molecular aspects of TDP-43 biochemical properties in order to try and identify abnormal expression and/or function.

Conclusion

The biochemical studies performed on TDP-43 suggest that the protein is essential to many aspects of cell cycle (especially RNA metabolism). Any alteration to the functional properties of TDP-43 will greatly enhance the protein’s ability to aggregate and consequently generate lethal effects in the organism. Although environmental effects may alter TDP functionality, studies suggest that aggregation should be a primary feature in all TDP-43 proteinopathies. There are promising indications that TDP-43 is indeed a vital biomarker molecule that detects disease onset or progression.

References

1. TDP-43: gumming up neurons through protein–protein and protein–RNA interactions
   Emanuele Buratti and Francisco E. Baralle

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