Talk about the “dark proteome” has become frequent recently. What lies behind this somewhat mysteriously labelled field of science? And why has it become such a popular topic among scientist and drug developers?
What is the dark proteome?
For a long time, proteomics held on to the firm believe that the function of a protein is determined by its’ structure – the “structure-function paradigm”. Only over the past 15 years has it become more and more obvious that a large part of all proteins is entirely or at least partly disordered – but still fully functional. These “intrinsically disordered proteins” – or IDPs, are also termed the “dark proteome”, as they are not easily observed with established methods.
Why is it relevant for proteomics?
Scientists have found that structural disorder is very common in the proteome of all species. Conservative predictions estimate that about 15-45% of eukaryotic proteins contain significant disorder (1). Estimates vary with the definition of disorder. In early definitions, disordered regions had to have 30 amino acid residues or more. But new findings show that intrinsically disordered protein regions can only consist of down to about 5 amino acids (2).
What are key features of the dark proteome?
Intrinsically disordered proteins of the dark proteome are fail to form specific structures and are highly dynamic in their secondary or tertiary structure. This makes them very adaptable when binding to a protein partner. There exist intrinsically disordered protein regions that can perform their function while remaining completely disorder. But most undergo an order-to-disorder transition during binding. In this case, binding can follow two different mechanisms. The protein can fold before binding and then choose the binding partner. This is termed conformational selection. It can also occur that the protein folds during or after binding, which is then termed induced folding. To find out which mechanisms applies for a specific protein, kinetic measurements are essential.
What are the functions of disordered proteins?
Proteins of the dark proteome are mostly involved in signalling and regulation. The intrinsically disordered protein regions are frequent targets of post translational modifications. Many of these domains exhibit a multiplicity of post-translational modification states. Many protein-protein interactions and enzymatic modifications are mediated by short disordered amino acid sequence motifs. They mostly act through weak but highly specific binding.
The dark proteome in disease
Due to their importance in regulation and signalling, intrinsically disordered proteins are often involved in disease states, e.g. cancer, neurodegenerative diseases, cardiovascular diseases and diabetes (3). This makes them prime targets for drug development. The challenge with developing drugs that target intrinsically disordered proteins is that they have no enzymatic activity and thereby cannot be targeted by traditional drug mechanism, which mostly rely on blocking active centre or binding pockets of enzymes. Novel drugs could target the protein-protein interactions of intrinsically disordered proteins, e.g. by small molecules.
How can we analyse the dark proteome?
A large part of what we know about the abundance and distribution of intrinsically disordered proteins comes from computational modelling based on known amino acid sequences. NMR spectroscopy is a common way to analyse dark proteins structure and self-organisation. Kinetics of the binding of intrinsically disordered protein have been studied by fluorescence anisotropy measurements.
What is your opinion?
Could label-free measurements of binding and kinetics help with shedding light into the dark proteome? How important is the screening of large libraries of short disordered peptide motifs to advance the field further?
(1) Tompa, P. (2012) Intrinsically disordered proteins: A 10-year recap. Trends in Biochemical Sciences 37: 509-516.
(2) Tompa, P. et al. (2014) A Million peptide motifs for the molecular biologist. Molecular Cell 55: 161-169.
(3) Uversky, V. et al. (2008) Intrinsically disordered proteins in human diseases: Introducing the D2 Concept. Annual Review of Biophysics 37: 215-246.