What are intrinsically disordered proteins (IDPs)? And how do they differ from ordered proteins? 

Jenny Pham

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May 18, 2024

Over the past two decades the functions and importance of intrinsically disordered proteins (IDPs) have become more widely appreciated, reflected in the persistent increase in their appearance in the peer-reviewed literature (Figure 1). This increased attention is reflected in the rise of articles being published that discuss how attractive IDPs are as drug targets [1]. But, despite the knowledge we have gained, there is still a lot more to learn about this important class of proteins. In this article we explain what IDPs are and how they differ from ordered globular proteins, both in terms of structure and their key characteristics.

IDP proteins- publications

Figure 1: A graph showing the number of publications covering IDPs over time. Data sourced from:  https://pubmed.ncbi.nlm.nih.gov/?term=intrinsically+disordered+protein

What are IDPs?

IDPs and proteins with intrinsically disordered regions (IDRs) make up around 30% of the human proteome [2]. The key characteristic of IDPs and IDRs is that they do not fold spontaneously into single, well-defined 3D structures, but instead fluctuate between multiple conformations. IDPs/IDRs cannot be readily characterized by the traditional methods of structural biology and so new technologies to investigate their structure and behavior are being sought.

The classical structure-function paradigm where two proteins (with highly structured states determined by their respective amino acid sequences) bind via a “lock and key” model has been taught for more than a century. However, many proteins have been discovered that do not require a unique structure to carry out their function [3]. These types of proteins, that carry structure-independent functions, are classified as IDPs. There are also proteins that exist with both ordered domains and IDRs (Figure 2). One important example is p53. It has IDRs in its N- and C-terminus, which are able to form binding sites for many partner proteins.

 

 

A comparison of the key characteristics between structured domains and intrinsically disordered regions

Figure 2: A comparison of the key characteristics between structured domains and intrinsically disordered regions. The inclusion of disordered regions and structured domains is shown to increase the versatility of proteins in eukaryotes. Adapted from Babu et al. 2012 [4].

How prevalent are IDPs?

IDPs and IDRs have now been found throughout nature in proteomes of organisms in all kingdoms of life [5]. Interestingly, it has now been shown through computational analyses that the abundance of disorder increases proportionally with organism complexity [5,6]. Bioinformatic studies have found that the number of sequences with predicted IDRs (>30 residues) is roughly consistent in bacteria and archaea, but is significantly higher in eukaryotes [7,8]. This increase is estimated to be due to the higher number of cell signaling pathways in higher organisms that rely on IDPs/IDRs.

Almost immediately after the biological world began to recognize IDPs as a new class of biologically active proteins, it became clear that they were not rare exceptions but highly prevalent in nature. The first collection of IDRs included 67 disordered regions found in 61 PDB proteins [9]. Recently researchers experimentally validated the disorder of the IDRs in 3133 different proteins [10]. The recognition of IDP importance has led an international consortium of researchers to establish and continue to maintain and expand a database of known IDPs, DisProt [11].

 

The characteristics of IDPs that inform their structure and function

IDPs do not follow the rules established by ordered globular proteins and domains. These structural differences appear to be rooted in the peculiarities of the amino acid sequences in IDPs. So-called “order promoting residues” such as tryptophan, cysteine, tyrosine and leucine are depleted in IDPs. On the other hand, “disorder promoting residues” such as arginine, proline, glycine and serine are found more frequently in IDPs compared to ordered proteins [12].

Just as with ordered proteins, whose biological structures are formed based on their amino acid sequences, the ability of IDPs to not fold and still be functional in the absence of unique structures is also encoded into the amino acid sequences of IDPs/IDRs. In extended IDPs, these features include multiple charged groups (typically negative) that give the IDP its characteristic high net charge at neutral pH and their extreme isoelectric values [13–15]. It is these features that allow IDP/IDRs to continue to function in conditions that ordered proteins would find too harsh such as environments with high pH.

These characteristics, coupled with their low frequency of hydrophobic amino acid residues [14], allow IDPs to be dis/ordered at one moment in time, but able to change state at a future point in time. Therefore, IDPs are not homogeneous, but represent a very complex mixture of partially foldable, potentially foldable, differently foldable, or completely unfoldable segments [16].

 

Conclusion

In this article we have covered what IDP/IDRs are and how they differ from ordered proteins in both their structure and their characteristics. There is still lots of mystery surrounding IDP/IDRs given that they contradict the basic logic of the “lock-and-key” theory of protein functionality and that they break multiple rules devised by the researchers studying structure, folding, and functions of ordered proteins. An accurate understanding of multilevel complexity of IDPs/IDRs will require the development of new rules and new technologies to study them.

 

Want to explore IDP interactions? Microfluidic Diffusional Sizing is here to help.

Microfluidic Diffusional Sizing (MDS) is a recently developed solution-phase protein interaction technology that is well suited to studying proximity-sensitive systems such as IDPs/IDRs. As well as detecting and characterizing binding events it is able to study compactness/foldedness of a protein of interest by measuring protein hydrodynamic radius in solution.

Follow the link below to learn more about MDS or contact us to discuss how MDS can assist your IDP study.

 

References

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