We recently had the wonderful opportunity to speak with Dr. Peter Wright about the history and future of the IDP field. Dr. Wright is a Professor in the Department of Integrative Structural and Computational Biology at the Scripps Research Institute in La Jolla; he published seminal works in the IDP literature and has been instrumental in the evolution of the field.
1. Can you describe the initial reception to the idea of intrinsically disordered proteins having function in their disordered state? Were people excited? Skeptical?
Complete and utter skepticism!There was the thought that IDPs wouldn’t survive in the cell; how on earth would they survive proteolysis? The whole idea met with skepticism for quite some time, it was beyond belief. The reason was the prevailing dogma that structure equals function and that recognition was by lock and key. Those ideas were firmly ingrained in the community, and they didn’t see that disorder had any role in biology. There are still some people who are skeptical, who think that IDPs are an artifact of studying them in isolation from their binding partners. Even last year they were called PWPs – proteins waiting for partners.
It took a lot of time for these views to change. Even now the idea of IDPs is in very few textbooks, not widely taught. It takes a long time to overcome the dogma. What has changed that view is the huge number of examples of IDPS that have been identified and studied in detail. A lot of biologists come across IDPs who wouldn’t have thought about their existence before. There’s been an explosion of data over the last few years on proteins that are clearly disordered and have extremely important biological functions.
2. In your opinion, what were some significant milestones in the history of IDP research?
- late 1980s: Paul Sigler published a seminal paper on transcriptional activation domains early to mid 1990s: We and others published examples of 3-4 proteins that were clearly unstructured. “We went to great lengths to prove they were functional.” Experimental recognition of disorder became more widespread in biology.
- early to mid 1990s: development of bioinformatics tools, which led to identification of disorder from sequence
- 1990s: development of NMR methods to allow characterization of conformational propensities in both the free and bound states.
- 2000s: identification of motifs that never fold when bound to targets: fuzzy complexes
3. Do you think the field has achieved a stable equilibrium or will it continue to grow? Where do you think IDP work will go in the future?
No way is it at equilibrium. Growth has been exponential over the past decade and I have no doubt that knowledge of IDPs will continue to grow exponentially. Technologies improve further and further all the time. Also, biologists are finally beginning to realize that disorder in their proteins may be what’s important for function... there are now many papers on IDPs in high profile journals that are not from known IDP researchers but from biologists. They don’t necessarily talk about them in the terms IDP researchers would, but they’re dealing with them.
Where are we going – dramatic growth. One really important thing for the future is development of technologies to characterize full-length proteins. To a large extent we still use a reductionist approach. But huge numbers of eukaryotic proteins have both globular domains and disordered regions. How do we characterize these? We need to move beyond a reductionist approach, studying domain by domain, region by region, to understand how the full length protein works synergistically. There are synergies and incredible complexities in these huge disordered proteins that will be hard to understand.
The other one is going to be tough: addressing structural and biophysical questions in the native environment in the cell. Are interaction domains of IDPs always bound to partners and folded in the cell? To what extent are they free and flexible? The challenge of studying regulatory and signaling IDPs in their native environment will be their low concentrations in the cell – developing technology for for such studies is going to be critical. Single molecule FRET experiments in the cell are going to be critical and are synergistic with NMR and other technologies.
So, the future is understanding the status of IDPs in the cell and characterization of full-length proteins. Biologists will contribute greatly to understanding of IDPs because more and more they are exploring problems involving disordered regions.
4. What do you think are the most exciting recent developments in the field?
The whole field is exploding! It’s extremely exciting.
- Identification of low complexity regions involved in assembly of nuclear bodies, RNA bodies – the recognition that proteins can self-assemble into organized particles in the cell.
- Prion-like domains which are completely disordered and fold into amyloid-like structures to form signaling complexes. They point toward a different level of organization than appreciated previously. It is now evident that protein disorder contributes to a level of organization in the cell. These assemblies are dynamic and proteins can more in and out of the bodies/particles for function.
- The sheer number of papers now appearing on disorder and signaling, and the massive extent of post-translational modifications observed in disordered regions that lead to combinatorial signaling processes.
5. Many of the more common structural biology and computational tools were developed based on folded proteins with crystal structures in the PDB. Do you think this has had an effect on IDP research, and has the situation changed or is it changing?
Yes, because of the prevailing dogma: that the folded structure was the key to the function. The whole focus until the 1990s was that structure equals function. That did slow the recognition of the importance of IDPs, and certainly slowed development of the field. It wasn’t until we overcame that bias that the field could gain recognition and expand the way it has been doing.
6. Your research covers both IDPs and dynamics in folded proteins. Could you talk about similarities and differences in this work? How do techniques developed for one application carry over or inform the other?
There are a lot of connections between them, and a lot of the technology is very much the same. What I’ve come to realize is that nature uses a continuum of protein conformational space. Some proteins are functional but fully unstructured, others form transient elements of secondary structure or are molten globules, some are well folded globular proteins with dynamic regions. The structure determined by crystallography is not unique – it’s the ground state structure. Proteins can fluctuate into higher energy substates that may be involved in function. We are beginning to understand that flexibility and dynamics of IDPs and globular proteins is all part of the same continuum.
NMR relaxation and single molecule techniques apply equally well to characterization of IDPs and to characterization of alternate conformational states and dynamics in folded globular proteins. Many of the technologies developed for studying globular protein dynamics are also used for studying the dynamics and protein-protein interactions of IDPs.
7. Do you think the methods and nuances of IDP research affect or will affect how we study proteins with stable folds? How?
IDP research is leading people to have a more open view of protein structure: that all proteins are part of one continuous landscape of structure and dynamics. Now that realization has hit home, it leaves people more open minded to the fact that you don’t just look at an x-ray or NMR structure and say “that is the structure and that is how it works”. Now people think about how the protein moves and how that motion relates to function. The flexibility of IDPs is an extreme case. The growth of technologies to look at dynamics is changing our view of all proteins, opening people’s minds to the fact that proteins move, that proteins are flexible.