Uncategorized Understanding Science

F for Folding or F for Fuzzy?

In one of our recent posts, we touched upon the intrinsically disordered proteins and regions (IDPs/IDRs, I will use IDP abbreviation in further text). There we explained how their specific primary structure and the choice of very hydrophilic, charged, and small amino acids enables them to exist in an extended conformation thereby defying one of the main paradigms of molecular biology – in order for a protein to be functional, it needs to exist in the most stable fold (called also the native fold). Today we know that not to always be the case, as we have characterized many functions of IDPs, even though they lack globular structure.

Since IDPs exist in this extended, stretched conformation with no distinct secondary or tertiary structure, a huge portion of their surface is exposed to the solvent, meaning that IDPs posses a high entropic energy. However, as soon as they bind to their target protein (and thereby form weak intermolecular bonds and interactions), their entropic energy decreases following the decrease in their exposed surface. As always, nature loves the equilibrium, so this drop in the entropy can’t be ignored – we need to find a way to compensate for this loss so that the overall energy of the system remains more or less the same. IDPs realized that if they follow up this entropy loss with some enthalpy gain, things could work out and nature won’t be forced to abandon IDPs. Once bound, IDPs start forming some sort of a secondary structure by creating intermolecular bonds and interactions. So the entropy that we lost because of the weak intermolecular bonds that were created between the IDP and the target protein is being balanced with the enthalpy gain due to the formation of intramolecular bonds within the IDP. This process, in which IDPs exit as completely disordered and then become ordered when bound to the target protein is called folding upon binding and it’s one of the coolest mechanisms in biochemistry (in my humble opinion at least).

Life is all about balance

In most cases, folding upon binding is energetically favorable for the majority of IDPs, but not everything is as simple as we would want it to be. If the entropic penalty (or decrease) is well compensated with enthalpic gain (in translation: if enough non-covalent bonds are created within the IDP and between IDP and target protein), a strong binding with a high affinity is achieved. However, since only basic secondary structure is being induced in the majority of IDPs (for example simple alpha-helix or beta strand), the number of those newly formed interactions is theoretically limited, meaning that the enthalpic contributions are usually not enough to counteract the entropic penalty and therefore the binding is usually of lower affinity. This is where the story gets messy, but don’t worry, nature has a few tricks up its sleeve…

Firstly, not all IDPs fold upon binding. Even though we said that folding is energetically more favorable than having the highly exposed surface of the extended IDP conformation, this would be the case in a perfect scenario where the gain in enthalpy is sufficient to cover for the loss of entropy. As explained, those newly formed bonds are usually not that strong and therefore we can’t always count that the energies will end add up in the end. Because of this a substantial amount of IDPs retain their disorder even when bound to the binding partner and they never really fold. We call those are “fuzzy” IDPs and they create “fuzzy” complexes with their binding partners where the “fuzziness” depends on the degree of disorder that IDP retains, which is also based upon the relative entropy inherent to the complex (the fuzziness helps to minimize the entropic penalty caused by binding of IDP and the binding partner, which would otherwise be too high to compensate with the increase in enthalpic energy of a newly formed complex, in which case there would be no binding whatsoever). The main characteristic of fuzzy complexes is that the interactions between the IDP and the binding partner protein are transient and coupled with a weak binding affinity (they come and go fast).

Ways to feel fuzzy

The fuzziness can be divided into 4 classes. It’s important to note that they are not mutually exclusive and the disorder at the bound state is a continuum, meaning that at any point in time a protein complex may exhibit the character of more than one class. 

  1. Polymorphic model : In this case the IDP adopts distinct well-defined extended conformations in the bound state, while remaining fully disordered. The 3D conformations of IDP and the protein that are a part of this fuzzy complex are unrelated, meaning that we can’t find traces of lock-key binding mechanism or induced-fit mechanism here.
Figure1: Representation of a polymorphic fuzzy complex (b),(c),(d) here IDP adopts a few conformations when bound to the binding partner. (Tompa & Fuxreiter 2008)

2. Clamp model: Clamp model is possible when we are dealing with a protein that has two structured globular regions connected with one intrinsically disordered region (IDR) that serves as a linker segment in this case. Two structured regions bind following a regular lock-key mechanism of binding, while the function of the IDR is just to link them. Because IDR is very flexible, it enables different 3D positions of the two structured regions, meaning that they can easily adapt to the binding protein surface.

Figure 2: Representation of a clamp mechanism in forming a fuzzy complex: two structured regions (orange alpha helices) are connected with a disordered linker segment (in orange dotted line). (Miskei et al 2016)

3. Flanking model : This mechanism is similar to the clamp model. The difference is that in the clamp model the only disordered part is the linker segment, while the two domains that actually bind to the binding partner are structured (globular/ordered). In the case of a flanking model, the two domains that bind to the binding partner are disordered, as well as the linker segment. The two (or more) domains that bind to the binding partner are SLiMs (short linear motifs) that undergo folding upon binding. Because the linker segment is disordered, it retains its conformational freedom and therefore reduces the entropic penalty caused by binding of the SLiMs to the binding partner. Importantly, the flanking regions modulate the nature of the interaction between the SLiMs and the binding partner by contributing to the affinity and specificity of the interaction (and by “keeping the binding sites safe”).

Figure 3: Representation of a flanking model: three SLiMs can be seen in orange, forming the alpha helices upon binding to a partner protein shown in gray. The orange dotted line represents a flanking region which is also a linker segment between different SLiMs. (Miskei et al 2016)

Flanking model is very interesting because there is a folding upon binding and static disorder upon binding present in the same IDP chain. We can further describe the modes of binding within the flanking model as: avidity and allovalency. In short, avidity is a mechanism of binding which entails two or more binding sites present on an IDP (so two or more SLiMs connected with a linker segment), that are complementary to two or more binding sites present on its target protein (remember here that in the case of a polymorphic model the IDP conformations didn’t need to be complementary to the binding partner 3D structure). In order to achieve avidity, it’s important that the number of binding sites on the IDP is equal to the number of binding sites on a binding partner and at no point in time should the contacts interchange. An advantage of this binding mechanism is that once the initial contact is made, a cooperative effect takes place, facilitating further interactions. Moreover, the increased local concentration from the first binding event, combined with the lowered entropic penalty when binding only one IDP results in a greater binding affinity and the interaction is more thermodynamically favorable. 

Conversely, allovalency models a system where there are multiple binding sites in tandem on an IDP that are complementary to a single binding site on its partner. Once the first contact is made, the rest of the complementary binding sites of the IDP start competing for this spot so that even when the first contact dissociates (due to low binding affinity which we discussed earlier), anoher complementary binding spot od an IDP is close enough to form a contatc. In this way, some part of an IDP is always bound to the binding partner, but the binding spots on the IDP are exchaning relatively quickly. 

Figure 4: Representation of the allovalency binding mechanism in the flanking mode – on the left we can see the first contact being made between an IDP and its binding partner. This contact dissolves quickly, but due to the high concentration of complementary binding sites on the IDP, the binding site is quickly filled with another binding domain from the IDP (another SLiM), as shown on the right hand side. (Morris et al 2021)

Back to the binding modes, finally we have

4. Random model: The random fuzzy model describes a situation where both the IDP and its target protein have a number of interaction sites and the interaction between each site is not restricted by any specificity. The random model works similar to the allovalency: first one nonspecific low affinity binding takes place between one binding site on the IDP and one on the binding partner protein. Even though this interaction dissolves quickly, because of the large number of putative binding sites in a close proximity, the binding is resumed even quicker. Random fuzziness represents the extreme case of disorder where there is little to no secondary structure induced upon binding of the IDP to a binding partner and the IDP retains a high degree of conformational freedom, making this model hard to characterise (both experimentaly and computationaly).

Figure 5: Representation of a random model of fuzzy complex. Each colored “blob” in orange and blue represent a binding site of an IDP, while the target protein is shown in gray. (source: Wikipedia)

To be continued

Even though it might seem like we have it all figured out with the classes and groups we formed in an attempt to describe and understand the wild nature of IDPs when they interact with other proteins, the reality might not be so optimistic. We are still far from fully understanding these complex mechanisms, let alone predicting this kind of behaviour, but with the growing interest in this very special group of proteins, we will surely soon be in a much better position. I will do my best to cover a part of that amazing journey here so stay with us for more stories about the world of the mischievous IDPs 🙂


  • Miskei M, Antal C, Fuxreiter M. FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies. Nuc Acid Res. (2017) 4;45(D1):D228-D235.
  • Morris O, Torpey J, Isaacscon RL. Intrinsically disordered proteins: Modes of binding with emphasis on disordered domains. Open Biol. (2021) 11: 210222.
  • Tompa P, Fuxreiter M. Fuzzy complexes: polymorphism and structural disorder in protein–protein interactions. Trends Biochem Sci. (2008) 33:1 (2-8).
  • Wikipedia. Fuzzy complex. (date of usage: 1.5.2023.)
Issue 25 Understanding Science

The perfect chaos

One of the main characteristics of all living beings, especially the more sophisticated ones like humans, is the amount of law and order that seems to exist inside every cell. The entire human body is a machine – well organized atoms that form molecules, which then form into cellular compartments which working together form a cell. Groups of cells further work together with the liquid space between them and form tissues which on a higher level become organs and organic systems that finally create a beautiful symphony called the human. And this goes for every multicellular organism.

Issue 24 Understanding Science

The Orphanage

Every year, an estimated 1 billion people worldwide are infected by seasonal influenza. In 1980 there were 50 000 reported cases of polio. One of the most infectious diseases of all time was mumps – up to 726 cases per population of 100 000 yearly have been detected around the globe. Unlike such highly contagious diseases, throughout history humankind has faced much rarer diseases, ones we don’t hear much about.

Issue 23 Science Shoutout

The Need, the Needle or the Needless?

Among the deadliest diseases worldwide is diabetes. Despite the exhausting public health campaigns designed to raise awareness of the fatal complications that develop within one year of untreated diabetes, one in ten people around the world suffer from it. The “hidden” sugar is added to virtually every soda, not to mention the abundance of sweets in our everyday diet. Kids as young as two years old are exposed to such high sugar food in every social encounter and there’s no way to protect them from it, even if we want to. The fact that so many of us have become accustomed to the taste of sugar is scary if not alarming already and is starting to cost us not only money, but lives. Lives of so many lost over a little 6 carbon ring molecule.

However, not all of it is our fault. According to their literature, even the ancient Greeks and Egyptians noticed a sweet taste of their urine. The term diabetes was first used over 2000 years ago and the first medical texts describing it appear in 1425 in Britain. The diabetes mellitus they talked about is, as we call it today, of type 1. The onset of the type 1 diabetes is usually already in childhood, due to genetics and congenital pancreatic insufficiency. With the modern world came the type 2 – caused by the overconsumption of sugar and carbohydrates, usually starting later in the adult life. The difference is – in type 1 diabetes pancreatic cells produce very little or no insulin due to the organ dysfunction, whereas in type 2 it’s either all other cells in our body stop recognizing the insulin our pancreas produces and become blind to it in a way, or the pancreas stops producing the insulin because of the exhaustion caused by constant high blood sugar levels.

Issue 22 Science Shoutout Understanding Science

Danger in disguise

The most prescribed drug in the world is atorvastatin (the inhibitor of cholesterol production in the liver, used to lower blood cholesterol levels). However, the most prescribed group of drugs are benzodiazepines. Behind the elegant and “clean” chemical structure of three rings – benzene, diazepine and phenyl ring lays a group of drugs so powerful and potentially harmful, and yet… so safe. Their list of indications is amongst the longest of all drugs, but they are also known as most commonly used drugs without doctors’ prescription. Not only are they being sold in the streets and on the black market, but they are also shared with friends and family as a “help” to get through a stressed or hard period in one’s life. What’s worse, because of their clinical efficiency when used properly, even doctors often prescribe them for minor problems and in the wrong dosages, or for too long of a time period. Although there are many positive sides of benzodiazepines and they can be extremely useful for many patients, which we will talk about in a minute, there is also a great risk attached to them, which not so many people are aware of. But let’s start from the beginning – how do they work?

Issue 21 Presenting Alumni

Julia Hamblin-Trué: “Seek discomfort – the uncomfortable things we say yes to make us grow the most”

This issue comes with yet another alumni interview. This time we wish to present to you Julia Hamblin-Trué, a pretty loyal alumni member and, as you’ll probably agree after getting to know her, a Swiss knife of Summer School of Science. Julia is currently an undergraduate student at CODE University of Applied Sciences in Berlin, where she studies Product Management. Her Summer School of Science journey started back in 2017 when she was a participant in S3++ camp. Continue reading and you’ll find out how her S3++ journey continued, where she is now and how she got there.

Issue 20 Understanding Science

HIV – a hero?

Several studies conducted in the 90’s suggested that prevalence of HIV infection was smaller in patients with sickle cell anemia than in healthy individuals. Although the mechanism behind that is still not fully understood, today we know a lot more than we did back at the end of the century. In order to understand the connection between sickle cell anemia and HIV infection, let us first take a look at both of them separately.

Issue 20 Science Shoutout

The most popular anti-procrastination method

Ah, the never-ending cycle of continuous working, feeling you haven’t done enough and then binging on YouTube self-improvement videos hoping to start fresh tomorrow… or on Monday… or, well, at least next year. We have all been there and we have all done that. The amount of money those self-help videos and books make is even more ridiculous when you realize how toxic they can get. However, among the noise there is legit advice and a few methods that have been proven to work and are even applied in school curriculums for children suffering from attention deficits. One of them, the most popular one for sure, is the Pomodoro method.

Issue 19 Understanding Science

Friedreich’s ataxia – a “not so rare” disease

Friedrich’a ataxia (FA) is a progressive neurodegenerative disease that affects 1 in every 50 000 people worldwide. Therefore, it falls under the umbrella of rare diseases. The thing with rare diseases is that it’s hard to get funding for researching their pathophysiology and possible therapies (ergo the name “orphan drugs”). However, with the recent rise of gene therapy, more and more private investors put their money towards finding a cure for 1 in 50 000 people. So don’t be misled by the title of this article – FA is still a rare disease, but its popularity among research groups and institutes has been growing for the past few years. The main reason for such blooming is the emerging field of gene therapy.

Issue 18 Understanding Science

Ultrasound, magnetic fields and brain tumors – only fiction or a possible reality?

I believe it is safe to say that those of us who were at some point (or maybe still are) glued to our screens watching Grey’s Anatomy often found yourselves intrigued by some of the innovative treatments used on the patients. One of my personal favorites was a clever use of ultrasound waves to treat a hypothalamic hamartoma in a young boy. After that episode, I rushed to the Internet trying to find anything published about the technique. I was amazed by the idea and was trying to find out more about it. Is it really possible? Can it really be used as a completely non-invasive way of treating brain masses, including tumors? Is it safe? Is it maybe already in use? To my disappointment, I found nothing. I’m not sure whether I did a very bad job at googling those facts back then, or maybe really nothing had been published yet. However, I recently stumbled upon a very interesting article about the use of a head-mounted magnetic device that shrinks tumors. Since it reminded me of the cutting-edge treatment from Grey’s Anatomy, I once again googled it, only this time with greater success. As it turns out, a lot has been done and published upon this subject over the past few years.