Disordered spaghetti-like proteins finally characterised

Breaking new ground 4. jul 2024 3 min Professor Kresten Lindorff-Larsen Written by Kristian Sjøgren

Many human proteins do not act in a well-defined and orderly way, and researchers have long had difficulty understanding them. A major study has now characterised these intrinsically disordered proteins.

The human body has about 21,000 proteins. Most are well ordered and structured and have a specific function, such as enzymes that cleave molecules or receptors that bind to signalling substances.

About 30% of these proteins, however, do not have a well-ordered structure, and researchers have long had difficulty in understanding how these disordered structures affect function.

In a new study, researchers addressed this by creating a tool that can describe intrinsically disordered proteins and explain how the sequence of these proteins is related to biological function and how these special proteins have developed over evolutionary time.

“We have been studying individual examples of these proteins for many years, but we decided to look at them all simultaneously and investigate their structural properties. Although the intrinsically disordered proteins do not have a well-defined structure, their structure can still be important, and we have now elucidated this,” explains Kresten Lindorff-Larsen, a researcher behind the study and Professor, Department of Biology, University of Copenhagen, Denmark.

The research, which began as a BSc project by Anna Ida Trolle co-supervised by Giulio Tesei, has been published in Nature.

Parts of proteins can be disordered

Describing 30% of human proteins as intrinsically disordered does not mean that three of 10 whole proteins are disordered. Many proteins can have disordered regions, and 30% of amino acid residues in the proteins do not conform to a well-defined structure.

Kresten Lindorff-Larsen says that the disordered proteins behave very differently from what researchers are used to understanding and describing.

“We know relatively little about these proteins. Their amino acid composition differs from that of ordinary proteins. which typically have a hydrophobic, or water-repelling, part that they hide and then a hydrophilic part facing the water or the cells. The disordered proteins do not have the same properties and cannot fold in the same way as normal proteins, because they lack the necessary amino acids to stabilise a folded structure,” he adds.

According to Kresten Lindorff-Larsen, proteins can be compared to pasta. Normal proteins are like fusilli with a well-defined shape, and the disordered proteins are like cooked spaghetti.

“This means that, unlike other proteins, the disordered proteins do not function well as enzymes or being used as structural proteins in constructing cells. But they have other roles. For example, they are important for regulating genes, can function as peptide hormones or can participate in other ways in cellular signalling. This is connected to the fact that their structure means that they can often bind to many other molecules,” says Kresten Lindorff-Larsen.

Answering fundamental questions

The researchers developed a molecular model that enabled them to study all the intrinsically disordered proteins simultaneously.

Humans have 21,000 proteins with 28,000 ensembles without a well-defined structure, and the researchers made molecular simulations of these to examine them in several ways.

The researchers investigated the relationship between the proteins’ sequences of amino acids and their structure. The model shows for the first time how certain types of sequences of amino acids lead to special properties in proteins, which gives them the spaghetti-like structure. The researchers also discovered how different sequences of amino acids lead to different spaghetti-like properties.

The researchers also showed how certain biological functions of disordered proteins are related to the structural properties mentioned above. For example, more compact disordered proteins are often involved in regulating gene expression. The proteins involved in signalling are often more elongated.

“We found that the protein sequences were associated with their structural properties and then that the structural properties were associated with function. This is the first time anyone has characterised these associations,” explains Kresten Lindorff-Larsen.

The researchers also investigated evolutionary conservation. Kresten Lindorff-Larsen explains that studying the evolution of these proteins is difficult because they act differently from other proteins. However, this part of the study revealed that the amino acid sequences do not need to be very similar between related disordered proteins in different organisms as long as the overall properties are similar. If a certain disordered protein with a special function is compact in humans, it is also often compact in mice and yeast, even though the amino acid sequences may be very different.

Implications for understanding disease

Kresten Lindorff-Larsen says that the research is basic science but can have great practical significance in the long term.

He leads the Protein Interactions and Stability in Medicine and Genomics (PRISM) research centre at the University of Copenhagen, where researchers investigate how genetic variation affects the risk of disease.

However, examining the disordered proteins and understanding how mutations in the genes that code for them can cause disease has been difficult because many of the proteins have been written in a language “that we can neither fully read nor write”.

Using the model developed now enables the researchers to determine the disordered proteins’ amino acid sequence, structure and function much more easily.

If the proteins have a role in health and disease, being able to characterise the proteins could also improve understanding of diseases and the opportunities for treatment.

“We have long studied how mutations in the well-ordered proteins have led to hereditary disease, but we have very poorly understood how disordered proteins contribute to this because we have not known how changes in the amino acid sequence can change function. We understand this better now, and it enables improved understanding of disease and opportunities to predict why hereditary diseases occur and eventually perhaps treat the people who have them,” concludes Kresten Lindorff-Larsen.

Conformational ensembles of the human intrinsically disordered proteome” has been published in Nature. The study received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Actions and the Novo Nordisk Foundation.

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