A new LMU study shows how proteins function reliably even without a stable 3D structure – and the crucial importance not only of short sequence motifs, but also of the chemical characteristics.
Many proteins do not only consist of stably folded components. They also contain flexible parts known as intrinsically disordered regions (IDRs), which do not form any stable three-dimensional structure and yet perform key tasks in the cell. “Such disordered protein domains comprise around one third of all protein structures. Recently, they received much attention, as it has become apparent that they engage in a particularly varied range of interactions, are able to form biomolecular condensates, and are involved in practically all major cell functions,” explains Professor Philipp Korber, group leader at the Chair of Molecular Biology at LMU’s Biomedical Center.
These disordered regions have long puzzled researchers: Their linear amino acid sequences are often hardly conserved during evolution, even though their function remains the same. A new study, which appeared recently in the journal Nature Cell Biology, resolves this apparent contradiction. According to the authors, the varied combinations of two properties are decisive: the linear amino acid sequence of short stretches (motifs) and the chemical characteristics of the broader region as a whole.
Flexible segments with crucial role
For their work, the researchers from LMU Munich, the Technical University of Munich (TUM), Helmholtz Munich, and Washington University in St. Louis investigated an essential disordered protein segment of the yeast protein Abf1. Using this easy-to-manipulate model system, they systematically experimented with over 150 Abf1 variants to see which modified and, in some cases, newly designed sequences could replace the function of the natural segment. Their results showed that short binding motifs play an important role – that is to say, small linear sequence segments that enable very specific molecular contacts. Another important contribution, they discovered, comes from the overall chemical context, such as the amount of negative charges and water-soluble or poorly soluble amino acids within the disordered region. It is the interplay of these two aspects – the linear motifs and the broader chemical context – that determines whether the protein region is functional.
“Intrinsically disordered regions appear contradictory at first glance: They are biologically very important, yet they are often insufficiently explained by classical sequence comparisons,” says Korber, who led the study together with Alex Holehouse, Professor of Biochemistry and Molecular Biophysics at Washington University. “Our results show that their function does not depend on a conserved linear blueprint, but on the variable interplay of different proportions of linear sequence motifs and physicochemical characteristics.”
When chemistry balances out an absent motif
Particularly surprising was a finding that is relevant beyond the specific model system: a binding motif that is indispensable in the naturally evolved protein region can become dispensable under certain conditions. This is because the chemical characteristics of the surrounding sequence context can be modified such that it balances out the loss of function. Conversely, it is not sufficient to just retain the rough composition of a region when the critical motif is destroyed or the chemical context is unfavorable. The study thus makes it clear that IDRs operate in a sort of functional landscape in which various molecular solutions can lead to the same result.
“This enormously expands the space of possible functional sequences,” notes Korber. “The evolution of intrinsically disordered regions can clearly use various molecular strategies and still retain the same biological function. This helps us understand why these protein regions can be so variable in the course of evolution without losing their function.”
New perspectives for evolutionary biology and medicine
The work thus provides a general framework for better understanding the evolution of disordered protein regions. At the same time, it opens up new perspectives for biomedical research. Many disease-relevant changes affect such flexible protein segments, whose importance has been difficult to gauge to date. If their function arises not solely from an exact sequence, but from an interplay of motifs and chemical characteristics, this could help researchers better interpret mutations in the future and design synthetic proteins in a more targeted manner.