What is the concept of fuzziness?
Fuzziness is a general concept that is used in many fields (mathematics, linguistics, electronics, psychology) when the boundary or value of an application varies according to the context or conditions. In fuzzy protein complexes the conformational ensemble is shifted according to the cellular context to fine-tune activity. Thus fuzziness establishes a direct relationship between structural heterogeneity and protein function, while 'intrinsic disorder' is a structural term that characterizes the unbound state of proteins.
Are fuzzy complexes intrinsically disordered?
Intrinsically disordered proteins often retain a significant degree of structural multiplicity/heterogeneity in their complexes, which will likely be fuzzy.
What is the difference between disordered proteins and fuzzy complexes?
Referred to as intrinsically disordered, proteins lack a well-defined structure in their unbound states. Referred to as fuzzy structures, IDRs may alternatively either fold into ensembles of structured conformations or remain largely disordered, exhibiting a fast exchange of conformations in their bound, complex states.
Why fuzzy complexes are not termed as disordered protein complexes?
The main difference between the two concepts is that fuzziness establishes a direct relationship between structural heterogeneity and protein function. In contrast, 'intrinsic disorder' is a structural term that is mostly used for unbound state of proteins.
How do I know that I have a fuzzy complex?
If a protein region is protease-sensitive in the complex, resists crystallization or is missing from electron density, does not exhibit permanent contacts even in solution-based spectroscopic techniques (NMR, FRET); yet changes affinity, transcriptional or enzymatic activity or regulatory pathways if removed or mutated.
How can I demonstrate the fuzziness of complex?
You will need to demonstrate the structural heterogeneity in the partner-bound form of your protein. You may compare the spectrum of the complex with that in the free form and show the lack of significant shifts. You may also use parameters characterizing the dynamics of proteins and show that they increase upon complex formation. In case you have static fuzziness, you need at least two complex structures of the same region and partner, but exhibiting different forms/interactions. Functionally, you need to have variant(s) with mutations, deletions, truncations affecting the heterogeneous region and compare the affinity/activity/localization to that of wild type protein, demonstrating considerable difference.
How the database helps to analyze my model system?
Fuzzy complexes in the database are categorized based on topology and mechanism. Please relate your protein to those in the same topological category (P,C,F,R) and similar activities. You can also select the organism of your protein. Once these filters are applied, you will see the experimental techniques, which were used to analyze related systems. You may use the PDB or BMRB link for more detailed analysis of spectral data. Each entry has an expanded description page, where the experimental data indicating fuzziness is presented, the molecular mechanisms are elaborated and are the significance of fuzziness is explained. You may compare your model system to other complexes to see the available scenarios within a specific topological setup.
What can I do if my model system turns out to be fuzzy?
Please use the upload page of the FuzDB database, and submit the name of your protein and its partner and the structural as well as the biochemical evidence for fuzziness. The detailed instructions can be found in the upload page. You will be contacted by email to complete the information for a database entry.
What is the significance of fuzziness in structural biology?
Structural biology is engraved in a deterministic relationship between protein sequence, structure and function. Proteins without a well-defined three dimensional conformation in their native state contradict this paradigm. Termed as intrinsically disordered (ID), these proteins transformed our thinking on the structural pre-requisites of biological functions. Upon interacting with their partners however, ID proteins were assumed to adopt a folded state and follow the classical principles.
The concept of fuzzy complexes brings the importance of structural multiplicity to a new level and establishes a direct relationship between structural heterogeneity and biological function. These proteins not only preserve conformational freedom in their bound forms, but this property also contributes to formation, activity or regulation of their complexes. The direct connection between the conformational ensembles and functions of proteins is the basis of a new, stochastic paradigm, which leads to a more holistic view on how proteins fulfill their biological roles.
How fuzziness can be applied to interpret protein function?
Shifting conformational ensembles of proteins upon signals or changes in context may have significant functional consequences. A specific activity can be up- or downregulated in a variety of ways (gradual, threshold etc.), but can also be switched to a different function. Furthermore, sequence requirements in fuzzy complexes are rather loose, mostly restricted to binding motifs. This allows a high degree of variability in sequence, and a series of different sequences with the same amino acid composition could perform same or similar functions, leading to a more stochastic relationship between sequences, structures and functions of proteins. We propose that this stochastic relationship is also applicable to other proteins, for example to enzymes with globular structures and promiscuous activities.