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In many ways, the disordered regions that contain SLiMs constitute flexible disorder as by the above classification, as their main role is to provide flexibility to enable access to the linear motif for proteins that will bind them as ligands or introduce post-translational modifications.
Constrained disordered residues also occur more often in annotated protein sequence families (domains) than flexible disorder, but both types are strongly depleted in domains compared to structured regions.
Flexible disorder is the most common of the three evolutionary classes with just over one-half of disordered residues in yeast.
For such flexible disordered regions, we speculate that the relatively small size of the antibody binding site provides insufficient binding energy to fold the flexible disorder and therefore cannot bind tightly enough for the generation of an immune response.
For flexible disorder, low sequence conservation is expected if the property of disorder itself, as opposed to disorder in combination with specific sequence, is the only requirement for function.
For example, assignment of evolutionarily constrained or flexible disorder requires automatic alignment of amino acid and disorder sequences, while gene expression subtypes can be derived from the wealth of microarray and RNA sequencing data.
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Most disorder prediction algorithms [such as DISOPRED, Ward et al. (2004)] perform well for stable globular domains or highly flexible disordered regions without a strong structural preference.
This is because the monomeric structures of the protomers are used, which may have flexible loops or disorder regions.
In human, both flexible and constrained disorder are enriched in proteins functioning in differentiation and development, which reflects the importance of IDPs in these processes.
Information about sequence conservation (see section 7.1) is another important aspect and could provide clues about evolutionarily constrained or flexible types of disorder, which are implicated in different types of functions.
Here, the evolutionary dynamics of structurally ordered and disordered (flexible) regions are investigated genome-wide in flaviviruses, revealing that the amount and location of structural disorder fluctuates highly among related proteins.
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