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Book ChapterDOI

Functions of intrinsically disordered proteins through evolutionary lenses.

TLDR
In this article, the authors give an overview of the different types of evolutionary behavior of disordered proteins and associated functions in normal and disease settings in both disease and normal settings. But, different evolutionary rules apply for the group of intrinsically disordered regions and proteins (IDR/IDPs) that exist as an ensemble of fluctuating conformations.
Abstract
Protein sequences are the result of an evolutionary process that involves the balancing act of experimenting with novel mutations and selecting out those that have an undesirable functional outcome. In the case of globular proteins, the function relies on a well-defined conformation, therefore, there is a strong evolutionary pressure to preserve the structure. However, different evolutionary rules might apply for the group of intrinsically disordered regions and proteins (IDR/IDPs) that exist as an ensemble of fluctuating conformations. The function of IDRs can directly originate from their disordered state or arise through different types of molecular recognition processes. There is an amazing variety of ways IDRs can carry out their functions, and this is also reflected in their evolutionary properties. In this chapter we give an overview of the different types of evolutionary behavior of disordered proteins and associated functions in normal and disease settings.

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Citations
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Journal ArticleDOI

Characterization of intrinsically disordered regions in proteins informed by human genetic diversity

TL;DR: This study presents a novel approach to assign functional importance to IDRs by leveraging the wealth of available genetic data, which will aid in a deeper understating of the role of IDRs in biological processes and disease mechanisms.
Journal ArticleDOI

The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors.

TL;DR: The early 2020s saw the advent of a new generation of deep learning-based protein structure prediction tools that offer the potential to predict structures based on any number of protein sequences as mentioned in this paper .
Journal ArticleDOI

The Cynosure of CtBP: Evolution of a Bilaterian Transcriptional Corepressor

TL;DR: A comparative phylogenetic study shows that CtBP is a bilaterian innovation whose CTD of about 100 residues is present in almost all orthologs, and highlights the rich regulatory potential of this previously unstudied domain of a central transcriptional regulator.
Journal ArticleDOI

Ten Plastomes of Crassula (Crassulaceae) and Phylogenetic Implications

TL;DR: In this article , the second largest genus in the family Crassulaceae, Crassula L. is the second most common genus in angiosperms, but variable in size, gene content, and evolutionary rates of genes.
Journal ArticleDOI

The DYW domain of RARE1 plays an indispensable role in regulating accD-C794 RNA editing in Arabidopsis thaliana.

TL;DR: In this paper , the authors investigate the correlation between Arabidopsis pentatricopeptide repeat (PPR) proteins and their respective DYW domain functions in RNA editing of accD-C794.
References
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Journal ArticleDOI

PED in 2021: A major update of the protein ensemble database for intrinsically disordered proteins

TL;DR: The renewed PED will be useful for researchers interested in the atomic-level understanding of IDPs function, and promote the rational, structure-based design of IDP-targeting drugs.
Journal ArticleDOI

Dynamic Behavior of an Intrinsically Unstructured Linker Domain Is Conserved in the Face of Negligible Amino Acid Sequence Conservation

TL;DR: The results of this analysis showed that many sites in the IULD are evolving neutrally, suggesting that dynamic behavior can be maintained in the absence of natural selection.
Journal ArticleDOI

Generalized affine gap costs for protein sequence alignment.

TL;DR: A simple generalization of affine gap costs is proposed that allows nonconserved regions to be effectively ignored and the distribution of scores from local alignments using these generalized gap Costs is shown empirically to follow an extreme value distribution.
Journal ArticleDOI

SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions

TL;DR: The use of evolutionary conservation as a discriminatory technique for motif discovery is evaluated, with a statistical framework introduced to assess the significance of relatively conserved residues, and a metric that forms the basis of SLiMPrints (short linear motif fingerprints), a de novo motif discovery tool.
Journal ArticleDOI

Conformational preferences and phase behavior of intrinsically disordered low complexity sequences: insights from multiscale simulations.

TL;DR: How simulations performed across distinct resolutions have provided different types of insights into the biological role of LC sequences is reviewed.
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