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.read more
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Journal ArticleDOI
Characterization of intrinsically disordered regions in proteins informed by human genetic diversity
Shehab S. Ahmed,Zaara T. Rifat,Ruchi Lohia,Arthur J. Campbell,A. Keith Dunker,Mohammad Sohel Rahman,Sumaiya Iqbal +6 more
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
Ana-Maria Raicu,Dhruva Kadiyala,Madeline Niblock,Aanchal Kumar Jain,Yahui Yang,Kalynn M. Bird,Kayla Bertholf,Akshay Seenivasan,David N. Arnosti +8 more
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
Hengwu Ding,Shiyun Han,Yuan Ye,D. Bi,Sijia Zhang,Ran Yi,Jinming Gao,Jianke Yang,Long-Fei Wu,Xianzhao Kan +9 more
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
Intrinsically unstructured proteins and their functions.
H. Jane Dyson,Peter E. Wright +1 more
TL;DR: Many gene sequences in eukaryotic genomes encode entire proteins or large segments of proteins that lack a well-structured three-dimensional fold, whereas others constitute flexible linkers that have a role in the assembly of macromolecular arrays.
Journal ArticleDOI
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Peter E. Wright,H. Jane Dyson +1 more
TL;DR: Many proteins that lack intrinsic globular structure under physiological conditions have now been recognized, and it appears likely that their rapid turnover, aided by their unstructured nature in the unbound state, provides a level of control that allows rapid and accurate responses of the cell to changing environmental conditions.
Journal ArticleDOI
Progressive sequence alignment as a prerequisite to correct phylogenetic trees.
Da-Fei Feng,Russell F. Doolittle +1 more
TL;DR: A progressive alignment method that utilizes the Needleman and Wunsch pairwise alignment algorithm iteratively to achieve the multiple alignment of a set of protein sequences and to construct an evolutionary tree depicting their relationship is described.
Journal ArticleDOI
Prediction and functional analysis of native disorder in proteins from the three kingdoms of life.
TL;DR: An automatic method for recognizing natively disordered regions from amino acid sequence is described and benchmarked against predictors that were assessed at the latest critical assessment of techniques for protein structure prediction (CASP) experiment and represents a statistically significant improvement on the methods evaluated on the same targets at CASP.
Journal ArticleDOI
Intrinsically disordered proteins in cellular signalling and regulation.
Peter E. Wright,H. Jane Dyson +1 more
TL;DR: Experimental, computational and bioinformatic analyses combine to identify and characterize disordered regions of proteins, leading to a greater appreciation of their widespread roles in biological processes.