Patterns of Dynamics Comprise a Conserved Evolutionary Trait

Zsolyomi, Fruzsina; Ambrus, Viktor; Fuxreiter, Mónika

doi:10.1016/j.jmb.2019.11.007

Cited by 8 publications

(3 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…www.nature.com/scientificreports/ However, IDDs indeed exist. The functions of IDDs have been investigated in previous studies 12,[52][53][54][55] , but the comprehensive analysis of the distribution and functional significance of IDDs is lacking. In this study, we investigated the functional and evolutionary characteristics of IDDs at the entire proteome level across three superkingdoms.…”

Section: Discussionmentioning

confidence: 99%

Intrinsic disorder in protein domains contributes to both organism complexity and clade-specific functions

Gao

Wang

et al. 2021

Sci Rep

View full text Add to dashboard Cite

Interestingly, some protein domains are intrinsically disordered (abbreviated as IDD), and the disorder degree of same domains may differ in different contexts. However, the evolutionary causes and biological significance of these phenomena are unclear. Here, we address these issues by genome-wide analyses of the evolutionary and functional features of IDDs in 1,870 species across the three superkingdoms. As the result, there is a significant positive correlation between the proportion of IDDs and organism complexity with some interesting exceptions. These phenomena may be due to the high disorder of clade-specific domains and the different disorder degrees of the domains shared in different clades. The functions of IDDs are clade-specific and the higher proportion of post-translational modification sites may contribute to their complex functions. Compared with metazoans, fungi have more IDDs with a consecutive disorder region but a low disorder ratio, which reflects their different functional requirements. As for disorder variation, it’s greater for domains among different proteins than those within the same proteins. Some clade-specific ‘no-variation’ or ‘high-variation’ domains are involved in clade-specific functions. In sum, intrinsic domain disorder is related to both the organism complexity and clade-specific functions. These results deepen the understanding of the evolution and function of IDDs.

show abstract

Section: Discussionmentioning

confidence: 99%

Intrinsic disorder in protein domains contributes to both organism complexity and clade-specific functions

Gao

Wang

et al. 2021

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Based on mounting evidence from ENMs [20] and parallel studies on residue flexibility [86], protein global dynamics has been suggested to be maximally conserved versus sequence and structure. Nevertheless, the degree of conservation of conformational spaces as well as the contributing factors are unclear.…”

Section: Lowest-frequency Modes and Evolutionmentioning

confidence: 99%

Are Protein Shape-Encoded Lowest-Frequency Motions a Key Phenotype Selected by Evolution?

Orellana

2023

Applied Sciences

View full text Add to dashboard Cite

At the very deepest molecular level, the mechanisms of life depend on the operation of proteins, the so-called “workhorses” of the cell. Proteins are nanoscale machines that transform energy into useful cellular work, such as ion or nutrient transport, information processing, or energy transformation. Behind every biological task, there is a nanometer-sized molecule whose shape and intrinsic motions, binding, and sensing properties have been evolutionarily polished for billions of years. With the emergence of structural biology, the most crucial property of biomolecules was thought to be their 3D shape, but how this relates to function was unclear. During the past years, Elastic Network Models have revealed that protein shape, motion and function are deeply intertwined, so that each structure displays robustly shape-encoded functional movements that can be extraordinarily conserved across the tree of life. Here, we briefly review the growing literature exploring the interplay between sequence evolution, protein shape, intrinsic motions and function, and highlight examples from our research in which fundamental movements are conserved from bacteria to mammals or selected by cancer cells to modulate function.

show abstract

“…In addition, comparative analysis of fuzzy regions can be used to derive evolutionary relationships. In case of low sequence similarity, evolutionary relationships can be indicated based on similar dynamical characteristics ( 48 ). The association of protein domains with fuzzy regions can also be systematically investigated.…”

Section: Database Descriptionmentioning

confidence: 99%

FuzDB: a new phase in understanding fuzzy interactions

Hatos

Monzón

Tosatto

et al. 2021

Nucleic Acids Research

View full text Add to dashboard Cite

Fuzzy interactions are specific, variable contacts between proteins and other biomolecules (proteins, DNA, RNA, small molecules) formed in accord to the cellular context. Fuzzy interactions have recently been demonstrated to regulate biomolecular condensates generated by liquid-liquid phase separation. The FuzDB v4.0 database (https://fuzdb.org) assembles experimentally identified examples of fuzzy interactions, where disordered regions mediate functionally important, context-dependent contacts between the partners in stoichiometric and higher-order assemblies. The new version of FuzDB establishes cross-links with databases on structure (PDB, BMRB, PED), function (ELM, UniProt) and biomolecular condensates (PhaSepDB, PhaSePro, LLPSDB). FuzDB v4.0 is a source to decipher molecular basis of complex cellular interaction behaviors, including those in protein droplets.

show abstract

Patterns of Dynamics Comprise a Conserved Evolutionary Trait

Cited by 8 publications

References 58 publications

Intrinsic disorder in protein domains contributes to both organism complexity and clade-specific functions

Intrinsic disorder in protein domains contributes to both organism complexity and clade-specific functions

Are Protein Shape-Encoded Lowest-Frequency Motions a Key Phenotype Selected by Evolution?

FuzDB: a new phase in understanding fuzzy interactions

Contact Info

Product

Resources

About