Biological soft matter: intrinsically disordered proteins in liquid–liquid phase separation and biomolecular condensates

AV Fonin, IA Antifeeva, IM Kuznetsova… - Essays in …, 2022 - portlandpress.com
The facts that many proteins with crucial biological functions do not have unique structures
and that many biological processes are compartmentalized into the liquid-like biomolecular …

Evolution of short linear motifs and disordered proteins Topic: yeast as model system to study evolution

AG Sangster, T Zarin, AM Moses - Current Opinion in Genetics & …, 2022 - Elsevier
Evolutionary preservation of protein structure had a major influence on the field of molecular
evolution: changes in individual amino acids that did not disrupt protein folding would either …

Proteome-wide signatures of function in highly diverged intrinsically disordered regions

T Zarin, B Strome, AN Nguyen Ba, S Alberti… - Elife, 2019 - elifesciences.org
Intrinsically disordered regions make up a large part of the proteome, but the sequence-to-
function relationship in these regions is poorly understood, in part because the primary …

Intrinsic disorder in human RNA-binding proteins

B Zhao, A Katuwawala, CJ Oldfield, G Hu, Z Wu… - Journal of Molecular …, 2021 - Elsevier
Although RNA-binding proteins (RBPs) are known to be enriched in intrinsic disorder, no
previous analysis focused on RBPs interacting with specific RNA types. We fill this gap with …

Strong evidence for the adaptive walk model of gene evolution in Drosophila and Arabidopsis

AF Moutinho, A Eyre-Walker, JY Dutheil - PLoS biology, 2022 - journals.plos.org
Understanding the dynamics of species adaptation to their environments has long been a
central focus of the study of evolution. Theories of adaptation propose that populations …

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

SS Ahmed, ZT Rifat, R Lohia, AJ Campbell… - PLoS Computational …, 2022 - journals.plos.org
All proteomes contain both proteins and polypeptide segments that don't form a defined
three-dimensional structure yet are biologically active—called intrinsically disordered …

Evolution of virus-like features and intrinsically disordered regions in retrotransposon-derived mammalian genes

R Cagliani, D Forni, A Mozzi, R Fuchs… - Molecular Biology …, 2024 - academic.oup.com
Several mammalian genes have originated from the domestication of retrotransposons,
selfish mobile elements related to retroviruses. Some of the proteins encoded by these …

Mediator subunit Med15 dictates the conserved “fuzzy” binding mechanism of yeast transcription activators Gal4 and Gcn4

LM Tuttle, D Pacheco, L Warfield, DB Wilburn… - Nature …, 2021 - nature.com
The acidic activation domain (AD) of yeast transcription factor Gal4 plays a dual role in
transcription repression and activation through binding to Gal80 repressor and Mediator …

[HTML][HTML] Evolution of the orthopoxvirus core genome

C Molteni, D Forni, R Cagliani, A Mozzi, M Clerici… - Virus Research, 2023 - Elsevier
Orthopoxviruses comprise several relevant pathogens, including the causative agent of
smallpox and monkeypox virus. Analysis of orthopoxvirus genome evolution mainly focused …

Evolution of weak cooperative interactions for biological specificity

A Gao, K Shrinivas, P Lepeudry… - Proceedings of the …, 2018 - National Acad Sciences
A hallmark of biological systems is that particular functions and outcomes are realized in
specific contexts, such as when particular signals are received. One mechanism for …