The Mediator complex as a master regulator of transcription by RNA polymerase II

WF Richter, S Nayak, J Iwasa, DJ Taatjes - Nature Reviews Molecular …, 2022 - nature.com
The Mediator complex, which in humans is 1.4 MDa in size and includes 26 subunits,
controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining …

Advances in targeting 'undruggable'transcription factors with small molecules

MJ Henley, AN Koehler - Nature Reviews Drug Discovery, 2021 - nature.com
Transcription factors (TFs) represent key biological players in diseases including cancer,
autoimmunity, diabetes and cardiovascular disease. However, outside nuclear receptors …

Multifunctional intrinsically disordered regions in transcription factors

M Már, K Nitsenko… - Chemistry–A European …, 2023 - Wiley Online Library
Eukaryotic transcription factors (TFs) are the final integrators of a complex molecular
feedback mechanism that interfaces with the genome, consolidating information for …

[HTML][HTML] On the potential of machine learning to examine the relationship between sequence, structure, dynamics and function of intrinsically disordered proteins

K Lindorff-Larsen, BB Kragelund - Journal of Molecular Biology, 2021 - Elsevier
Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and
many diverging properties. IDPs—and intrinsically disordered regions (IDRs) interspersed …

Quantification of conformational entropy unravels effect of disordered flanking region in coupled folding and binding

FF Theisen, L Staby, FG Tidemand… - Journal of the …, 2021 - ACS Publications
Intrinsic disorder (ID) constitutes a new dimension to the protein structure–function
relationship. The ability to undergo conformational changes upon binding is a key property …

Transcription factor dynamics

F Lu, T Lionnet - Cold Spring Harbor Perspectives in …, 2021 - cshperspectives.cshlp.org
To predict transcription, one needs a mechanistic understanding of how the numerous
required transcription factors (TFs) explore the nuclear space to find their target genes …

Sequence-and chemical specificity define the functional landscape of intrinsically disordered regions

I Langstein-Skora, A Schmid, F Huth, D Shabani… - BioRxiv, 2022 - biorxiv.org
Intrinsically disordered protein regions (IDRs) pervasively engage in essential molecular
functions, yet they are often poorly conserved as assessed by sequence alignment. To …

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 …

Commonly asked questions about transcriptional activation domains

A Udupa, SR Kotha, MV Staller - Current Opinion in Structural Biology, 2024 - Elsevier
Eukaryotic transcription factors activate gene expression with their DNA-binding domains
and activation domains. DNA-binding domains bind the genome by recognizing structurally …

[HTML][HTML] Unveiling induced folding of intrinsically disordered proteins–Protein engineering, frustration and emerging themes

F Malagrinò, A Diop, L Pagano, C Nardella… - Current Opinion in …, 2022 - Elsevier
Intrinsically disordered proteins (IDPs) can be generally described as a class of proteins that
lack a well-defined ordered structure in isolation at physiological conditions. Upon binding to …