Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains

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

(2021) Lisa M. Tuttle et al.   Nature Communications

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator

(2021) Adrian L Sanborn et al.   eLife

A High-Throughput Screen for Transcription Activation Domains Reveals Their Sequence Features and Permits Prediction by Deep Learning

(2020) Ariel Erijman et al.   MOLECULAR CELL

Disordered proteins follow diverse transition paths as they fold and bind to a partner

(2020) Jae-Yeol Kim et al.   SCIENCE

High-Throughput Discovery and Characterization of Human Transcriptional Effectors

(2020) Josh Tycko et al.   CELL

Inferring protein 3D structure from deep mutation scans

(2019) Nathan J. Rollins et al.   NATURE GENETICS

Determining protein structures using deep mutagenesis

(2019) Jörn M. Schmiedel et al.   NATURE GENETICS

Logomaker: beautiful sequence logos in Python

(2019) Ammar Tareen et al.   BIOINFORMATICS

Transcription Activation Domains of the Yeast Factors Met4 and Ino2: Tandem Activation Domains with Properties Similar to the Yeast Gcn4 Activator

(2018) Derek Pacheco et al.   MOLECULAR AND CELLULAR BIOLOGY

High‐throughput discovery of functional disordered regions: investigation of transactivation domains

(2018) Charles NJ Ravarani et al.   Molecular Systems Biology

Indel-correcting DNA barcodes for high-throughput sequencing

(2018) John A. Hawkins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genetic landscape of a physical interaction

(2018) Guillaume Diss et al.   eLife

A High-Throughput Mutational Scan of an Intrinsically Disordered Acidic Transcriptional Activation Domain

(2018) Max V. Staller et al.   Cell Systems

Mutational processes shape the landscape of TP53 mutations in human cancer

(2018) Andrew O. Giacomelli et al.   NATURE GENETICS

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Engineering Epigenetic Regulation Using Synthetic Read-Write Modules

(2018) Minhee Park et al.   CELL

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Long-range regulation of p53 DNA binding by its intrinsically disordered N-terminal transactivation domain

(2018) Alexander S. Krois et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diffusion-limited association of disordered protein by non-native electrostatic interactions

(2018) Jae-Yeol Kim et al.   Nature Communications

Analysis of Large-Scale Mutagenesis Data To Assess the Impact of Single Amino Acid Substitutions

(2017) Vanessa E. Gray et al.   GENETICS

ETV4 and AP1 Transcription Factors Form Multivalent Interactions with three Sites on the MED25 Activator-Interacting Domain

(2017) Simon L. Currie et al.   JOURNAL OF MOLECULAR BIOLOGY

Hypersensitive termination of the hypoxic response by a disordered protein switch

(2017) Rebecca B. Berlow et al.   NATURE

Structural characterization of interactions between transactivation domain 1 of the p65 subunit of NF-κB and transcription regulatory factors

(2017) Lauriane Lecoq et al.   NUCLEIC ACIDS RESEARCH

Analysis of Large-Scale Mutagenesis Data To Assess the Impact of Single Amino Acid Substitutions

(2017) Vanessa E. Gray et al.   GENETICS

Role of Intrinsic Protein Disorder in the Function and Interactions of the Transcriptional Coactivators CREB-binding Protein (CBP) and p300

(2016) H. Jane Dyson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Sequence Determinants of the Conformational Properties of an Intrinsically Disordered Protein Prior to and upon Multisite Phosphorylation

(2016) Erik W. Martin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Prospective functional classification of all possible missense variants in PPARG

(2016) Amit R Majithia et al.   NATURE GENETICS

The Transactivation Domains of the p53 Protein

(2016) Nitin Raj et al.   Cold Spring Harbor Perspectives in Medicine

The Ying and Yang of STAT3 in Human Disease

(2015) Tiphanie P. Vogel et al.   JOURNAL OF CLINICAL IMMUNOLOGY

Conformation and Dynamics of the Troponin I C-Terminal Domain: Combining Single-Molecule and Computational Approaches for a Disordered Protein Region

(2015) Lauren Ann Metskas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

A sequence-specific transcription activator motif and powerful synthetic variants that bind Mediator using a fuzzy protein interface

(2014) L. Warfield et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast

(2012) R. Scott McIsaac et al.   NUCLEIC ACIDS RESEARCH

Transient structure and dynamics in the disordered c-Myc transactivation domain affect Bin1 binding

(2012) Cecilia Andresen et al.   NUCLEIC ACIDS RESEARCH

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Distinct p53 Transcriptional Programs Dictate Acute DNA-Damage Responses and Tumor Suppression

(2011) Colleen A. Brady et al.   CELL

The Acidic Transcription Activator Gcn4 Binds the Mediator Subunit Gal11/Med15 Using a Simple Protein Interface Forming a Fuzzy Complex

(2011) Peter S. Brzovic et al.   MOLECULAR CELL

Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation

(2010) James A. Goodrich et al.   NATURE REVIEWS GENETICS

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

(2010) J. B. Kinney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Charge as a Selection Criterion for Translocation through the Nuclear Pore Complex

(2010) Lucy J. Colwell et al.   PLoS Computational Biology

Structural basis for recruitment of CBP/p300 coactivators by STAT1 and STAT2 transactivation domains

(2009) Jonathan M Wojciak et al.   EMBO JOURNAL

Multiple Intrinsically Disordered Sequences Alter DNA Binding by the Homeodomain of theDrosophilaHox Protein Ultrabithorax

(2008) Ying Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions

(2008) Andreas Vitalis et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY