AlphaFold and Implications for Intrinsically Disordered Proteins

Recent Developments in the Field of Intrinsically Disordered Proteins: Intrinsic Disorder–Based Emergence in Cellular Biology in Light of the Physiological and Pathological Liquid–Liquid Phase Transitions

(2021) Vladimir N. Uversky   Annual Review of Biophysics

Physics-based computational and theoretical approaches to intrinsically disordered proteins

(2021) Joan-Emma Shea et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Critical assessment of protein intrinsic disorder prediction

(2021) Marco Necci et al.   NATURE METHODS

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome

(2021) Maxwell I. Zimmerman et al.   Nature Chemistry

Discovery of drugs that directly target the intrinsically disordered region of the androgen receptor

(2020) Marianne D. Sadar   Expert Opinion on Drug Discovery

Controlling Structural Bias in Intrinsically Disordered Proteins Using Solution Space Scanning

(2020) Alex S. Holehouse et al.   Journal of Chemical Theory and Computation

Sequence-based determinants and prediction of fuzzy interactions in protein complexes

(2020) Marton Miskei et al.   JOURNAL OF MOLECULAR BIOLOGY

Valence and patterning of aromatic residues determine the phase behavior of prion-like domains

(2020) Erik W. Martin et al.   SCIENCE

Flanking Regions Determine the Structure of the Poly-Glutamine in Huntingtin through Mechanisms Common among Glutamine-Rich Human Proteins

(2020) Annika Urbanek et al.   STRUCTURE

Making the Case for Disordered Proteins and Biomolecular Condensates in Bacteria

(2020) Megan C. Cohan et al.   TRENDS IN BIOCHEMICAL SCIENCES

Interactions by Disorder – A Matter of Context

(2020) Katrine Bugge et al.   Frontiers in Molecular Biosciences

Robust Cell-Free Expression of Sub-Pathological and Pathological Huntingtin Exon-1 for NMR Studies. General Approaches for the Isotopic Labeling of Low-Complexity Proteins

(2020) Anna Morató et al.   Biomolecules

Revealing the Hidden Sensitivity of Intrinsically Disordered Proteins to their Chemical Environment

(2020) David Moses et al.   Journal of Physical Chemistry Letters

MobiDB: intrinsically disordered proteins in 2021

(2020) Damiano Piovesan et al.   NUCLEIC ACIDS RESEARCH

Improvements to the ABSINTH forcefield for proteins based on experimentally derived amino-acid specific backbone conformational statistics

(2019) Jeong-Mo Choi et al.   Journal of Chemical Theory and Computation

Efficient Ensemble Refinement by Reweighting

(2019) Jürgen Köfinger et al.   Journal of Chemical Theory and Computation

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

(2019) Taraneh Zarin et al.   eLife

Information theoretic measures for quantifying sequence–ensemble relationships of intrinsically disordered proteins

(2019) Megan C Cohan et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Relationship of Sequence and Phase Separation in Protein Low-Complexity Regions

(2018) Erik W. Martin et al.   BIOCHEMISTRY

Tadpole-like Conformations of Huntingtin Exon 1 Are Characterized by Conformational Heterogeneity that Persists regardless of Polyglutamine Length

(2018) Estella A. Newcombe et al.   JOURNAL OF MOLECULAR BIOLOGY

Sequence-to-Conformation Relationships of Disordered Regions Tethered to Folded Domains of Proteins

(2018) Anuradha Mittal et al.   JOURNAL OF MOLECULAR BIOLOGY

Idiosyncrasies of hnRNP A1-RNA recognition: Can binding mode influence function

(2018) Jeffrey D. Levengood et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

An ultraweak interaction in the intrinsically disordered replication machinery is essential for measles virus function

(2018) Sigrid Milles et al.   Science Advances

Experimentally derived and computationally optimized backbone conformational statistics for blocked amino acids

(2018) Jeong-Mo Choi et al.   Journal of Chemical Theory and Computation

The Cellular Environment Affects Monomeric α-Synuclein Structure

(2018) Amberley D. Stephens et al.   TRENDS IN BIOCHEMICAL SCIENCES

Monomeric Huntingtin Exon 1 Has Similar Overall Structural Features for Wild-Type and Pathological Polyglutamine Lengths

(2017) John B. Warner et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mutation effects predicted from sequence co-variation

(2017) Thomas A Hopf et al.   NATURE BIOTECHNOLOGY

Selection maintains signaling function of a highly diverged intrinsically disordered region

(2017) Taraneh Zarin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Control of transcriptional activity by design of charge patterning in the intrinsically disordered RAM region of the Notch receptor

(2017) Kathryn P. Sherry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design Principles Involving Protein Disorder Facilitate Specific Substrate Selection and Degradation by the Ubiquitin-Proteasome System

(2016) Mainak Guharoy et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Electric-field-stimulated protein mechanics

(2016) Doeke R. Hekstra et al.   NATURE

FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies

(2016) Marton Miskei et al.   NUCLEIC ACIDS RESEARCH

Computational identification of MoRFs in protein sequences

(2015) Nawar Malhis et al.   BIOINFORMATICS

Relating sequence encoded information to form and function of intrinsically disordered proteins

(2015) Rahul K Das et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A Rigorous and Efficient Method To Reweight Very Large Conformational Ensembles Using Average Experimental Data and To Determine Their Relative Information Content

(2015) Hoi Tik Alvin Leung et al.   Journal of Chemical Theory and Computation

Visualizing the Molecular Recognition Trajectory of an Intrinsically Disordered Protein Using Multinuclear Relaxation Dispersion NMR

(2015) Robert Schneider et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins

(2015) Mihaly Varadi et al.   PLoS One

Classification of Intrinsically Disordered Regions and Proteins

(2014) Robin van der Lee et al.   CHEMICAL REVIEWS

Long-Range Correlated Dynamics in Intrinsically Disordered Proteins

(2014) Giacomo Parigi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Small-Angle X-Ray Scattering- and Nuclear Magnetic Resonance-Derived Conformational Ensemble of the Highly Flexible Antitoxin PaaA2

(2014) Yann G.J. Sterckx et al.   STRUCTURE

Sequence co-evolution gives 3D contacts and structures of protein complexes

(2014) Thomas A Hopf et al.   eLife

A quantitative measure for protein conformational heterogeneity

(2013) Nicholas Lyle et al.   JOURNAL OF CHEMICAL PHYSICS

Homonuclear decoupling for enhancing resolution and sensitivity in NOE and RDC measurements of peptides and proteins

(2013) Jinfa Ying et al.   JOURNAL OF MAGNETIC RESONANCE

Emerging methods in protein co-evolution

(2013) David de Juan et al.   NATURE REVIEWS GENETICS

pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins

(2013) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

Genome-scale prediction of proteins with long intrinsically disordered regions

(2013) Zhenling Peng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Describing sequence–ensemble relationships for intrinsically disordered proteins

(2012) Albert H. Mao et al.   BIOCHEMICAL JOURNAL

Improved Atomistic Monte Carlo Simulations Demonstrate That Poly-l-Proline Adopts Heterogeneous Ensembles of Conformations of Semi-Rigid Segments Interrupted by Kinks

(2012) Aditya Radhakrishnan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Chemical composition is maintained in poorly conserved intrinsically disordered regions and suggests a means for their classification

(2012) Harry Amri Moesa et al.   Molecular BioSystems

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites

(2012) G. R. Bowman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy

(2012) H. Hofmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution and disorder

(2011) Celeste J Brown et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intrinsic disorder in measles virus nucleocapsids

(2011) M. R. Jensen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analyzing protein structure and function using ancestral gene reconstruction

(2010) Michael J Harms et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Target gene context influences the transcriptional requirement for the KAT3 family of CBP and p300 histone acetyltransferases

(2010) David C. Bedford et al.   Epigenetics

NMR Characterization of Long-Range Order in Intrinsically Disordered Proteins

(2010) Loïc Salmon et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Net charge per residue modulates conformational ensembles of intrinsically disordered proteins

(2010) A. H. Mao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linking folding and binding

(2009) Peter E Wright et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Prediction of Protein Binding Regions in Disordered Proteins

(2009) Bálint Mészáros et al.   PLoS Computational Biology

The effects of conformational heterogeneity on the binding of the Notch intracellular domain to effector proteins: a case of biologically tuned disorder

(2008) Angela Bertagna et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

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

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

Malleable Machines in Transcription Regulation: The Mediator Complex

(2008) Ágnes Tóth-Petróczy et al.   PLoS Computational Biology

A simple model for polyproline II structure in unfolded states of alanine-based peptides

(2002) Rohit V. Pappu et al.   PROTEIN SCIENCE