Intrinsically Disordered Proteins: Where Computation Meets Experiment

Minimal Model of Self-Assembly: Emergence of Diversity and Complexity

(2014) Bogdan Barz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Discrete Molecular Dynamics Can Predict Helical Prestructured Motifs in Disordered Proteins

(2014) Dániel Szöllősi et al.   PLoS One

Temperature-dependent solvation modulates the dimensions of disordered proteins

(2014) R. Wuttke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting the Predictive Power of IDP Ensembles

(2014) Peter Tompa et al.   STRUCTURE

Prion-like aggregation of mutant p53 in cancer

(2014) Jerson L. Silva et al.   TRENDS IN BIOCHEMICAL SCIENCES

Combining Experiments and Simulations Using the Maximum Entropy Principle

(2014) Wouter Boomsma et al.   PLoS Computational Biology

Contribution of proline to the pre-structuring tendency of transient helical secondary structure elements in intrinsically disordered proteins

(2013) Chewook Lee et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Comparative Studies of Disordered Proteins with Similar Sequences: Application to Aβ40 and Aβ42

(2013) Charles K. Fisher et al.   BIOPHYSICAL JOURNAL

Effect of the amyloid β hairpin's structure on the handedness of helices formed by its aggregates

(2013) Pavan K. GhattyVenkataKrishna et al.   FEBS LETTERS

A Novel Sirtuin 2 (SIRT2) Inhibitor with p53-dependent Pro-apoptotic Activity in Non-small Cell Lung Cancer

(2013) Gesine Hoffmann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Variational Optimization of an All-Atom Implicit Solvent Force Field To Match Explicit Solvent Simulation Data

(2013) Sandro Bottaro et al.   Journal of Chemical Theory and Computation

Native-Based Simulations of the Binding Interaction Between RAP74 and the Disordered FCP1 Peptide

(2013) Sushant Kumar et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Energetic Basis of Uncoupling Folding from Binding for an Intrinsically Disordered Protein

(2013) Igor Drobnak et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Dynamic Structure of α-Synuclein Multimers

(2013) Thomas Gurry et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural Characterization of Intrinsically Disordered Proteins by NMR Spectroscopy

(2013) Simone Kosol et al.   MOLECULES

Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion

(2013) Yongheng Chen et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

Structure and Stability Insights into Tumour Suppressor p53 Evolutionary Related Proteins

(2013) Bruno Pagano et al.   PLoS One

Experiments and simulations show how long-range contacts can form in expanded unfolded proteins with negligible secondary structure

(2013) W. Meng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic structure and hierarchical assembly of a cross-  amyloid fibril

(2013) A. W. P. Fitzpatrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proliferation of amyloid- 42 aggregates occurs through a secondary nucleation mechanism

(2013) S. I. A. Cohen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predictive Atomic Resolution Descriptions of Intrinsically Disordered hTau40 and α-Synuclein in Solution from NMR and Small Angle Scattering

(2013) Martin Schwalbe et al.   STRUCTURE

High-speed atomic force microscopy

(2013) Toshio Ando   Microscopy

Towards the physical basis of how intrinsic disorder mediates protein function

(2012) Jianhan Chen   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Characterization of disordered proteins with ENSEMBLE

(2012) Mickaël Krzeminski et al.   BIOINFORMATICS

Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables

(2012) V. Ozenne et al.   BIOINFORMATICS

Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer

(2012) Yu-Shan Lin et al.   BIOPHYSICAL JOURNAL

Understanding Pre-Structured Motifs (PreSMos) in Intrinsically Unfolded Proteins

(2012) Si-Hyung Lee et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

On the Use of Experimental Observations to Bias Simulated Ensembles

(2012) Jed W. Pitera et al.   Journal of Chemical Theory and Computation

Structural basis for heteromeric assembly and perinuclear organization of keratin filaments

(2012) Chang-Hun Lee et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dimer Formation Enhances Structural Differences between Amyloid β-Protein (1–40) and (1–42): An Explicit-Solvent Molecular Dynamics Study

(2012) Bogdan Barz et al.   PLoS One

Atomic View of a Toxic Amyloid Small Oligomer

(2012) Arthur Laganowsky et al.   SCIENCE

HMGB1-Facilitated p53 DNA Binding Occurs via HMG-Box/p53 Transactivation Domain Interaction, Regulated by the Acidic Tail

(2012) John P. Rowell et al.   STRUCTURE

High-Speed AFM Reveals the Dynamics of Single Biomolecules at the Nanometer Scale

(2011) Allard J. Katan et al.   CELL

Constructing ensembles for intrinsically disordered proteins

(2011) Charles K Fisher et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Unstructural biology coming of age

(2011) Peter Tompa   CURRENT OPINION IN STRUCTURAL BIOLOGY

Anchoring Intrinsically Disordered Proteins to Multiple Targets: Lessons from N-Terminus of the p53 Protein

(2011) Yongqi Huang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Structural Basis for Aβ1–42 Toxicity Inhibition by Aβ C-Terminal Fragments: Discrete Molecular Dynamics Study

(2011) B. Urbanc et al.   JOURNAL OF MOLECULAR BIOLOGY

Crystal Structure of the Amyloid-  p3 Fragment Provides a Model for Oligomer Formation in Alzheimer's Disease

(2011) V. A. Streltsov et al.   JOURNAL OF NEUROSCIENCE

Direct Observations of Conformational Distributions of Intrinsically Disordered p53 Peptides Using UV Raman and Explicit Solvent Simulations

(2011) Kan Xiong et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Protein Structure along the Order–Disorder Continuum

(2011) Charles K. Fisher et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Understanding the structural ensembles of a highly extended disordered protein

(2011) Gary W. Daughdrill et al.   Molecular BioSystems

Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering

(2011) Pau Bernadó et al.   Molecular BioSystems

Structural biology: Breaking the protein rules

(2011) Tanguy Chouard   NATURE

α-Synuclein occurs physiologically as a helically folded tetramer that resists aggregation

(2011) Tim Bartels et al.   NATURE

Amyloid-β forms fibrils by nucleated conformational conversion of oligomers

(2011) Jiyong Lee et al.   Nature Chemical Biology

The amyloid cascade hypothesis for Alzheimer's disease: an appraisal for the development of therapeutics

(2011) Eric Karran et al.   NATURE REVIEWS DRUG DISCOVERY

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

Structure of the p53 Transactivation Domain in Complex with the Nuclear Receptor Coactivator Binding Domain of CREB Binding Protein

(2010) Chul Won Lee et al.   BIOCHEMISTRY

Molecular simulations of protein disorderThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

(2010) Sarah Rauscher et al.   Biochemistry and Cell Biology

Understanding protein non-folding

(2010) Vladimir N. Uversky et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Micelle-Like Architecture of the Monomer Ensemble of Alzheimer’s Amyloid-β Peptide in Aqueous Solution and Its Implications for Aβ Aggregation

(2010) Andreas Vitalis et al.   JOURNAL OF MOLECULAR BIOLOGY

Mechanism of Fiber Assembly: Treatment of Aβ Peptide Aggregation with a Coarse-Grained United-Residue Force Field

(2010) Ana Rojas et al.   JOURNAL OF MOLECULAR BIOLOGY

Elucidation of Amyloid β-Protein Oligomerization Mechanisms: Discrete Molecular Dynamics Study

(2010) B. Urbanc et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Defining Conformational Ensembles of Intrinsically Disordered and Partially Folded Proteins Directly from Chemical Shifts

(2010) Malene Ringkjøbing Jensen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Modeling Intrinsically Disordered Proteins with Bayesian Statistics

(2010) Charles K. Fisher et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A causative link between the structure of aberrant protein oligomers and their toxicity

(2010) Silvia Campioni et al.   Nature Chemical Biology

Structural conversion of neurotoxic amyloid-β1–42 oligomers to fibrils

(2010) Mahiuddin Ahmed et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Stabilization of neurotoxic Alzheimer amyloid-  oligomers by protein engineering

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

Drug discovery and mutant p53

(2010) Magda M. Maslon et al.   TRENDS IN CELL BIOLOGY

The Tumor Suppressor p53: From Structures to Drug Discovery

(2010) A. C. Joerger et al.   Cold Spring Harbor Perspectives in Biology

Thermodynamics of β-Sheet Formation in Polyglutamine

(2009) Andreas Vitalis et al.   BIOPHYSICAL JOURNAL

Probing Energetics of Aβ Fibril Elongation by Molecular Dynamics Simulations

(2009) Takako Takeda et al.   BIOPHYSICAL JOURNAL

Blinded by the Light: The Growing Complexity of p53

(2009) Karen H. Vousden et al.   CELL

Structural biology of the p53 tumour suppressor

(2009) Andrei L Okorokov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Biophysical characterization of intrinsically disordered proteins

(2009) David Eliezer   CURRENT OPINION IN STRUCTURAL BIOLOGY

Finding order within disorder: elucidating the structure of proteins associated with neurodegenerative disease

(2009) Austin Huang et al.   Future Medicinal Chemistry

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structural Interpretation of Paramagnetic Relaxation Enhancement-Derived Distances for Disordered Protein States

(2009) Debabani Ganguly et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure and Disorder in an Unfolded State under Nondenaturing Conditions from Ensemble Models Consistent with a Large Number of Experimental Restraints

(2009) Joseph A. Marsh et al.   JOURNAL OF MOLECULAR BIOLOGY

Kinetic Advantage of Intrinsically Disordered Proteins in Coupled Folding–Binding Process: A Critical Assessment of the “Fly-Casting” Mechanism

(2009) Yongqi Huang et al.   JOURNAL OF MOLECULAR BIOLOGY

Effect of pathogenic mutations on the structure and dynamics of Alzheimer’s Aβ42-amyloid oligomers

(2009) Kristin Kassler et al.   JOURNAL OF MOLECULAR MODELING

Influence of Preformed Asp23−Lys28 Salt Bridge on the Conformational Fluctuations of Monomers and Dimers of Aβ Peptides with Implications for Rates of Fibril Formation

(2009) Govardhan Reddy et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Intrinsically Disordered p53 Extreme C-Terminus Binds to S100B(ββ) through “Fly-Casting”

(2009) Jianhan Chen   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Determination of the Free Energy Landscape of α-Synuclein Using Spin Label Nuclear Magnetic Resonance Measurements

(2009) Jane R. Allison et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Amyloid-β protein oligomerization and the importance of tetramers and dodecamers in the aetiology of Alzheimer's disease

(2009) Summer L. Bernstein et al.   Nature Chemistry

Quantitative Determination of the Conformational Properties of Partially Folded and Intrinsically Disordered Proteins Using NMR Dipolar Couplings

(2009) Malene Ringkjøbing Jensen et al.   STRUCTURE

Structural Basis for p300 Taz2-p53 TAD1 Binding and Modulation by Phosphorylation

(2009) Hanqiao Feng et al.   STRUCTURE

Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners

(2008) Christopher J Oldfield et al.   BMC GENOMICS

Visualization of Intrinsically Disordered Regions of Proteins by High-Speed Atomic Force Microscopy

(2008) Atsushi Miyagi et al.   CHEMPHYSCHEM

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

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

Chirality of Amyloid Suprastructures

(2008) Noa Rubin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Crystal structure of the λ repressor and a model for pairwise cooperative operator binding

(2008) Steven Stayrook et al.   NATURE

Stabilization of a β-hairpin in monomeric Alzheimer's amyloid-β peptide inhibits amyloid formation

(2008) Wolfgang Hoyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular structural basis for polymorphism in Alzheimer's  -amyloid fibrils

(2008) A. K. Paravastu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tight Regulation of Unstructured Proteins: From Transcript Synthesis to Protein Degradation

(2008) J. Gsponer et al.   SCIENCE

The Effect of a ΔK280 Mutation on the Unfolded State of a Microtubule-Binding Repeat in Tau

(2008) Austin Huang et al.   PLoS Computational Biology

Structural disorder serves as a weak signal for intracellular protein degradation

(2007) P. Tompa et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Fuzzy complexes: polymorphism and structural disorder in protein–protein interactions

(2007) Peter Tompa et al.   TRENDS IN BIOCHEMICAL SCIENCES