Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein

A Folded Excited State of Ligand-Free Nuclear Coactivator Binding Domain (NCBD) Underlies Plasticity in Ligand Recognition

(2013) Magnus Kjaergaard et al.   BIOCHEMISTRY

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

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

Towards the physical basis of how intrinsic disorder mediates protein function

(2012) Jianhan Chen   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Unusual biophysics of intrinsically disordered proteins

(2012) Vladimir N. Uversky   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

How is functional specificity achieved through disordered regions of proteins?

(2012) Rahul K. Das et al.   BIOESSAYS

Coupled Folding-Binding in a Hydrophobic/Polar Protein Model: Impact of Synergistic Folding and Disordered Flanks

(2012) Arnab Bhattacherjee et al.   BIOPHYSICAL JOURNAL

Plasticity in Structural and Functional Interactions between the Phosphoprotein and Nucleoprotein of Measles Virus

(2012) Yaoling Shu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Investigation of the Polymeric Properties of α-Synuclein and Comparison with NMR Experiments: A Replica Exchange Molecular Dynamics Study

(2012) Chitra Narayanan et al.   Journal of Chemical Theory and Computation

The Transition State of Coupled Folding and Binding for a Flexible β-Finger

(2012) O. Andreas Karlsson et al.   JOURNAL OF MOLECULAR BIOLOGY

Assembly of the Five-Way Junction in the Ribosomal Small Subunit Using Hybrid MD-Go̅ Simulations

(2012) Ke Chen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Disorder-to-Order Transition of an Intrinsically Disordered Region of Sortase Revealed by Multiscale Enhanced Sampling

(2012) Kei Moritsugu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multidomain Protein Solves the Folding Problem by Multifunnel Combined Landscape: Theoretical Investigation of a Y-Family DNA Polymerase

(2012) Yong Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure and Dynamics of an Unfolded Protein Examined by Molecular Dynamics Simulation

(2012) Kresten Lindorff-Larsen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Rate constants and mechanisms of intrinsically disordered proteins binding to structured targets

(2012) Huan-Xiang Zhou et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The Impact of Small Molecule Binding on the Energy Landscape of the Intrinsically Disordered Protein C-Myc

(2012) Julien Michel et al.   PLoS One

Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding

(2012) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interaction between the C-terminal domains of measles virus nucleoprotein and phosphoprotein: A tight complex implying one binding site

(2012) David Blocquel et al.   PROTEIN SCIENCE

Residual Structures, Conformational Fluctuations, and Electrostatic Interactions in the Synergistic Folding of Two Intrinsically Disordered Proteins

(2012) Weihong Zhang et al.   PLoS Computational Biology

A Preformed Binding Interface in the Unbound Ensemble of an Intrinsically Disordered Protein: Evidence from Molecular Simulations

(2012) Michael Knott et al.   PLoS Computational Biology

Exploration of Multi-State Conformational Dynamics and Underlying Global Functional Landscape of Maltose Binding Protein

(2012) Yong Wang et al.   PLoS Computational Biology

Importance of Electrostatic Interactions in the Association of Intrinsically Disordered Histone Chaperone Chz1 and Histone H2A.Z-H2B

(2012) Xiakun Chu et al.   PLoS Computational Biology

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Intrinsically disordered proteins from A to Z

(2011) Vladimir N. Uversky   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH

(2011) Magnus Kjaergaard et al.   JOURNAL OF BIOMOLECULAR NMR

A Hybrid All-Atom Structure-Based Model for Protein Folding and Large Scale Conformational Transitions

(2011) Ludovico Sutto et al.   Journal of Chemical Theory and Computation

Energy Landscape Analyses of Disordered Histone Tails Reveal Special Organization of Their Conformational Dynamics

(2011) Davit A. Potoyan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Native Ensemble and Folding of a Protein Molten-Globule: Functional Consequence of Downhill Folding

(2011) Athi N. Naganathan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Free-Energy Landscape for Coupled Folding and Binding of an Intrinsically Disordered Protein in Explicit Solvent from Detailed All-Atom Computations

(2011) Junichi Higo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Synergistic folding of two intrinsically disordered proteins: searching for conformational selection

(2011) Debabani Ganguly et al.   Molecular BioSystems

Intrinsically disordered regions as affinity tuners in protein–DNA interactions

(2011) Dana Vuzman et al.   Molecular BioSystems

Modulation of an IDP binding mechanism and rates by helix propensity and non-native interactions: association of HIF1α with CBP

(2011) David De Sancho et al.   Molecular BioSystems

Structural disorder within paramyxovirus nucleoproteins and phosphoproteins

(2011) Johnny Habchi et al.   Molecular BioSystems

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

Expanding the proteome: disordered and alternatively folded proteins

(2011) H. Jane Dyson   QUARTERLY REVIEWS OF BIOPHYSICS

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Automated Prediction of Protein Association Rate Constants

(2011) Sanbo Qin et al.   STRUCTURE

Intrinsic disorder: signaling via highly specific but short-lived association

(2011) Huan-Xiang Zhou   TRENDS IN BIOCHEMICAL SCIENCES

Multi-Scaled Explorations of Binding-Induced Folding of Intrinsically Disordered Protein Inhibitor IA3 to its Target Enzyme

(2011) Jin Wang et al.   PLoS Computational Biology

Understanding protein non-folding

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

Conformational Analysis of the Partially Disordered Measles Virus NTAIL-XD Complex by SDSL EPR Spectroscopy

(2010) Aleh Kavalenka et al.   BIOPHYSICAL JOURNAL

Multitude of binding modes attainable by intrinsically disordered proteins: a portrait gallery of disorder-based complexes

(2010) Vladimir N. Uversky   CHEMICAL SOCIETY REVIEWS

The Effect of Electrostatics on the Marginal Cooperativity of an Ultrafast Folding Protein

(2010) Tanay M. Desai et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Solution structure of the C-terminal X domain of the measles virus phosphoprotein and interaction with the intrinsically disordered C-terminal domain of the nucleoprotein

(2010) Stéphane Gely et al.   JOURNAL OF MOLECULAR RECOGNITION

Balance between α and β Structures in Ab Initio Protein Folding

(2010) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

(2010) Jeffrey K. Noel et al.   NUCLEIC ACIDS RESEARCH

Nonnative Interactions in Coupled Folding and Binding Processes of Intrinsically Disordered Proteins

(2010) Yongqi Huang et al.   PLoS One

Conformational selection in the molten globule state of the nuclear coactivator binding domain of CBP

(2010) Magnus Kjaergaard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topology-based modeling of intrinsically disordered proteins: Balancing intrinsic folding and intermolecular interactions

(2010) Debabani Ganguly et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structure/Function Implications in a Dynamic Complex of the Intrinsically Disordered Sic1 with the Cdc4 Subunit of an SCF Ubiquitin Ligase

(2010) Tanja Mittag et al.   STRUCTURE

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

Reconciling binding mechanisms of intrinsically disordered proteins

(2009) L. Michel Espinoza-Fonseca   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Thermally induced structural changes of intrinsically disordered small heat shock protein Hsp22

(2009) Alexey S. Kazakov et al.   BIOPHYSICAL CHEMISTRY

Slowing Down Downhill Folding: A Three-Probe Study

(2009) Seung Joong Kim et al.   BIOPHYSICAL JOURNAL

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Linking folding and binding

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

A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1

(2009) Fabio Pietrucci et al.   Journal of Chemical Theory and Computation

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

Dynamics of one-state downhill protein folding

(2009) P. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational selection or induced fit: A flux description of reaction mechanism

(2009) G. G. Hammes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Proteins with weakly funneled energy landscapes challenge the classical structure-function paradigm

(2008) G. A. Papoian   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor

(2008) T. Mittag et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping α-helical induced folding within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein by site-directed spin-labeling EPR spectroscopy

(2008) Valérie Belle et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Binding-Induced Folding of a Natively Unstructured Transcription Factor

(2008) Adrian Gustavo Turjanski et al.   PLoS Computational Biology

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

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