Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

Helical Propensity in an Intrinsically Disordered Protein Accelerates Ligand Binding

(2014) Vytautas Iešmantavičius et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

(2013) Magnus Kjaergaard et al.   BIOCHEMISTRY

Describing intrinsically disordered proteins at atomic resolution by NMR

(2013) Malene Ringkjøbing Jensen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Folding and Binding of an Intrinsically Disordered Protein: Fast, but Not ‘Diffusion-Limited’

(2013) Joseph M. Rogers et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A "slow" protein folds quickly in the end

(2013) R. B. Best   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Folding the proteome

(2013) Esther Braselmann et al.   TRENDS IN BIOCHEMICAL SCIENCES

The transition state structure for coupled binding and folding of disordered protein domains

(2013) Jakob Dogan et al.   Scientific Reports

Insights into the binding of intrinsically disordered proteins from molecular dynamics simulation

(2013) Christopher M. Baker et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Impact of N-Terminal Acetylation of α-Synuclein on Its Random Coil and Lipid Binding Properties

(2012) Alexander S. Maltsev et al.   BIOCHEMISTRY

Slow, Reversible, Coupled Folding and Binding of the Spectrin Tetramerization Domain

(2012) S.L. Shammas et al.   BIOPHYSICAL JOURNAL

An α Helix to β Barrel Domain Switch Transforms the Transcription Factor RfaH into a Translation Factor

(2012) Björn M. Burmann et al.   CELL

Fast Association and Slow Transitions in the Interaction between Two Intrinsically Disordered Protein Domains

(2012) Jakob Dogan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

From A to B: A ride in the free energy surfaces of protein G domains suggests how new folds arise

(2012) Ludovico Sutto et al.   JOURNAL OF CHEMICAL PHYSICS

Exploring the Dynamic Functional Landscape of Adenylate Kinase Modulated by Substrates

(2012) Yong Wang et al.   Journal of Chemical Theory and Computation

Structural Ensemble of an Intrinsically Disordered Polypeptide

(2012) Jeetain Mittal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Escape from Adaptive Conflict follows from weak functional trade-offs and mutational robustness

(2012) T. Sikosek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy

(2012) A. Soranno 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

Exploring the binding diversity of intrinsically disordered proteins involved in one-to-many binding

(2012) Wei-Lun Hsu et al.   PROTEIN SCIENCE

Mutational Tipping Points for Switching Protein Folds and Functions

(2012) Yanan He et al.   STRUCTURE

Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts

(2012) Tobias Sikosek et al.   PLoS Computational Biology

Binding of Two Intrinsically Disordered Peptides to a Multi-Specific Protein: A Combined Monte Carlo and Molecular Dynamics Study

(2012) Iskra Staneva et al.   PLoS Computational Biology

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

Cooperativity, Local-Nonlocal Coupling, and Nonnative Interactions: Principles of Protein Folding from Coarse-Grained Models

(2011) Hue Sun Chan et al.   Annual Review of Physical Chemistry

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

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

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

(2011) Debabani Ganguly 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

Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins

(2011) Madeleine B. Borgia et al.   NATURE

Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction

(2011) A. Bachmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interconversion of Functional Motions between Mesophilic and Thermophilic Adenylate Kinases

(2011) Michael D. Daily et al.   PLoS Computational Biology

In Silico Elucidation of the Recognition Dynamics of Ubiquitin

(2011) Dong Long et al.   PLoS Computational Biology

From Induced Fit to Conformational Selection: A Continuum of Binding Mechanism Controlled by the Timescale of Conformational Transitions

(2010) Huan-Xiang Zhou   BIOPHYSICAL JOURNAL

Enzyme dynamics point to stepwise conformational selection in catalysis

(2010) Buyong Ma et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Many Local Motions Cooperate to Produce the Adenylate Kinase Conformational Transition

(2010) Michael D. Daily et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

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

Linking folding and binding

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

CHARMM: The biomolecular simulation program

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

The Limited Role of Nonnative Contacts in the Folding Pathways of a Lattice Protein

(2009) Brian C. Gin et al.   JOURNAL OF MOLECULAR BIOLOGY

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Molecular simulation of conformational transitions in biomolecules using a combination of structure-based potential and empirical valence bond theory

(2009) Giuseppe de Marco et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

(2009) T. Wlodarski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A minimal sequence code for switching protein structure and function

(2009) Patrick A. Alexander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

Conformer Selection and Induced Fit in Flexible Backbone Protein–Protein Docking Using Computational and NMR Ensembles

(2008) Sidhartha Chaudhury et al.   JOURNAL OF MOLECULAR BIOLOGY

Malleable machines take shape in eukaryotic transcriptional regulation

(2008) Monika Fuxreiter et al.   Nature Chemical Biology

Interconversion between two unrelated protein folds in the lymphotactin native state

(2008) Robbyn L. Tuinstra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms

(2008) K.-i. Okazaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

(2008) O. F. Lange et al.   SCIENCE

Binding-Induced Folding of a Natively Unstructured Transcription Factor

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

Coarse-grained Models for Simulations of Multiprotein Complexes: Application to Ubiquitin Binding

(2007) Young C. Kim et al.   JOURNAL OF MOLECULAR BIOLOGY

The origins of asymmetry in the folding transition states of protein L and protein G

(2002) John Karanicolas et al.   PROTEIN SCIENCE