Toward a quantitative description of microscopic pathway heterogeneity in protein folding

A General Mechanism for the Propagation of Mutational Effects in Proteins

(2016) Nandakumar Rajasekaran et al.   BIOCHEMISTRY

High-Resolution Mapping of the Folding Transition State of a WW Domain

(2016) Kapil Dave et al.   JOURNAL OF MOLECULAR BIOLOGY

Quantifying Protein Disorder through Measures of Excess Conformational Entropy

(2016) Nandakumar Rajasekaran et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Microscopic interpretation of folding ϕ-values using the transition path ensemble

(2016) Robert B. Best et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A simple two-state protein unfolds mechanically via multiple heterogeneous pathways at single-molecule resolution

(2016) Jörg Schönfelder et al.   Nature Communications

Charged Termini on the Trp-Cage Roughen the Folding Energy Landscape

(2015) Charles A. English et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Bridging Experiments and Native-Centric Simulations of a Downhill Folding Protein

(2015) Athi N. Naganathan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Are Protein Folding Intermediates the Evolutionary Consequence of Functional Constraints?

(2015) Athi N. Naganathan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations

(2015) Lorenzo Sborgi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mapping the Topography of a Protein Energy Landscape

(2015) Richard D. Hutton et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Comparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations

(2015) Anna Jean Wirth et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Imprints of function on the folding landscape: functional role for an intermediate in a conserved eukaryotic binding protein

(2015) Sneha Munshi et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Energetic and topological determinants of a phosphorylation-induced disorder-to-order protein conformational switch

(2015) Soundhararajan Gopi et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Sequence, structure, and cooperativity in folding of elementary protein structural motifs

(2015) Jason K. Lai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule chemo-mechanical unfolding reveals multiple transition state barriers in a small single-domain protein

(2015) Emily J. Guinn et al.   Nature Communications

Direct Observation of Parallel Folding Pathways Revealed Using a Symmetric Repeat Protein System

(2014) Tural Aksel et al.   BIOPHYSICAL JOURNAL

Thermodynamics of Downhill Folding: Multi-Probe Analysis of PDD, a Protein that Folds Over a Marginal Free Energy Barrier

(2014) Athi N. Naganathan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Evidence for the Sequential Folding Mechanism in RNase H from an Ensemble-Based Model

(2014) Abhishek Narayan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Probing the Free Energy Landscape of the Fast-Folding gpW Protein by Relaxation Dispersion NMR

(2014) Celia Sanchez-Medina et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements

(2014) Rui Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Temporal Variation of a Protein Folding Energy Landscape in the Cell

(2013) Anna Jean Wirth et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers

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

Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations

(2013) E. R. Henry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Folding of a large protein at high structural resolution

(2013) B. T. Walters et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry

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

A Disorder-Induced Domino-Like Destabilization Mechanism Governs the Folding and Functional Dynamics of the Repeat Protein IκBα

(2013) Srinivasan Sivanandan et al.   PLoS Computational Biology

To milliseconds and beyond: challenges in the simulation of protein folding

(2012) Thomas J Lane et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Predictions from an Ising-like Statistical Mechanical Model on the Dynamic and Thermodynamic Effects of Protein Surface Electrostatics

(2012) Athi N. Naganathan   Journal of Chemical Theory and Computation

Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment

(2012) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Denaturant-dependent folding of GFP

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

Is there an en route folding intermediate for cold shock proteins?

(2012) Lei Huang et al.   PROTEIN SCIENCE

Single-Molecule Fluorescence Experiments Determine Protein Folding Transition Path Times

(2012) H. S. Chung et al.   SCIENCE

Identification of Multiple Folding Pathways of Monellin Using Pulsed Thiol Labeling and Mass Spectrometry

(2011) Santosh Kumar Jha et al.   BIOCHEMISTRY

Analysis of the equilibrium and kinetics of the ankyrin repeat protein myotrophin

(2011) Mauro Faccin et al.   JOURNAL OF CHEMICAL PHYSICS

Quantitative Prediction of Protein Folding Behaviors from a Simple Statistical Model

(2011) Pierpaolo Bruscolini et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories

(2011) Thomas J. Lane et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Estimation of protein folding free energy barriers from calorimetric data by multi-model Bayesian analysis

(2011) Athi N. Naganathan et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The Complex Folding Network of Single Calmodulin Molecules

(2011) J. Stigler et al.   SCIENCE

How Fast-Folding Proteins Fold

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

Taming the complexity of protein folding

(2010) Gregory R Bowman et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Navigating the Downhill Protein Folding Regime via Structural Homologues

(2010) Athi N. Naganathan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Atomistic Folding Simulations of the Five-Helix Bundle Protein λ6−85

(2010) Gregory R. Bowman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Insights into protein folding mechanisms from large scale analysis of mutational effects

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

Thermodynamic Characterization of the Folding Equilibrium of the Human Nedd4-WW4 Domain: At the Frontiers of Cooperative Folding

(2009) Eva S. Cobos et al.   BIOCHEMISTRY

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conservation of Transition State Structure in Fast Folding Peripheral Subunit-Binding Domains

(2008) Timothy D. Sharpe et al.   JOURNAL OF MOLECULAR BIOLOGY

Expanding the Realm of Ultrafast Protein Folding: gpW, a Midsize Natural Single-Domain with α+β Topology that Folds Downhill

(2008) Adam Fung et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Rerouting the Folding Pathway of the Notch Ankyrin Domain by Reshaping the Energy Landscape

(2008) Katherine W. Tripp et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Chemical, physical, and theoretical kinetics of an ultrafast folding protein

(2008) J. Kubelka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

All-atom replica exchange molecular simulation of protein BBL

(2008) Jian Zhang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of One-Dimensional Architectures

(2008) Diego U. Ferreiro et al.   PLoS Computational Biology