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

Are Protein Folding Intermediates the Evolutionary Consequence of Functional Constraints?

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

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

Concerted Dihedral Rotations Give Rise to Internal Friction in Unfolded Proteins

(2014) Ignacia Echeverria et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Frustration in biomolecules

(2014) Diego U. Ferreiro et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Molecular origins of internal friction effects on protein-folding rates

(2014) David de Sancho et al.   Nature Communications

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Exploring the Minimally Frustrated Energy Landscape of Unfolded ACBP

(2013) Valéry Ozenne et al.   JOURNAL OF MOLECULAR BIOLOGY

The Conformational Landscape of an Intrinsically Disordered DNA-Binding Domain of a Transcription Regulator

(2013) Athi N. Naganathan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Rapid, Ensemble and Free Energy Based Method for Engineering Protein Stabilities

(2013) Athi N. Naganathan   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

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

Quantitative Prediction of Protein Folding Behaviors from a Simple Statistical Model

(2011) Pierpaolo Bruscolini 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

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 protein folding transition-state ensemble from a Gō-like model

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

Visualization of the nanospring dynamics of the I B  ankyrin repeat domain in real time

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

Capturing the essence of folding and functions of biomolecules using coarse-grained models

(2011) Changbong Hyeon et al.   Nature Communications

Navigating the Downhill Protein Folding Regime via Structural Homologues

(2010) Athi N. Naganathan 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

Charge interactions can dominate the dimensions of intrinsically disordered proteins

(2010) S. Muller-Spath et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cooperative formation of native-like tertiary contacts in the ensemble of unfolded states of a four-helix protein

(2010) S. W. Bruun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Direct Observation of Downhill Folding of λ -Repressor in a Microfluidic Mixer

(2009) Stephen J. DeCamp et al.   BIOPHYSICAL JOURNAL

A one-dimensional free energy surface does not account for two-probe folding kinetics of protein α3D

(2009) Feng Liu et al.   JOURNAL OF CHEMICAL PHYSICS

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Fundamental Link between Folding States and Functional States of Proteins

(2009) Hans Robert Kalbitzer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical 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

Exploiting the downhill folding regime via experiment

(2008) Victor Muñoz et al.   HFSP Journal

Large-scale modulation of thermodynamic protein folding barriers linked to electrostatics

(2008) O. Halskau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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