Structural–Energetic Basis for Coupling between Equilibrium Fluctuations and Phosphorylation in a Protein Native Ensemble

Diverse Native Ensembles Dictate the Differential Functional Responses of Nuclear Receptor Ligand-Binding Domains

(2021) Soundhararajan Gopi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Electrostatic Frustration Shapes Folding Mechanistic Differences in Paralogous Bacterial Stress Response Proteins

(2020) Abhishek Narayan et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein dynamics enables phosphorylation of buried residues in Cdk2/Cyclin A-bound p27

(2020) João Henriques et al.   BIOPHYSICAL JOURNAL

Local frustration around enzyme active sites

(2019) Maria I. Freiberger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A binding cooperativity switch driven by synergistic structural swelling of an osmo-regulatory protein pair

(2019) Abhishek Narayan et al.   Nature Communications

Binding-induced folding under unfolding conditions: Switching between induced fit and conformational selection mechanisms

(2019) Sreemantee Sen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Frustration, function and folding

(2018) Diego U Ferreiro et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Mechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2

(2018) Ricardo A. P. Pádua et al.   Nature Communications

Native State Volume Fluctuations in Proteins as a Mechanism for Dynamic Allostery

(2017) Anthony B. Law et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways

(2017) Wen-Ting Chu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Physicochemical code for quinary protein interactions inEscherichia coli

(2017) Xin Mu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the link between conformational changes, ligand binding and heat capacity

(2016) S. Vega et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

(2016) Guanghong Wei et al.   CHEMICAL REVIEWS

Interaction of p190A RhoGAP with eIF3A and Other Translation Preinitiation Factors Suggests a Role in Protein Biosynthesis

(2016) Prasanna Parasuraman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Quantifying Protein Disorder through Measures of Excess Conformational Entropy

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

Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics

(2016) R. Gonzalo Parra et al.   NUCLEIC ACIDS RESEARCH

Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection

(2016) Joseph J. Maciag et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allostery: An Overview of Its History, Concepts, Methods, and Applications

(2016) Jin Liu et al.   PLoS Computational Biology

Alterations of Nonconserved Residues Affect Protein Stability and Folding Dynamics through Charge–Charge Interactions

(2015) Swarnendu Tripathi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Electrostatics, structure prediction, and the energy landscapes for protein folding and binding

(2015) Min-Yeh Tsai et al.   PROTEIN SCIENCE

A Designed Conformational Shift To Control Protein Binding Specificity

(2014) Servaas Michielssens et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

Biophysics of protein evolution and evolutionary protein biophysics

(2014) T. Sikosek et al.   Journal of the Royal Society Interface

Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit

(2014) N. Greives et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Conformational selection and adaptation to ligand binding in T4 lysozyme cavity mutants

(2013) C. J. Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein recognition and selection through conformational and mutually induced fit

(2013) Q. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allostery and the Monod-Wyman-Changeux Model After 50 Years

(2012) Jean-Pierre Changeux   Annual Review of Biophysics

Dynamics and mechanisms of coupled protein folding and binding reactions

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

Probing the diverse landscape of protein flexibility and binding

(2012) Joseph A Marsh 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

Exploiting a natural conformational switch to engineer an interleukin-2 ‘superkine’

(2012) Aron M. Levin et al.   NATURE

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites

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

Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles

(2011) R. Bryn Fenwick et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Nonnative Interactions in the FF Domain Folding Pathway from an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study

(2011) Dmitry M. Korzhnev et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Global Dynamics of Proteins: Bridging Between Structure and Function

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

Folding and binding cascades: Dynamic landscapes and population shifts

(2010) Sandeep Kumar et al.   PROTEIN SCIENCE

GelBandFitter - A computer program for analysis of closely spaced electrophoretic and immunoblotted bands

(2009) Mihail I. Mitov et al.   ELECTROPHORESIS

NMR Structural Studies on Human p190-A RhoGAPFF1 Revealed that Domain Phosphorylation by the PDGF-Receptor α Requires Its Previous Unfolding

(2009) R. Bonet et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

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

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