Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework

Binding Kinetics of Glucose and Allosteric Activators to Human Glucokinase Reveal Multiple Conformational States

(2009) Mathias Antoine et al.   BIOCHEMISTRY

Prion Proteins with Pathogenic and Protective Mutations Show Similar Structure and Dynamics

(2009) Sung-Hun Bae et al.   BIOCHEMISTRY

Application of Elastic Network Models to Proteins in the Crystalline State

(2009) Demian Riccardi et al.   BIOPHYSICAL JOURNAL

Arc-Repressor Dimerization on DNA: Folding Rate Enhancement by Colocalization

(2009) Amir Marcovitz et al.   BIOPHYSICAL JOURNAL

Instantaneous Normal Modes and the Protein Glass Transition

(2009) Roland Schulz et al.   BIOPHYSICAL JOURNAL

Frequency-resolved communication maps for proteins and other nanoscale materials

(2009) David M. Leitner   JOURNAL OF CHEMICAL PHYSICS

Reactive flux and folding pathways in network models of coarse-grained protein dynamics

(2009) Alexander Berezhkovskii et al.   JOURNAL OF CHEMICAL PHYSICS

Apo Adenylate Kinase Encodes Its Holo Form: A Principal Component and Varimax Analysis

(2009) Robert I. Cukier   JOURNAL OF PHYSICAL CHEMISTRY B

Deconstructing the Native State: Energy Landscapes, Function, and Dynamics of Globular Proteins

(2009) Pavel I. Zhuravlev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms

(2009) Chung-Jung Tsai et al.   Molecular BioSystems

Hidden alternative structures of proline isomerase essential for catalysis

(2009) James S. Fraser et al.   NATURE

Mapping GFP structure evolution during proton transfer with femtosecond Raman spectroscopy

(2009) Chong Fang et al.   NATURE

How Adequate are One- and Two-Dimensional Free Energy Landscapes for Protein Folding Dynamics?

(2009) Gia G. Maisuradze et al.   PHYSICAL REVIEW LETTERS

NMR analysis of G-protein    subunit complexes reveals a dynamic G -G   subunit interface and multiple protein recognition modes

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

Enzyme millisecond conformational dynamics do not catalyze the chemical step

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

Ligand-induced global transitions in the catalytic domain of protein kinase A

(2009) C. Hyeon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of two distinct inactive conformations of the  2-adrenergic receptor reconciles structural and biochemical observations

(2009) R. O. Dror et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multi-scale characterization of the energy landscape of proteins with application to the C3D/Efb-C complex

(2009) Nurit Haspel et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics

(2009) Barry J. Grant et al.   PLoS Computational Biology

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

Energy Flow in Proteins

(2008) David M. Leitner   Annual Review of Physical Chemistry

Free-Energy Landscape of Enzyme Catalysis†

(2008) Stephen J. Benkovic et al.   BIOCHEMISTRY

Exploring the Energy Landscape of Antibody−Antigen Complexes: Protein Dynamics, Flexibility, and Molecular Recognition

(2008) Megan C. Thielges et al.   BIOCHEMISTRY

A Unification of the Elastic Network Model and the Gaussian Network Model for Optimal Description of Protein Conformational Motions and Fluctuations

(2008) Wenjun Zheng   BIOPHYSICAL JOURNAL

High Resolution Approach to the Native State Ensemble Kinetics and Thermodynamics

(2008) Sangwook Wu et al.   BIOPHYSICAL JOURNAL

Energy landscape along an enzymatic reaction trajectory: Hinges or cracks?

(2008) Paul Charles Whitford et al.   HFSP Journal

The spectrum of biomolecular states and motions

(2008) Joseph A. Hegler et al.   HFSP Journal

Two-State Allosteric Modeling Suggests Protein Equilibrium as an Integral Component for Cyclic AMP (cAMP) Specificity in the cAMP Receptor Protein of Escherichia coli

(2008) H. Youn et al.   JOURNAL OF BACTERIOLOGY

An Allosteric Circuit in Caspase-1

(2008) Debajyoti Datta et al.   JOURNAL OF MOLECULAR BIOLOGY

Principal Component Analysis for Protein Folding Dynamics

(2008) Gia G. Maisuradze et al.   JOURNAL OF MOLECULAR BIOLOGY

Allostery Wiring Diagrams in the Transitions that Drive the GroEL Reaction Cycle

(2008) Riina Tehver et al.   JOURNAL OF MOLECULAR BIOLOGY

Pathways for Conformational Change in Nitrogen Regulatory Protein C from Discrete Path Sampling

(2008) Mey Khalili et al.   JOURNAL OF PHYSICAL CHEMISTRY B

One-Dimensional Barrier-Preserving Free-Energy Projections of a β-sheet Miniprotein: New Insights into the Folding Process

(2008) Sergei V. Krivov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse Master Equations for Peptide Folding Dynamics†

(2008) Nicolae-Viorel Buchete et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mapping of Two Networks of Residues That Exhibit Structural and Dynamical Changes upon Binding in a PDZ Domain Protein

(2008) Anne Dhulesia et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein Sequence- and pH-Dependent Hydration Probed by Terahertz Spectroscopy

(2008) Simon Ebbinghaus et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement

(2008) G. Marius Clore   Molecular BioSystems

Visualizing transient events in amino-terminal autoprocessing of HIV-1 protease

(2008) Chun Tang et al.   NATURE

Protein Dynamical Transition Does Not Require Protein Structure

(2008) Yunfen He et al.   PHYSICAL REVIEW LETTERS

Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions

(2008) C. K. Materese et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Computing the stability diagram of the Trp-cage miniprotein

(2008) D. Paschek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the relationship between folding and chemical landscapes in enzyme catalysis

(2008) M. Roca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reassessing a sparse energetic network within a single protein domain

(2008) C. N. Chi 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

Folding energy landscape and network dynamics of small globular proteins

(2008) N. Hori et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Induced-fit or preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design

(2008) Yechun Xu et al.   PROTEIN SCIENCE

Quantifying information transfer by protein domains: Analysis of the Fyn SH2 domain structure

(2008) Tom Lenaerts et al.   BMC STRUCTURAL BIOLOGY

Binding-Induced Folding of a Natively Unstructured Transcription Factor

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

Protein folding: Then and now

(2007) Yiwen Chen et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Metal-Coupled Folding of Cys2His2Zinc-Finger

(2007) Wenfei Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY