Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning

Crystallographic and Nuclear Magnetic Resonance Evaluation of the Impact of Peptide Binding to the Second PDZ Domain of Protein Tyrosine Phosphatase 1E

(2010) Jun Zhang et al.   BIOCHEMISTRY

Manipulation of Conformational Change in Proteins by Single-Residue Perturbations

(2010) C. Atilgan et al.   BIOPHYSICAL JOURNAL

Interaction Energy Based Protein Structure Networks

(2010) M.S. Vijayabaskar et al.   BIOPHYSICAL JOURNAL

Biophysical Characterization of the Complex between Human Papillomavirus E6 Protein and Synapse-associated Protein 97

(2010) Celestine N. Chi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An Ensemble View of Allostery

(2010) V. J. Hilser   SCIENCE

Coupling between Normal Modes Drives Protein Conformational Dynamics: Illustrations Using Allosteric Transitions in Myosin II

(2009) Wenjun Zheng et al.   BIOPHYSICAL JOURNAL

Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins

(2009) Ivet Bahar et al.   CHEMICAL REVIEWS

Allosteric Transitions in Biological Nanomachines are Described by Robust Normal Modes of Elastic Networks

(2009) Wenjun Zheng et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Protein elastic network models and the ranges of cooperativity

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hidden dynamic allostery in a PDZ domain

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

On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: Illustrations using lattice model

(2009) Zhenxing Liu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior

(2009) Z. Nevin Gerek et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Sending Signals Dynamically

(2009) R. G. Smock et al.   SCIENCE

The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways

(2009) Antonio del Sol et al.   STRUCTURE

Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations

(2009) Bosco K. Ho et al.   PLoS Computational Biology

Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein

(2009) Canan Atilgan et al.   PLoS Computational Biology

Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL

(2009) Zheng Yang et al.   PLoS Computational Biology

Flexible ligand docking to multiple receptor conformations: a practical alternative

(2008) Maxim Totrov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein−Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking

(2008) Andreas May et al.   JOURNAL OF MEDICINAL CHEMISTRY

Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play

(2008) Chung-Jung Tsai et al.   JOURNAL OF MOLECULAR BIOLOGY

RosettaLigand Docking with Full Ligand and Receptor Flexibility

(2008) Ian W. Davis 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

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

Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL

(2008) Chakra Chennubhotla et al.   Molecular BioSystems

Allosteric regulation and catalysis emerge via a common route

(2008) Nina M Goodey et al.   Nature Chemical Biology

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

Deriving protein dynamical properties from weighted protein contact number

(2008) Chih-Peng Lin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Signaling pathways of PDZ2 domain: A molecular dynamics interaction correlation analysis

(2008) Yifei Kong et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Surface Sites for Engineering Allosteric Control in Proteins

(2008) J. Lee et al.   SCIENCE