Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases
Published 2011 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases
Authors
Keywords
-
Journal
PLoS Computational Biology
Volume 7, Issue 10, Pages e1002179
Publisher
Public Library of Science (PLoS)
Online
2011-10-07
DOI
10.1371/journal.pcbi.1002179
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Molecular dynamics analysis of conserved hydrophobic and hydrophilic bond-interaction networks in ErbB family kinases
- (2011) Andrew J. Shih et al. BIOCHEMICAL JOURNAL
- Structural Analysis of the Mechanism of Inhibition and Allosteric Activation of the Kinase Domain of HER2 Protein
- (2011) Kathleen Aertgeerts et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- A multiscale modeling approach to investigate molecular mechanisms of pseudokinase activation and drug resistance in the HER3/ErbB3 receptor tyrosine kinase signaling network
- (2011) Shannon E. Telesco et al. Molecular BioSystems
- Catalytic Control in the EGF Receptor and Its Connection to General Kinase Regulatory Mechanisms
- (2011) Natalia Jura et al. MOLECULAR CELL
- Allosteric Interactions between the Myristate- and ATP-Site of the Abl Kinase
- (2011) Roxana E. Iacob et al. PLoS One
- Discovery of a small-molecule type II inhibitor of wild-type and gatekeeper mutants of BCR-ABL, PDGFR , Kit, and Src kinases: novel type II inhibitor of gatekeeper mutants
- (2010) E. Weisberg et al. BLOOD
- Structural Mechanism of the Pan-BCR-ABL Inhibitor Ponatinib (AP24534): Lessons for Overcoming Kinase Inhibitor Resistance
- (2010) Tianjun Zhou et al. Chemical Biology & Drug Design
- Targeting the BCR-ABL Signaling Pathway in Therapy-Resistant Philadelphia Chromosome-Positive Leukemia
- (2010) T. O'Hare et al. CLINICAL CANCER RESEARCH
- Molecular Dynamics Simulations and Elastic Network Analysis of Protein Kinase B (Akt/PKB) Inactivation
- (2010) Shu Cheng et al. Journal of Chemical Information and Modeling
- Asymmetric tyrosine kinase arrangements in activation or autophosphorylation of receptor tyrosine kinases
- (2010) Jae Hyun Bae et al. MOLECULES AND CELLS
- Targeting Bcr–Abl by combining allosteric with ATP-binding-site inhibitors
- (2010) Jianming Zhang et al. NATURE
- Co-Conserved Features Associated with cis Regulation of ErbB Tyrosine Kinases
- (2010) Amar Mirza et al. PLoS One
- Conformational regulation of the EGFR kinase core by the juxtamembrane and C-terminal tail: A molecular dynamics study
- (2010) Morad Mustafa et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Protein kinases: evolution of dynamic regulatory proteins
- (2010) Susan S. Taylor et al. TRENDS IN BIOCHEMICAL SCIENCES
- Identification of small-molecule inhibitors of the JIP–JNK interaction
- (2009) Tracy Chen et al. BIOCHEMICAL JOURNAL
- Crystal Structures of MEK1 Binary and Ternary Complexes with Nucleotides and Inhibitors
- (2009) Thierry O. Fischmann et al. BIOCHEMISTRY
- Defining the conserved internal architecture of a protein kinase
- (2009) Alexandr P. Kornev et al. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
- Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics
- (2009) Lee-Wei Yang et al. BIOINFORMATICS
- Atomistic Insights into Regulatory Mechanisms of the HER2 Tyrosine Kinase Domain: A Molecular Dynamics Study
- (2009) Shannon E. Telesco et al. BIOPHYSICAL JOURNAL
- Computational Modeling of Structurally Conserved Cancer Mutations in the RET and MET Kinases: The Impact on Protein Structure, Dynamics, and Stability
- (2009) Anshuman Dixit et al. BIOPHYSICAL JOURNAL
- Coupling between Normal Modes Drives Protein Conformational Dynamics: Illustrations Using Allosteric Transitions in Myosin II
- (2009) Wenjun Zheng et al. BIOPHYSICAL JOURNAL
- AP24534, a Pan-BCR-ABL Inhibitor for Chronic Myeloid Leukemia, Potently Inhibits the T315I Mutant and Overcomes Mutation-Based Resistance
- (2009) Thomas O'Hare et al. CANCER CELL
- Mechanism for Activation of the EGF Receptor Catalytic Domain by the Juxtamembrane Segment
- (2009) Natalia Jura et al. CELL
- Identification of Allosteric PIF-Pocket Ligands for PDK1 using NMR-Based Fragment Screening and1H-15N TROSY Experiments
- (2009) Brian J. Stockman et al. Chemical Biology & Drug Design
- Allosteric Coupling and Conformational Fluctuations in Proteins
- (2009) H. Onaran et al. CURRENT PROTEIN & PEPTIDE SCIENCE
- Allosteric Transitions in Biological Nanomachines are Described by Robust Normal Modes of Elastic Networks
- (2009) Wenjun Zheng et al. CURRENT PROTEIN & PEPTIDE SCIENCE
- Structural and Computational Biology of the Molecular Chaperone Hsp90: From Understanding Molecular Mechanisms to Computer-Based Inhibitor Design
- (2009) Gennady Verkhivker et al. CURRENT TOPICS IN MEDICINAL CHEMISTRY
- Her4 and Her2/neu Tyrosine Kinase Domains Dimerize and Activate in a Reconstitutedin VitroSystem
- (2009) John Monsey et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms
- (2009) Chung-Jung Tsai et al. Molecular BioSystems
- The Juxtamembrane Region of the EGF Receptor Functions as an Activation Domain
- (2009) Monica Red Brewer et al. MOLECULAR CELL
- A new screening assay for allosteric inhibitors of cSrc
- (2009) Jeffrey R Simard et al. Nature Chemical Biology
- Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories
- (2009) S. Yang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Conformational disturbance in Abl kinase upon mutation and deregulation
- (2009) R. E. Iacob et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- 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
- 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
- Structural analysis of the catalytically inactive kinase domain of the human EGF receptor 3
- (2009) N. Jura et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Extracting the multiscale backbone of complex weighted networks
- (2009) M. A. Serrano et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Trapping Moving Targets with Small Molecules
- (2009) G. M. Lee et al. SCIENCE
- The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways
- (2009) Antonio del Sol et al. STRUCTURE
- Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model
- (2009) Wenjun Zheng et al. BMC STRUCTURAL BIOLOGY
- Role of a Novel PH-Kinase Domain Interface in PKB/Akt Regulation: Structural Mechanism for Allosteric Inhibition
- (2009) Véronique Calleja et al. PLOS BIOLOGY
- Computation of Conformational Coupling in Allosteric Proteins
- (2009) Brian A. Kidd et al. PLoS Computational Biology
- Structure-Based Predictive Models for Allosteric Hot Spots
- (2009) Omar N. A. Demerdash et al. PLoS Computational Biology
- Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer
- (2009) Giulia Morra et al. PLoS Computational Biology
- Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations
- (2009) Bosco K. Ho et al. PLoS Computational Biology
- Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations
- (2009) Anshuman Dixit et al. PLoS Computational Biology
- Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins
- (2009) Michael D. Daily 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
- Mechanism of Signal Propagation upon Retinal Isomerization: Insights from Molecular Dynamics Simulations of Rhodopsin Restrained by Normal Modes
- (2008) Basak Isin et al. BIOPHYSICAL JOURNAL
- Solution Conformations and Dynamics of ABL Kinase-Inhibitor Complexes Determined by NMR Substantiate the Different Binding Modes of Imatinib/Nilotinib and Dasatinib
- (2008) Navratna Vajpai et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Structure and Clinical Relevance of the Epidermal Growth Factor Receptor in Human Cancer
- (2008) Amit Kumar et al. JOURNAL OF CLINICAL ONCOLOGY
- 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
- Extensive Conformational Transitions Are Required to Turn On ATP Hydrolysis in Myosin
- (2008) Yang Yang 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
- Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations
- (2008) Anna Berteotti 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
- The T790M "gatekeeper" mutation in EGFR mediates resistance to low concentrations of an irreversible EGFR inhibitor
- (2008) N. Godin-Heymann et al. MOLECULAR CANCER THERAPEUTICS
- A quantitative analysis of kinase inhibitor selectivity
- (2008) Mazen W Karaman et al. NATURE BIOTECHNOLOGY
- Allosteric regulation and catalysis emerge via a common route
- (2008) Nina M Goodey et al. Nature Chemical Biology
- Activation of tyrosine kinases by mutation of the gatekeeper threonine
- (2008) Mohammad Azam et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Detection of Mutations inEGFRin Circulating Lung-Cancer Cells
- (2008) Shyamala Maheswaran et al. NEW ENGLAND JOURNAL OF MEDICINE
- BIBW2992, an irreversible EGFR/HER2 inhibitor highly effective in preclinical lung cancer models
- (2008) D Li et al. ONCOGENE
- Direct analysis of cooperativity in multisubunit allosteric proteins
- (2008) N. Zandany et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Identification of a new JNK inhibitor targeting the JNK-JIP interaction site
- (2008) J. L. Stebbins et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A helix scaffold for the assembly of active protein kinases
- (2008) A. P. Kornev et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- 6-Ethynylthieno[3,2-d]- and 6-ethynylthieno[2,3-d]pyrimidin-4-anilines as tunable covalent modifiers of ErbB kinases
- (2008) E. R. Wood et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A conserved protonation-dependent switch controls drug binding in the Abl kinase
- (2008) Y. Shan et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP
- (2008) C.-H. Yun et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- An electrostatic network and long-range regulation of Src kinases
- (2008) Elif Ozkirimli et al. PROTEIN SCIENCE
- Allostery and cooperativity revisited
- (2008) Qiang Cui et al. PROTEIN SCIENCE
- Detailed conformational dynamics of juxtamembrane region and activation loop in c-Kit kinase activation process
- (2008) Jun Zou et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Conformational dynamics of the EGFR kinase domain reveals structural features involved in activation
- (2008) Athanasios Papakyriakou et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases
- (2008) Nilesh K. Banavali et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Mechanism of Activation and Inhibition of the HER4/ErbB4 Kinase
- (2008) Chen Qiu et al. STRUCTURE
- Exploring allosteric coupling in the α-subunit of Heterotrimeric G proteins using evolutionary and ensemble-based approaches
- (2008) Kemal Sayar et al. BMC STRUCTURAL BIOLOGY
- Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements
- (2008) M. Cecchini et al. PLoS Computational Biology
- Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms
- (2008) Sichun Yang et al. PLoS Computational Biology
- Contact rearrangements form coupled networks from local motions in allosteric proteins
- (2007) Michael D. Daily et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreDiscover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversation