The Structural Basis of Oncogenic Mutations G12, G13 and Q61 in Small GTPase K-Ras4B

Ras Conformational Ensembles, Allostery, and Signaling

(2016) Shaoyong Lu et al.   CHEMICAL REVIEWS

The disordered hypervariable region and the folded catalytic domain of oncogenic K-Ras4B partner in phospholipid binding

(2016) Avik Banerjee et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The higher level of complexity of K-Ras4B activation at the membrane

(2016) Hyunbum Jang et al.   FASEB JOURNAL

ASBench: benchmarking sets for allosteric discovery: Fig. 1.

(2015) Wenkang Huang et al.   BIOINFORMATICS

High-Affinity Interaction of the K-Ras4B Hypervariable Region with the Ras Active Site

(2015) Tanmay S. Chavan et al.   BIOPHYSICAL JOURNAL

The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin

(2015) Avishek Kumar et al.   BIOPHYSICAL JOURNAL

A New View of Ras Isoforms in Cancers

(2015) R. Nussinov et al.   CANCER RESEARCH

Inhibitors of Ras-SOS Interactions

(2015) Shaoyong Lu et al.   ChemMedChem

Mechanisms of Membrane Binding of Small GTPase K-Ras4B Farnesylated Hypervariable Region

(2015) Hyunbum Jang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site

(2015) Shaoyong Lu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Differential dynamics of RAS isoforms in GDP- and GTP-bound states

(2015) Abhijeet Kapoor et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Mechanism of ATP-Dependent Allosteric Protection of Akt Kinase Phosphorylation

(2015) Shaoyong Lu et al.   STRUCTURE

GTP-Dependent K-Ras Dimerization

(2015) Serena Muratcioglu et al.   STRUCTURE

Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD

(2015) Susan K. Fetics et al.   STRUCTURE

Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations

(2015) Huiyong Sun et al.   Scientific Reports

Insights into the key interactions between human protein phosphatase 5 and cantharidin using molecular dynamics and site-directed mutagenesis bioassays

(2015) Ji-Yuan Liu et al.   Scientific Reports

Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm

(2015) Rudy Clausen et al.   PLoS Computational Biology

The structural basis for cancer treatment decisions

(2015) Ruth Nussinov et al.   Oncotarget

Investigation of Inhibition Mechanism of Chemokine Receptor CCR5 by Micro-second Molecular Dynamics Simulations

(2015) Ramin Ekhteiari Salmas et al.   Scientific Reports

Modeling the Role of G12V and G13V Ras Mutations in the Ras-GAP-Catalyzed Hydrolysis Reaction of Guanosine Triphosphate

(2014) Maria G. Khrenova et al.   BIOCHEMISTRY

Kinesin-5 Allosteric Inhibitors Uncouple the Dynamics of Nucleotide, Microtubule, and Neck-Linker Binding Sites

(2014) Guido Scarabelli et al.   BIOPHYSICAL JOURNAL

RAS’s Cloak of Invincibility Slips at Last?

(2014) Julian Downward   CANCER CELL

Stability of Iowa mutant and wild type Aβ-peptide aggregates

(2014) Erik J. Alred et al.   JOURNAL OF CHEMICAL PHYSICS

Harnessing Allostery: A Novel Approach to Drug Discovery

(2014) Shaoyong Lu et al.   MEDICINAL RESEARCH REVIEWS

Small-molecule modulation of Ras signaling

(2014) Jochen Spiegel et al.   Nature Chemical Biology

Drugging the undruggable RAS: Mission Possible?

(2014) Adrienne D. Cox et al.   NATURE REVIEWS DRUG DISCOVERY

The free energy landscape in translational science: how can somatic mutations result in constitutive oncogenic activation?

(2014) Chung-Jung Tsai et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

In situ selectivity profiling and crystal structure of SML-8-73-1, an active site inhibitor of oncogenic K-Ras G12C

(2014) J. C. Hunter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ras activation by SOS: Allosteric regulation by altered fluctuation dynamics

(2014) L. Iversen et al.   SCIENCE

KRAS: feeding pancreatic cancer proliferation

(2014) Kirsten L. Bryant et al.   TRENDS IN BIOCHEMICAL SCIENCES

Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops

(2014) Gaetano Invernizzi et al.   PLoS Computational Biology

The Structural Basis of ATP as an Allosteric Modulator

(2014) Shaoyong Lu et al.   PLoS Computational Biology

P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape

(2014) Huiyong Sun et al.   PLoS Computational Biology

Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant

(2014) Paraskevi Gkeka et al.   PLoS Computational Biology

Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications

(2014) Kristin Blacklock et al.   PLoS Computational Biology

K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions

(2013) Jonathan M. Ostrem et al.   NATURE

Regulation of Small GTPases by GEFs, GAPs, and GDIs

(2013) Jacqueline Cherfils et al.   PHYSIOLOGICAL REVIEWS

NMR-based functional profiling of RASopathies and oncogenic RAS mutations

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

Discovery of Small Molecules that Bind to K-Ras and Inhibit Sos-Mediated Activation

(2012) Qi Sun et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A Comprehensive Survey of Ras Mutations in Cancer

(2012) I. A. Prior et al.   CANCER RESEARCH

Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity

(2012) T. Maurer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ras and GTPase-activating protein (GAP) drive GTP into a precatalytic state as revealed by combining FTIR and biomolecular simulations

(2012) T. Rudack et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Solution Structure of the State 1 Conformer of GTP-bound H-Ras Protein and Distinct Dynamic Properties between the State 1 and State 2 Conformers

(2011) Mitsugu Araki et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Nucleotide Binding Switches the Information Flow in Ras GTPases

(2011) Francesco Raimondi et al.   PLoS Computational Biology

Structural Basis for Conformational Dynamics of GTP-bound Ras Protein

(2010) Fumi Shima et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Distinct Conformational Dynamics of K-Ras and H-Ras A59G

(2010) Suryani Lukman et al.   PLoS Computational Biology

Self-guided Langevin dynamics study of regulatory interactions in NtrC

(2009) Ana Damjanović 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 GAP arginine finger movement into the catalytic site of Ras increases the activation entropy

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

Mapping the Nucleotide and Isoform-Dependent Structural and Dynamical Features of Ras Proteins

(2008) Alemayehu A. Gorfe et al.   STRUCTURE