Relation between the Conformational Heterogeneity and Reaction Cycle of Ras: Molecular Simulation of Ras Chigusa Kobayashi, Shinji Saito Biophysical.

Slides:

Advertisements

Similar presentations

How Do Thermophilic Proteins and Proteomes Withstand High Temperature? Lucas Sawle, Kingshuk Ghosh Biophysical Journal Volume 101, Issue 1, Pages

Advertisements

Inhibitor Binding Increases the Mechanical Stability of Staphylococcal Nuclease Chien-Chung Wang, Tian-Yow Tsong, Yau-Heiu Hsu, Piotr E. Marszalek Biophysical.

X-Ray Absorption Spectroscopy of Dinuclear Metallohydrolases David L. Tierney, Gerhard Schenk Biophysical Journal Volume 107, Issue 6, Pages

A Hydrodynamic Model for Hindered Diffusion of Proteins and Micelles in Hydrogels Ronald J. Phillips Biophysical Journal Volume 79, Issue 6, Pages

Photochemical Reaction Dynamics of the Primary Event of Vision Studied by Means of a Hybrid Molecular Simulation Shigehiko Hayashi, Emad Tajkhorshid, Klaus.

Lever-Arm Mechanics of Processive Myosins Yujie Sun, Yale E. Goldman Biophysical Journal Volume 101, Issue 1, Pages 1-11 (July 2011) DOI: /j.bpj

Mesoscale Simulation of Blood Flow in Small Vessels Prosenjit Bagchi Biophysical Journal Volume 92, Issue 6, Pages (March 2007) DOI: /biophysj

The Importance of the Hook Region of the Cochlea for Bone-Conduction Hearing Namkeun Kim, Charles R. Steele, Sunil Puria Biophysical Journal Volume 107,

Cell Traction Forces Direct Fibronectin Matrix Assembly Christopher A. Lemmon, Christopher S. Chen, Lewis H. Romer Biophysical Journal Volume 96, Issue.

Effects of Macromolecular Crowding on the Structure of a Protein Complex: A Small- Angle Scattering Study of Superoxide Dismutase Ajith Rajapaksha, Christopher.

Nonlinear Poisson Equation for Heterogeneous Media Langhua Hu, Guo-Wei Wei Biophysical Journal Volume 103, Issue 4, Pages (August 2012) DOI: /j.bpj

Direct Measurements of the Mechanical Stability of Zinc-Thiolate Bonds in Rubredoxin by Single-Molecule Atomic Force Microscopy Peng Zheng, Hongbin Li.

Volume 107, Issue 9, Pages (November 2014)

A Protein Dynamics Study of Photosystem II: The Effects of Protein Conformation on Reaction Center Function Sergej Vasil’ev, Doug Bruce Biophysical.

Changing Chromatin Fiber Conformation by Nucleosome Repositioning

Induced Fit and the Entropy of Structural Adaptation in the Complexation of CAP and λ- Repressor with Cognate DNA Sequences Surjit B. Dixit, David Q.

Yufeng Liu, Meng Ke, Haipeng Gong Biophysical Journal

Pedro R. Magalhães, Miguel Machuqueiro, António M. Baptista

Maik Goette, Martin C. Stumpe, Ralf Ficner, Helmut Grubmüller

Volume 101, Issue 5, Pages (September 2011)

Olivier Fisette, Stéphane Gagné, Patrick Lagüe Biophysical Journal

Volume 110, Issue 2, Pages (January 2016)

Molecular Dynamics Free Energy Calculations to Assess the Possibility of Water Existence in Protein Nonpolar Cavities Masataka Oikawa, Yoshiteru Yonetani

Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer Yu-Shan Lin, Gregory R. Bowman, Kyle A.

Modeling Zymogen Protein C

Volume 113, Issue 12, Pages (December 2017)

A Model of H-NS Mediated Compaction of Bacterial DNA

Henry van den Bedem, Ellen Kuhl Biophysical Journal

Construction, MD Simulation, and Hydrodynamic Validation of an All-Atom Model of a Monoclonal IgG Antibody J. Paul Brandt, Thomas W. Patapoff, Sergio.

Volume 92, Issue 11, Pages (June 2007)

Volume 86, Issue 6, Pages (June 2004)

Large-Scale Conformational Dynamics of the HIV-1 Integrase Core Domain and Its Catalytic Loop Mutants Matthew C. Lee, Jinxia Deng, James M. Briggs, Yong.

Mechanism and Energetics of Charybdotoxin Unbinding from a Potassium Channel from Molecular Dynamics Simulations Po-chia Chen, Serdar Kuyucak Biophysical.

Mechanism of the αβ Conformational Change in F1-ATPase after ATP Hydrolysis: Free- Energy Simulations Yuko Ito, Mitsunori Ikeguchi Biophysical Journal

Rainer A. Böckmann, Helmut Grubmüller Biophysical Journal

Christian Kappel, Ulrich Zachariae, Nicole Dölker, Helmut Grubmüller

Brittny C. Davis, Jodian A. Brown, Ian F. Thorpe Biophysical Journal

Volume 113, Issue 10, Pages (November 2017)

L. Makowski, J. Bardhan, D. Gore, D.J. Rodi, R.F. Fischetti

Molecular Recognition of CXCR4 by a Dual Tropic HIV-1 gp120 V3 Loop

Volume 74, Issue 1, Pages (January 1998)

Binding of the Bacteriophage P22 N-Peptide to the boxB RNA Motif Studied by Molecular Dynamics Simulations Ranjit P. Bahadur, Srinivasaraghavan Kannan,

Adam W. Van Wynsberghe, Qiang Cui Biophysical Journal

Volume 96, Issue 7, Pages (April 2009)

Azobenzene Photoisomerization-Induced Destabilization of B-DNA

Comparative Molecular Dynamics Simulation Studies of Protegrin-1 Monomer and Dimer in Two Different Lipid Bilayers Huan Rui, Jinhyuk Lee, Wonpil Im

Sundeep S. Deol, Peter J. Bond, Carmen Domene, Mark S.P. Sansom

Intrinsic Bending and Structural Rearrangement of Tubulin Dimer: Molecular Dynamics Simulations and Coarse-Grained Analysis Yeshitila Gebremichael, Jhih-Wei.

Volume 110, Issue 2, Pages (January 2016)

Molecular Interactions of Alzheimer's Biomarker FDDNP with Aβ Peptide

Activation of the Edema Factor of Bacillus anthracis by Calmodulin: Evidence of an Interplay between the EF-Calmodulin Interaction and Calcium Binding

Amir H.G. Isfahani, Jonathan B. Freund Biophysical Journal

Volume 107, Issue 9, Pages (November 2014)

Elucidation of Single Hydrogen Bonds in GTPases via Experimental and Theoretical Infrared Spectroscopy Daniel Mann, Udo Höweler, Carsten Kötting, Klaus.

Min Wang, Mary Prorok, Francis J. Castellino Biophysical Journal

Volume 83, Issue 6, Pages (December 2002)

Volume 111, Issue 4, Pages (August 2016)

The Selectivity of K+ Ion Channels: Testing the Hypotheses

Accurate Flexible Fitting of High-Resolution Protein Structures to Small-Angle X-Ray Scattering Data Using a Coarse-Grained Model with Implicit Hydration.

Mechanism of Anionic Conduction across ClC

Christina Bergonzo, Thomas E. Cheatham Biophysical Journal

A Superresolution Census of RNA Polymerase

Nevra Ozer, Celia A. Schiffer, Turkan Haliloglu Biophysical Journal

The Relation between α-Helical Conformation and Amyloidogenicity

Mechanism of Interaction between the General Anesthetic Halothane and a Model Ion Channel Protein, III: Molecular Dynamics Simulation Incorporating a.

Shayantani Mukherjee, Sean M. Law, Michael Feig Biophysical Journal

Christian Kappel, Ulrich Zachariae, Nicole Dölker, Helmut Grubmüller

Volume 111, Issue 4, Pages (August 2016)

A Model of H-NS Mediated Compaction of Bacterial DNA

Volume 98, Issue 4, Pages (February 2010)

Presentation transcript:

Relation between the Conformational Heterogeneity and Reaction Cycle of Ras: Molecular Simulation of Ras Chigusa Kobayashi, Shinji Saito Biophysical Journal Volume 99, Issue 11, Pages 3726-3734 (December 2010) DOI: 10.1016/j.bpj.2010.09.063 Copyright © 2010 Biophysical Society Terms and Conditions

Figure 1 Conformational switches in the GTP-bound (A) and GDP-bound (B) states. Switch I consists of residues 30–38 and switch II consists of residues 60–72. The figures were generated with the open-source version of PyMOL (75). Biophysical Journal 2010 99, 3726-3734DOI: (10.1016/j.bpj.2010.09.063) Copyright © 2010 Biophysical Society Terms and Conditions

Figure 2 Configurations of switches I and II in the GTP2 (A and B), GDP (C and D), GTP1w/HB (E and F), and GTP1w/oHB (G and H) states. The sphere represents Mg2+. The figures were generated with the open-source version of PyMOL (75). Biophysical Journal 2010 99, 3726-3734DOI: (10.1016/j.bpj.2010.09.063) Copyright © 2010 Biophysical Society Terms and Conditions

Figure 3 Backbone ϕ and ψ dihedral angles of the residues in switch I (A) and switch II (B). The upper and lower graphs display the ϕ and ψ angles, respectively. The circles, diamonds, squares, and triangles show the angles in the GTP2, GTP1w/HB, GTP1w/oHB, and GDP states, respectively. The error bars represent the standard deviations. Biophysical Journal 2010 99, 3726-3734DOI: (10.1016/j.bpj.2010.09.063) Copyright © 2010 Biophysical Society Terms and Conditions

Figure 4 RMSF of the Cα atoms in (A) switch I and (B) switch II. The circles, diamonds, squares, and triangles show the RMSF in the GTP2, GTP1w/HB, GTP1w/oHB, and GDP states, respectively. Biophysical Journal 2010 99, 3726-3734DOI: (10.1016/j.bpj.2010.09.063) Copyright © 2010 Biophysical Society Terms and Conditions

Figure 5 The first (A) and second (B) PCs of the four states. The structure averaged over the four states is shown as the thin tube. The shades represent the first and second PCs as displacements from the averaged structure. The projections of the GTP2, GTP1w/HB, GTP1w/oHB, and GDP states onto the first and second PCs are shown with the contour lines (C). The x-ray structures of the GTP-bound Ras in a complex with the effectors and nucleotide-free Ras binding to GEF are shown by triangles and circles, respectively. Biophysical Journal 2010 99, 3726-3734DOI: (10.1016/j.bpj.2010.09.063) Copyright © 2010 Biophysical Society Terms and Conditions