Aurélie Gouron, Anne Milet, Helene Jamet Biophysical Journal

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

Analysis of Kinetic Intermediates in Single-Particle Dwell-Time Distributions Daniel L. Floyd, Stephen C. Harrison, Antoine M. van Oijen Biophysical Journal.

Counter-Intuitive Stochastic Behavior of Simple Gene Circuits with Negative Feedback Tatiana T. Marquez-Lago, Jörg Stelling Biophysical Journal Volume.

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

Structure and Dynamics of ER: Minimal Networks and Biophysical Constraints Congping Lin, Yiwei Zhang, Imogen Sparkes, Peter Ashwin Biophysical Journal.

Calibration of Optical Tweezers for In Vivo Force Measurements: How do Different Approaches Compare? Yonggun Jun, Suvranta K. Tripathy, Babu R.J. Narayanareddy,

Tryptophan-Lipid Interactions in Membrane Protein Folding Probed by Ultraviolet Resonance Raman and Fluorescence Spectroscopy Katheryn M. Sanchez, Guipeun.

Yield Strength of Human Erythrocyte Membranes to Impulsive Stretching Fenfang Li, Chon U Chan, Claus Dieter Ohl Biophysical Journal Volume 105, Issue 4,

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

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,

The Interrelations among Stochastic Pacing, Stability, and Memory in the Heart Hila Dvir, Sharon Zlochiver Biophysical Journal Volume 107, Issue 4, Pages.

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

Quantifying the Rheological and Hemodynamic Characteristics of Sickle Cell Anemia Huan Lei, George Em Karniadakis Biophysical Journal Volume 102, Issue.

2015 Alzheimer's disease facts and figures Alzheimer's & Dementia: The Journal of the Alzheimer's Association Volume 11, Issue 3, Pages (March.

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.

Clamping Down on Tumor Proliferation

Maryam Sayadi, Seiichiro Tanizaki, Michael Feig Biophysical Journal

Dechang Li, Ming S. Liu, Baohua Ji Biophysical Journal

Volume 109, Issue 6, Pages (September 2015)

Volume 111, Issue 7, Pages (October 2016)

Volume 107, Issue 2, Pages (July 2014)

A Dynamics Criterion to Determine Allostery

Dejun Lin, Alan Grossfield Biophysical Journal

Peter J. Mulligan, Yi-Ju Chen, Rob Phillips, Andrew J. Spakowitz

Shaogui Wu, Laicai Li, Quan Li Biophysical Journal

M. Maraldi, C. Valero, K. Garikipati Biophysical Journal

SAXS versus FRET: A Matter of Heterogeneity?

Thermo- and Mesostabilizing Protein Interactions Identified by Temperature-Dependent Statistical Potentials Benjamin Folch, Yves Dehouck, Marianne Rooman

Volume 96, Issue 12, Pages (June 2009)

Nanopore Sequencing: Forcing Improved Resolution

How Does Protein Architecture Facilitate the Transduction of ATP Chemical-Bond Energy into Mechanical Work? The Cases of Nitrogenase and ATP Binding-Cassette.

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.

Emel Ficici, Daun Jeong, Ioan Andricioaei Biophysical Journal

Simulations of HIV Capsid Protein Dimerization Reveal the Effect of Chemistry and Topography on the Mechanism of Hydrophobic Protein Association Naiyin.

Volume 108, Issue 6, Pages (March 2015)

Nadine Keller, Jiří Mareš, Oliver Zerbe, Markus G. Grütter Structure

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

Volume 98, Issue 2, Pages (January 2010)

Volume 110, Issue 11, Pages (June 2016)

Volume 102, Issue 1, Pages (January 2012)

Conformational Recognition of an Intrinsically Disordered Protein

Tzur Paldi, Michael Gurevitz Biophysical Journal

Let’s Twist (the S4) Again

“DFG-Flip” in the Insulin Receptor Kinase Is Facilitated by a Helical Intermediate State of the Activation Loop Harish Vashisth, Luca Maragliano, Cameron F.

The Movement of tRNA Through the Ribosome

Atomistic Ensemble Modeling and Small-Angle Neutron Scattering of Intrinsically Disordered Protein Complexes: Applied to Minichromosome Maintenance Protein

Protein Collective Motions Coupled to Ligand Migration in Myoglobin

Volume 108, Issue 10, Pages (May 2015)

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

Volume 101, Issue 2, Pages (July 2011)

Protein Grabs a Ligand by Extending Anchor Residues: Molecular Simulation for Ca2+ Binding to Calmodulin Loop Chigusa Kobayashi, Shoji Takada Biophysical.

Ozge Kurkcuoglu, Paul A. Bates Biophysical Journal

Dynamics of the BH3-Only Protein Binding Interface of Bcl-xL

Volume 92, Issue 3, Pages (February 1998)

The Talin Dimer Structure Orientation Is Mechanically Regulated

Christina Bergonzo, Thomas E. Cheatham Biophysical Journal

Huan-Xiang Zhou, Osman Bilsel Biophysical Journal

Cooperative Nucleotide Binding in Hsp90 and Its Regulation by Aha1

Computational Modeling of Structurally Conserved Cancer Mutations in the RET and MET Kinases: The Impact on Protein Structure, Dynamics, and Stability

Insights from Free-Energy Calculations: Protein Conformational Equilibrium, Driving Forces, and Ligand-Binding Modes Yu-ming M. Huang, Wei Chen, Michael J.

Systems Biophysics: Multiscale Biophysical Modeling of Organ Systems

Xiaodong Pang, Huan-Xiang Zhou Biophysical Journal

Volume 96, Issue 12, Pages (June 2009)

Volume 98, Issue 2, Pages (January 2010)

Volume 112, Issue 6, Pages (March 2017)

Alexander S. Moffett, Kyle W. Bender, Steven C. Huber, Diwakar Shukla

Presentation transcript:

Conformational Flexibility of Human Casein Kinase Catalytic Subunit Explored by Metadynamics Aurélie Gouron, Anne Milet, Helene Jamet Biophysical Journal Volume 106, Issue 5, Pages 1134-1141 (March 2014) DOI: 10.1016/j.bpj.2014.01.031 Copyright © 2014 Biophysical Society Terms and Conditions

Figure 1 Overview of the flexible regions near the ATP binding site of the catalytic subunit of protein kinase in the totally active conformation (PDB: 2PVR). (a) Two conformations are superposed: in blue the collapsed p-loop, in green the stretched p-loop conformation. (b) The two conformations superposed are the closed and the open hinge region conformation respectively in blue and green. Figures were prepared with PYMOL (DeLano Scientific, San Carlos, CA, http://www.pymol.org). To see this figure in color, go online. Biophysical Journal 2014 106, 1134-1141DOI: (10.1016/j.bpj.2014.01.031) Copyright © 2014 Biophysical Society Terms and Conditions

Figure 2 FES reconstructed as a function of s and z of the p-loop equilibrium. The energy separation between contours is 2 kcal/mol. Basins A–E are referring to the conformations in Fig. 3, a–e. To see this figure in color, go online. Biophysical Journal 2014 106, 1134-1141DOI: (10.1016/j.bpj.2014.01.031) Copyright © 2014 Biophysical Society Terms and Conditions

Figure 3 (a–e) Steps of the p-loop collapse. Typical structure of basins A–E defined in Fig 2. Figures were prepared with PYMOL (DeLano Scientific, http://www.pymol.org). To see this figure in color, go online. Biophysical Journal 2014 106, 1134-1141DOI: (10.1016/j.bpj.2014.01.031) Copyright © 2014 Biophysical Society Terms and Conditions

Figure 4 FES reconstructed as a function of s and z of the hinge region equilibrium. The energy separation between contours is 2 kcal/mol. Basins A–D are referring to the conformations below the FES. Figures were prepared with PYMOL (Delano Scientific, http://www.pymol.org). To see this figure in color, go online. Biophysical Journal 2014 106, 1134-1141DOI: (10.1016/j.bpj.2014.01.031) Copyright © 2014 Biophysical Society Terms and Conditions

Scheme 1 Hypothetical equilibrium of CK2α proposed by Niefind et al. (9) Biophysical Journal 2014 106, 1134-1141DOI: (10.1016/j.bpj.2014.01.031) Copyright © 2014 Biophysical Society Terms and Conditions