Volume 107, Issue 8, Pages (October 2014)

Slides:



Advertisements
Similar presentations
Fabio Trovato, Edward P. O’Brien  Biophysical Journal 
Advertisements

Po-chia Chen, Jochen S. Hub  Biophysical Journal 
Dechang Li, Ming S. Liu, Baohua Ji  Biophysical Journal 
Koen E. Merkus, Menno W.J. Prins, Cornelis Storm  Biophysical Journal 
Volume 15, Issue 3, Pages (April 2016)
Volume 112, Issue 7, Pages (April 2017)
Multi-Image Colocalization and Its Statistical Significance
Volume 98, Issue 3, Pages (February 2010)
Structural States and Dynamics of the D-Loop in Actin
Wenjun Zheng, Han Wen, Gary J. Iacobucci, Gabriela K. Popescu 
Peter J. Mulligan, Yi-Ju Chen, Rob Phillips, Andrew J. Spakowitz 
Zhanghan Wu, Jianhua Xing  Biophysical Journal 
Volume 112, Issue 7, Pages (April 2017)
Olivier Fisette, Stéphane Gagné, Patrick Lagüe  Biophysical Journal 
SAXS versus FRET: A Matter of Heterogeneity?
Dynamics of Active Semiflexible Polymers
Jing Han, Kristyna Pluhackova, Tsjerk A. Wassenaar, Rainer A. Böckmann 
Partially Assembled Nucleosome Structures at Atomic Detail
William Y.C. Huang, Han-Kuei Chiang, Jay T. Groves  Biophysical Journal 
Carlos R. Baiz, Andrei Tokmakoff  Biophysical Journal 
Volume 95, Issue 9, Pages (November 2008)
Volume 111, Issue 2, Pages (July 2016)
Po-Chao Wen, Emad Tajkhorshid  Biophysical Journal 
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.
Monika Sharma, Alexander V. Predeus, Nicholas Kovacs, Michael Feig 
Volume 96, Issue 2, Pages (January 2009)
Volume 107, Issue 3, Pages (August 2014)
Volume 100, Issue 6, Pages (March 2011)
Brittny C. Davis, Jodian A. Brown, Ian F. Thorpe  Biophysical Journal 
Quantifying Biomolecule Diffusivity Using an Optimal Bayesian Method
Volume 99, Issue 9, Pages (November 2010)
Carlos R. Baiz, Andrei Tokmakoff  Biophysical Journal 
Xiao-Han Li, Elizabeth Rhoades  Biophysical Journal 
Volume 16, Issue 5, Pages (May 2008)
Kinesin Moving through the Spotlight: Single-Motor Fluorescence Microscopy with Submillisecond Time Resolution  Sander Verbrugge, Lukas C. Kapitein, Erwin.
Volume 96, Issue 7, Pages (April 2009)
Volume 108, Issue 7, Pages (April 2015)
Volume 103, Issue 2, Pages (July 2012)
Quantifying the Interaction between EGFR Dimers and Grb2 in Live Cells
Protein Collective Motions Coupled to Ligand Migration in Myoglobin
Karunesh Arora, Tamar Schlick  Biophysical Journal 
Volume 96, Issue 5, Pages (March 2009)
Comparative Studies of Microtubule Mechanics with Two Competing Models Suggest Functional Roles of Alternative Tubulin Lateral Interactions  Zhanghan.
Volume 107, Issue 12, Pages (December 2014)
Volume 98, Issue 11, Pages (June 2010)
Grischa R. Meyer, Justin Gullingsrud, Klaus Schulten, Boris Martinac 
Cholesterol Modulates the Dimer Interface of the β2-Adrenergic Receptor via Cholesterol Occupancy Sites  Xavier Prasanna, Amitabha Chattopadhyay, Durba.
Replica Exchange Molecular Dynamics Simulations Provide Insight into Substrate Recognition by Small Heat Shock Proteins  Sunita Patel, Elizabeth Vierling,
The Effect of Dye-Dye Interactions on the Spatial Resolution of Single-Molecule FRET Measurements in Nucleic Acids  Nicolas Di Fiori, Amit Meller  Biophysical.
Structural Flexibility of CaV1. 2 and CaV2
Volume 77, Issue 1, Pages (July 1999)
Richa Dave, Daniel S. Terry, James B. Munro, Scott C. Blanchard 
Dynamics of Active Semiflexible Polymers
Mariana Levi, Kien Nguyen, Liah Dukaye, Paul Charles Whitford 
Dynamics of the BH3-Only Protein Binding Interface of Bcl-xL
Blocking of Single α-Hemolysin Pore by Rhodamine Derivatives
Allosteric Control of Syntaxin 1a by Munc18-1: Characterization of the Open and Closed Conformations of Syntaxin  Damian Dawidowski, David S. Cafiso 
Multi-Image Colocalization and Its Statistical Significance
Volume 111, Issue 11, Pages (December 2016)
Nevra Ozer, Celia A. Schiffer, Turkan Haliloglu  Biophysical Journal 
Partially Assembled Nucleosome Structures at Atomic Detail
Yongli Zhang, Junyi Jiao, Aleksander A. Rebane  Biophysical Journal 
Po-chia Chen, Jochen S. Hub  Biophysical Journal 
Shayantani Mukherjee, Sean M. Law, Michael Feig  Biophysical Journal 
Amir Marcovitz, Yaakov Levy  Biophysical Journal 
Volume 95, Issue 9, Pages (November 2008)
Volume 98, Issue 4, Pages (February 2010)
Volume 102, Issue 9, Pages (May 2012)
Volume 114, Issue 4, Pages (February 2018)
Volume 105, Issue 8, Pages (October 2013)
Presentation transcript:

Volume 107, Issue 8, Pages 1913-1923 (October 2014) Conformational State Distributions and Catalytically Relevant Dynamics of a Hinge- Bending Enzyme Studied by Single-Molecule FRET and a Coarse-Grained Simulation  Matteo Gabba, Simón Poblete, Tobias Rosenkranz, Alexandros Katranidis, Daryan Kempe, Tina Züchner, Roland G. Winkler, Gerhard Gompper, Jörg Fitter  Biophysical Journal  Volume 107, Issue 8, Pages 1913-1923 (October 2014) DOI: 10.1016/j.bpj.2014.08.016 Copyright © 2014 Biophysical Society Terms and Conditions

Figure 1 Model of the three-dimensional structure of PGK from yeast (PDB:1QPG). The color code describes both domains (cyan, N-terminal domain; yellow, C-terminal domain) and the hinge region (magenta). The substrates (ATP and 3-PG) as bound to the individual domains are shown in a calotte-model display. The dyes (green) C5-Alexa488 and (red) C2-Alexa647 are shown at positions Q135C and S290C, respectively. Representation created with the software VMD (Ver. 1.9) (10). Biophysical Journal 2014 107, 1913-1923DOI: (10.1016/j.bpj.2014.08.016) Copyright © 2014 Biophysical Society Terms and Conditions

Figure 2 smFRET data from ligand-free PGK. (A) FRET efficiency histograms. Two populations with different mean efficiencies were fitted with Gaussian distributions (black and yellow solid lines). The distribution width caused by shot noise, and variation of the acceptor quantum yield, is given (blue dashed and yellow sawtoothed lines, respectively). (B) The same data is shown in a two-dimensional contour plot of F′ versus the donor lifetime τDA. Both populations are falling on the corrected static FRET line (red solid line), which considers fast fluctuations of the interdye distances (linker dynamics and/or rigid body interdomain movements). (Red dashed line) Uncorrected static FRET line. Biophysical Journal 2014 107, 1913-1923DOI: (10.1016/j.bpj.2014.08.016) Copyright © 2014 Biophysical Society Terms and Conditions

Figure 3 (A) Histograms of apparent FRET efficiencies of ligand-free PGK calculated for different bin durations T. The largest bin time was set to 7.5 ms, a value slightly higher than the mean burst duration of ∼7.0 ms (see Fig. S11 in the Supporting Material). (B and C) Normalized ratio GDD(τ)/GDA(τ) between the donor autocorrelation function GDD(τ) and the donor-acceptor cross-correlation function GDA(τ). The data are normalized to the plateau for a better comparison. No difference between ligand-bound/-free PGK and the DNA rigid control is observed. The original curves are shown in Fig. S11 and Fig. S12. Color code for both panels B and C: double-labeled DNA with dyes separated by 10 basepairs (black) and 17 basepairs (gray). Panel B: ligand-free PGK (red). Panel C: ATP-bound (cyan), ADP-bound (orange), 3-PG-bound (green), and 3-PG∗ADP-bound (yellow) PGK. Biophysical Journal 2014 107, 1913-1923DOI: (10.1016/j.bpj.2014.08.016) Copyright © 2014 Biophysical Society Terms and Conditions

Figure 4 Here, the FRET efficiency histograms and the two-dimensional contour plots are shown for substrate-bound PGK forming binary and ternary complexes. (Blue dashed line) Position of the major population of ligand-free PGK in the efficiency histogram (for full symbol code, see Fig. 2 A). Biophysical Journal 2014 107, 1913-1923DOI: (10.1016/j.bpj.2014.08.016) Copyright © 2014 Biophysical Society Terms and Conditions

Figure 5 Transition scheme of PGK conformers between a compact (PGKC) and an expanded (PGKe) state with (∗S) and without substrates. Occupation probabilities p were determined from the FRET efficiency histograms to derive the equilibrium constants Keq. Corresponding values of these two parameters are unknown for the transitions between the ligand-free and liganded form of PGK, which are represented here by vertical transitions. The pairs of p and Keq values reported for the ligand-bound protein refer to ADP-/ATP-bound and 3-PG-/3-PG∗ADP-bound PGK. Biophysical Journal 2014 107, 1913-1923DOI: (10.1016/j.bpj.2014.08.016) Copyright © 2014 Biophysical Society Terms and Conditions

Figure 6 (A) Radius of gyration Rg and the FRET-averaged interdye distance 〈rDA〉E calculated along the three slowest normal modes: the hinge bending (blue line), the rocking (red line), and the propeller twist (green line) motions. (B) The rPP-distances (black line) and their projections on the normal modes (for color code, see panel A) are shown as a function of time (for details, see Coarse-Grained Model in the Supporting Material). The whole trajectory is shown in Fig. S7. Biophysical Journal 2014 107, 1913-1923DOI: (10.1016/j.bpj.2014.08.016) Copyright © 2014 Biophysical Society Terms and Conditions