scholarly journals Extracting Complex Network and Effective Free Energy Landscape of Protein Fluctuation from Single-Molecule Time Series

2010 ◽  
Vol 98 (3) ◽  
pp. 184a
Author(s):  
Tamiki Komatsuzaki ◽  
Chun-Biu Li ◽  
Akinori Baba
Keyword(s):  
Time Series ◽  
Free Energy ◽  
Complex Network ◽  
Single Molecule ◽  
Energy Landscape ◽  
Free Energy Landscape

scholarly journals Slow domain reconfiguration causes power-law kinetics in a two-state enzyme

2018 ◽  
Vol 115 (3) ◽  
pp. 513-518 ◽  
Author(s):  
Iris Grossman-Haham ◽  
Gabriel Rosenblum ◽  
Trishool Namani ◽  
Hagen Hofmann
Keyword(s):  
Free Energy ◽  
Single Molecule ◽  
Power Law ◽  
Energy Landscape ◽  
Rate Equations ◽  
Free Energy Landscape ◽  
Closed Domain ◽  
Single Molecule Fret ◽  
Power Law Kinetics ◽  
Interdomain Interactions

Protein dynamics are typically captured well by rate equations that predict exponential decays for two-state reactions. Here, we describe a remarkable exception. The electron-transfer enzyme quiescin sulfhydryl oxidase (QSOX), a natural fusion of two functionally distinct domains, switches between open- and closed-domain arrangements with apparent power-law kinetics. Using single-molecule FRET experiments on time scales from nanoseconds to milliseconds, we show that the unusual open-close kinetics results from slow sampling of an ensemble of disordered domain orientations. While substrate accelerates the kinetics, thus suggesting a substrate-induced switch to an alternative free energy landscape of the enzyme, the power-law behavior is also preserved upon electron load. Our results show that the slow sampling of open conformers is caused by a variety of interdomain interactions that imply a rugged free energy landscape, thus providing a generic mechanism for dynamic disorder in multidomain enzymes.

scholarly journals A new view of protein synthesis: Mapping the free energy landscape of the ribosome using single-molecule FRET

Biopolymers ◽  
2008 ◽  
Vol 89 (7) ◽  
pp. 565-577 ◽  
Author(s):  
James B. Munro ◽  
Andrea Vaiana ◽  
Kevin Y. Sanbonmatsu ◽  
Scott C. Blanchard
Keyword(s):  
Free Energy ◽  
Protein Synthesis ◽  
Single Molecule ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Single Molecule Fret ◽  
New View

Single-Molecule FRET Studies of Counterion Effects on the Free Energy Landscape of Human Mitochondrial Lysine tRNA

Biochemistry ◽  
2011 ◽  
Vol 50 (15) ◽  
pp. 3107-3115 ◽  
Author(s):  
Kirsten Dammertz ◽  
Martin Hengesbach ◽  
Mark Helm ◽  
G. Ulrich Nienhaus ◽  
Andrei Yu. Kobitski
Keyword(s):  
Free Energy ◽  
Single Molecule ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Single Molecule Fret ◽  
Lysine Trna
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