Fast-Folding Kinetics Using Nanosecond Laser-Induced Temperature-Jump Methods

2021 ◽  
pp. 117-134
Author(s):  
Michele Cerminara
2019 ◽  
Vol 116 (17) ◽  
pp. 8137-8142 ◽  
Author(s):  
Malwina Szczepaniak ◽  
Manuel Iglesias-Bexiga ◽  
Michele Cerminara ◽  
Mourad Sadqi ◽  
Celia Sanchez de Medina ◽  
...  

Protein (un)folding rates depend on the free-energy barrier separating the native and unfolded states and a prefactor term, which sets the timescale for crossing such barrier or folding speed limit. Because extricating these two factors is usually unfeasible, it has been common to assume a constant prefactor and assign all rate variability to the barrier. However, theory and simulations postulate a protein-specific prefactor that contains key mechanistic information. Here, we exploit the special properties of fast-folding proteins to experimentally resolve the folding rate prefactor and investigate how much it varies among structural homologs. We measure the ultrafast (un)folding kinetics of five natural WW domains using nanosecond laser-induced temperature jumps. All five WW domains fold in microseconds, but with a 10-fold difference between fastest and slowest. Interestingly, they all produce biphasic kinetics in which the slower phase corresponds to reequilibration over the small barrier (<3RT) and the faster phase to the downhill relaxation of the minor population residing at the barrier top [transition state ensemble (TSE)]. The fast rate recapitulates the 10-fold range, demonstrating that the folding speed limit of even the simplest all-β fold strongly depends on the amino acid sequence. Given this fold’s simplicity, the most plausible source for such prefactor differences is the presence of nonnative interactions that stabilize the TSE but need to break up before folding resumes. Our results confirm long-standing theoretical predictions and bring into focus the rate prefactor as an essential element for understanding the mechanisms of folding.


2005 ◽  
Vol 76 (8) ◽  
pp. 083120 ◽  
Author(s):  
Eefei Chen ◽  
Youxian Wen ◽  
James W. Lewis ◽  
Robert A. Goldbeck ◽  
David S. Kliger ◽  
...  

2004 ◽  
Vol 101 (12) ◽  
pp. 4077-4082 ◽  
Author(s):  
C. D. Snow ◽  
L. Qiu ◽  
D. Du ◽  
F. Gai ◽  
S. J. Hagen ◽  
...  

2013 ◽  
Vol 85 (20) ◽  
pp. 9439-9443 ◽  
Author(s):  
Kazuhiko Yamasaki ◽  
Yuji Obara ◽  
Manabu Hasegawa ◽  
Hideki Tanaka ◽  
Tomoko Yamasaki ◽  
...  

2012 ◽  
Vol 102 (3) ◽  
pp. 448a-449a
Author(s):  
Mark E. Polinkovsky ◽  
Yann Gambin ◽  
Michael Erickstad ◽  
Ashok Deniz ◽  
Alex Groisman

2009 ◽  
Vol 106 (14) ◽  
pp. 5651-5656 ◽  
Author(s):  
T. Hart ◽  
L. L. P. Hosszu ◽  
C. R. Trevitt ◽  
G. S. Jackson ◽  
J. P. Waltho ◽  
...  

Author(s):  
T. Wichertjes ◽  
E.J. Kwak ◽  
E.F.J. Van Bruggen

Hemocyanin of the horseshoe crab (Limulus polyphemus) has been studied in nany ways. Recently the structure, dissociation and reassembly was studied using electron microscopy of negatively stained specimens as the method of investigation. Crystallization of the protein proved to be possible and X-ray crystallographic analysis was started. Also fluorescence properties of the hemocyanin after dialysis against Tris-glycine buffer + 0.01 M EDTA pH 8.9 (so called “stripped” hemocyanin) and its fractions II and V were studied, as well as functional properties of the fractions by NMR. Finally the temperature-jump method was used for assaying the oxygen binding of the dissociating molecule and of preparations of isolated subunits. Nevertheless very little is known about the structure of the intact molecule. Schutter et al. suggested that the molecule possibly consists of two halves, combined in a staggered way, the halves themselves consisting of four subunits arranged in a square.


2020 ◽  
Vol 92 (2) ◽  
pp. 20701
Author(s):  
Bo Li ◽  
Xiaofeng Li ◽  
Zhifeng Zhu ◽  
Qiang Gao

Laser-induced breakdown spectroscopy (LIBS) is a powerful technique for quantitative diagnostics of gases. The spatial resolution of LIBS, however, is limited by the volume of plasma. Here femtosecond-nanosecond dual-pulsed LIBS was demonstrated. Using this method, the breakdown threshold was reduced by 80%, and decay of continuous radiation was shortened. In addition, the volume of the plasma was shrunk by 85% and hence, the spatial resolution of LIBS was significantly improved.


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