scholarly journals Exploiting the downhill folding regime via experiment

HFSP Journal ◽  
2008 ◽  
Vol 2 (6) ◽  
pp. 342-353 ◽  
Author(s):  
Victor Muñoz ◽  
Mourad Sadqi ◽  
Athi N. Naganathan ◽  
David de Sancho
Keyword(s):  
Downhill Folding

scholarly journals A Survey of λ Repressor Fragments from Two-State to Downhill Folding

2010 ◽  
Vol 397 (3) ◽  
pp. 789-798 ◽  
Author(s):  
Feng Liu ◽  
Yi Gui Gao ◽  
Martin Gruebele
Keyword(s):  
Downhill Folding

scholarly journals Revisiting the NMR Structure of the Ultrafast Downhill Folding Protein gpW from Bacteriophage λ

PLoS ONE ◽  
2011 ◽  
Vol 6 (11) ◽  
pp. e26409 ◽  
Author(s):  
Lorenzo Sborgi ◽  
Abhinav Verma ◽  
Victor Muñoz ◽  
Eva de Alba
Keyword(s):  
Nmr Structure ◽  
Bacteriophage Λ ◽  
Downhill Folding

A Simple Thermodynamic Test To Discriminate between Two-State and Downhill Folding

2004 ◽  
Vol 126 (28) ◽  
pp. 8596-8597 ◽  
Author(s):  
Fabiana Y. Oliva ◽  
Victor Muñoz
Keyword(s):  
Downhill Folding

Robustness of Downhill Folding:  Guidelines for the Analysis of Equilibrium Folding Experiments on Small Proteins

Biochemistry ◽  
2005 ◽  
Vol 44 (20) ◽  
pp. 7435-7449 ◽  
Author(s):  
Athi N. Naganathan ◽  
Raúl Perez-Jimenez ◽  
Jose M. Sanchez-Ruiz ◽  
Victor Muñoz
Keyword(s):  
Downhill Folding ◽  
Small Proteins

scholarly journals 1I1645 Nonglassy downhill folding in a 3D lattice Go model protein

2002 ◽  
Vol 42 (supplement2) ◽  
pp. S52
Author(s):  
H. Nakamura ◽  
M. Sasai ◽  
M. Takano
Keyword(s):  
Downhill Folding ◽  
Go Model ◽  
Model Protein

A new way to recognize downhill folding based on generalized path length

2020 ◽  
Vol 19 (04) ◽  
pp. 2040005 ◽  
Author(s):  
Xuewei Jiang ◽  
Zhengwu Wu ◽  
Zhenyuan Fan ◽  
Junhua Yin ◽  
Lu Zheng
Keyword(s):  
Protein Folding ◽  
Molecular Mechanism ◽  
Path Length ◽  
Energy Profile ◽  
Scientific Problem ◽  
Downhill Folding ◽  
Barrier Energy ◽  
Insight Into

The protein folding is an important scientific problem and many methods were designed to elucidate the protein folding and obtain insight into the molecular mechanism. A novel means is presented to identify the downhill pathways of protein folding in this paper. This method is based on barrier energy profile projected onto the generalized path length (GPL) with Breadth-first searching (BFS) algorithm. We show the effectiveness of this approach by constructing the barrier energy profile of trpzip2 and comparing with other methods.

scholarly journals Substitution of the Native Zn(II) with Cd(II), Co(II) and Ni(II) Changes the Downhill Unfolding Mechanism of Ros87 to a Completely Different Scenario

2020 ◽  
Vol 21 (21) ◽  
pp. 8285
Author(s):  
Rinaldo Grazioso ◽  
Sara García-Viñuales ◽  
Luigi Russo ◽  
Gianluca D’Abrosca ◽  
Sabrina Esposito ◽  
...  
Keyword(s):  
Zinc Finger ◽  
Metal Ion ◽  
Zinc Ion ◽  
Hydrophobic Core ◽  
Downhill Folding ◽  
Key Factor ◽  
Model Protein ◽  
Nmr Techniques ◽  
The One

The structural effects of zinc replacement by xenobiotic metal ions have been widely studied in several eukaryotic and prokaryotic zinc-finger-containing proteins. The prokaryotic zinc finger, that presents a bigger βββαα domain with a larger hydrophobic core with respect to its eukaryotic counterpart, represents a valuable model protein to study metal ion interaction with metallo-proteins. Several studies have been conducted on Ros87, the DNA binding domain of the prokaryotic zinc finger Ros, and have demonstrated that the domain appears to structurally tolerate Ni(II), albeit with important structural perturbations, but not Pb(II) and Hg(II), and it is in vitro functional when the zinc ion is replaced by Cd(II). We have previously shown that Ros87 unfolding is a two-step process in which a zinc binding intermediate converts to the native structure thorough a delicate downhill folding transition. Here, we explore the folding/unfolding behaviour of Ros87 coordinated to Co(II), Ni(II) or Cd(II), by UV-Vis, CD, DSC and NMR techniques. Interestingly, we show how the substitution of the native metal ion results in complete different folding scenarios. We found a two-state unfolding mechanism for Cd-Ros87 whose metal affinity Kd is comparable to the one obtained for the native Zn-Ros87, and a more complex mechanism for Co-Ros87 and Ni-Ros87, that show higher Kd values. Our data outline the complex cross-correlation between the protein–metal ion equilibrium and the folding mechanism proposing such an interplay as a key factor in the proper metal ion selection by a specific metallo-protein.

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