scholarly journals Perturbations of the denatured state ensemble: Modeling their effects on protein stability and folding kinetics

1996 ◽  
Vol 5 (11) ◽  
pp. 2343-2352 ◽  
Author(s):  
James O. Wrabl ◽  
David Shortle
Keyword(s):  
Protein Stability ◽  
Ensemble Modeling ◽  
Folding Kinetics ◽  
Denatured State ◽  
State Ensemble

scholarly journals Electrostatic interactions in the denatured state ensemble: Their effect upon protein folding and protein stability

2008 ◽  
Vol 469 (1) ◽  
pp. 20-28 ◽  
Author(s):  
Jae-Hyun Cho ◽  
Satoshi Sato ◽  
Jia-Cherng Horng ◽  
Burcu Anil ◽  
Daniel P. Raleigh
Keyword(s):  
Protein Folding ◽  
Protein Stability ◽  
Electrostatic Interactions ◽  
Denatured State ◽  
State Ensemble

scholarly journals Charge-charge interactions influence the denatured state ensemble and contribute to protein stability

2000 ◽  
Vol 9 (7) ◽  
pp. 1395-1398 ◽  
Author(s):  
C. Nick Pace ◽  
Roy W. Alston ◽  
Kevin L. Shaw
Keyword(s):  
Protein Stability ◽  
Denatured State ◽  
State Ensemble ◽  
Charge Interactions

scholarly journals Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein

2021 ◽  
Vol 119 (1) ◽  
pp. e2109169119
Author(s):  
Kristen A. Gaffney ◽  
Ruiqiong Guo ◽  
Michael D. Bridges ◽  
Shaima Muhammednazaar ◽  
Daoyang Chen ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Lipid Bilayer ◽  
Lipid Bilayers ◽  
Limited Proteolysis ◽  
Water Soluble ◽  
Disordered Proteins ◽  
Resonance Spectroscopy ◽  
Denatured State ◽  
E Coli ◽  
State Ensemble

Defining the denatured state ensemble (DSE) and disordered proteins is essential to understanding folding, chaperone action, degradation, and translocation. As compared with water-soluble proteins, the DSE of membrane proteins is much less characterized. Here, we measure the DSE of the helical membrane protein GlpG of Escherichia coli (E. coli) in native-like lipid bilayers. The DSE was obtained using our steric trapping method, which couples denaturation of doubly biotinylated GlpG to binding of two streptavidin molecules. The helices and loops are probed using limited proteolysis and mass spectrometry, while the dimensions are determined using our paramagnetic biotin derivative and double electron–electron resonance spectroscopy. These data, along with our Upside simulations, identify the DSE as being highly dynamic, involving the topology changes and unfolding of some of the transmembrane (TM) helices. The DSE is expanded relative to the native state but only to 15 to 75% of the fully expanded condition. The degree of expansion depends on the local protein packing and the lipid composition. E. coli’s lipid bilayer promotes the association of TM helices in the DSE and, probably in general, facilitates interhelical interactions. This tendency may be the outcome of a general lipophobic effect of proteins within the cell membranes.

scholarly journals Protein Stability and Folding Kinetics in the Nucleus and Endoplasmic Reticulum of Eucaryotic Cells

2011 ◽  
Vol 101 (2) ◽  
pp. 421-430 ◽  
Author(s):  
A. Dhar ◽  
K. Girdhar ◽  
D. Singh ◽  
H. Gelman ◽  
S. Ebbinghaus ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Protein Stability ◽  
Folding Kinetics

Characterizing the denatured state ensemble of ubiquitin under native conditions using replica exchange molecular dynamics

RSC Advances ◽  
2016 ◽  
Vol 6 (98) ◽  
pp. 95584-95589
Author(s):  
Nai-yuan Chang ◽  
Yi-Ci Li ◽  
Cheng-Ping Jheng ◽  
Yu-Ting Kuo ◽  
Cheng-I Lee
Keyword(s):  
Molecular Dynamics ◽  
Replica Exchange ◽  
Denatured State ◽  
Replica Exchange Molecular Dynamics ◽  
Extended Conformation ◽  
State Ensemble ◽  
Native Condition ◽  
Fully Extended Conformation

The representative structures of the denatured state ensemble of ubiquitin under a native condition and heat-denatured ubiquitin simulated from a fully extended conformation.

Effects of Heme on the Structure of the Denatured State and Folding Kinetics of Cytochrome b562

2005 ◽  
Vol 346 (1) ◽  
pp. 331-344 ◽  
Author(s):  
Pascal Garcia ◽  
Marta Bruix ◽  
Manuel Rico ◽  
Simone Ciofi-Baffoni ◽  
Lucia Banci ◽  
...  
Keyword(s):  
Folding Kinetics ◽  
Denatured State ◽  
Cytochrome B562 ◽  
Kinetics Of
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