scholarly journals To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element

2021 ◽  
Author(s):  
Tamar Schlick ◽  
Qiyao Zhu ◽  
Abhishek Dey ◽  
Swati Jain ◽  
Shuting Yan ◽  
...  
Keyword(s):  
Multiple Conformations

scholarly journals Targeting multiple conformations of SARS-CoV2 Papain-Like Protease for drug repositioning: An in-silico study

2021 ◽  
Vol 131 ◽  
pp. 104295
Author(s):  
Muhammad I. Ismail ◽  
Hanan M. Ragab ◽  
Adnan A. Bekhit ◽  
Tamer M. Ibrahim
Keyword(s):  
In Silico ◽  
Drug Repositioning ◽  
In Silico Study ◽  
Multiple Conformations

scholarly journals Large domain movements upon UvrD dimerization and helicase activation

2017 ◽  
Vol 114 (46) ◽  
pp. 12178-12183 ◽  
Author(s):  
Binh Nguyen ◽  
Yerdos Ordabayev ◽  
Joshua E. Sokoloski ◽  
Elizabeth Weiland ◽  
Timothy M. Lohman
Keyword(s):  
Escherichia Coli ◽  
Single Molecule ◽  
Self Assembly ◽  
Total Internal Reflection ◽  
Dna Helicase ◽  
Conformational State ◽  
Helicase Activity ◽  
Multiple Conformations ◽  
Dna Substrate

Escherichia coli UvrD DNA helicase functions in several DNA repair processes. As a monomer, UvrD can translocate rapidly and processively along ssDNA; however, the monomer is a poor helicase. To unwind duplex DNA in vitro, UvrD needs to be activated either by self-assembly to form a dimer or by interaction with an accessory protein. However, the mechanism of activation is not understood. UvrD can exist in multiple conformations associated with the rotational conformational state of its 2B subdomain, and its helicase activity has been correlated with a closed 2B conformation. Using single-molecule total internal reflection fluorescence microscopy, we examined the rotational conformational states of the 2B subdomain of fluorescently labeled UvrD and their rates of interconversion. We find that the 2B subdomain of the UvrD monomer can rotate between an open and closed conformation as well as two highly populated intermediate states. The binding of a DNA substrate shifts the 2B conformation of a labeled UvrD monomer to a more open state that shows no helicase activity. The binding of a second unlabeled UvrD shifts the 2B conformation of the labeled UvrD to a more closed state resulting in activation of helicase activity. Binding of a monomer of the structurally similar Escherichia coli Rep helicase does not elicit this effect. This indicates that the helicase activity of a UvrD dimer is promoted via direct interactions between UvrD subunits that affect the rotational conformational state of its 2B subdomain.

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