The Folding of Knotted Proteins: Distinguishing the Distinct Behavior of Shallow and Deep Knots

2020 ◽  
Vol 60 (7) ◽  
pp. 713-724
Author(s):  
Maciej Piejko ◽  
Szymon Niewieczerzal ◽  
Joanna I. Sulkowska
Keyword(s):  
Knotted Proteins

Structural statistical properties of knotted proteins

2009 ◽  
Vol 18 (4) ◽  
pp. 1684-1690 ◽  
Author(s):  
Wang Xiang-Hong ◽  
Shen Yu ◽  
Zhang Lin-Xi
Keyword(s):  
Statistical Properties ◽  
Knotted Proteins

scholarly journals The Role of Non-Native Interactions in the Folding of Knotted Proteins

2012 ◽  
Vol 8 (6) ◽  
pp. e1002504 ◽  
Author(s):  
Tatjana Škrbić ◽  
Cristian Micheletti ◽  
Pietro Faccioli
Keyword(s):  
Knotted Proteins

Structures and folding pathways of topologically knotted proteins

2010 ◽  
Vol 23 (3) ◽  
pp. 033101 ◽  
Author(s):  
Peter Virnau ◽  
Anna Mallam ◽  
Sophie Jackson
Keyword(s):  
Folding Pathways ◽  
Knotted Proteins

scholarly journals Subknots in ideal knots, random knots and knotted proteins

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Eric J. Rawdon ◽  
Kenneth C. Millett ◽  
Andrzej Stasiak
Keyword(s):  
Knotted Proteins ◽  
Random Knots

scholarly journals Mechanistic Insights into the Folding of Knotted Proteins In Vitro and In Vivo

2015 ◽  
Vol 427 (2) ◽  
pp. 248-258 ◽  
Author(s):  
Nicole C.H. Lim ◽  
Sophie E. Jackson
Keyword(s):  
Knotted Proteins

scholarly journals Computer simulation of knotted proteins unfold and translocation through nano-pores

2018 ◽  
Author(s):  
M. A. Shahzad
Keyword(s):  
Computer Simulation ◽  
Computational Model ◽  
Coarse Grained ◽  
Kinetic Properties ◽  
Constant Force ◽  
Translocation Mechanism ◽  
Translocation Time ◽  
Knotted Protein ◽  
Knotted Proteins ◽  
Pulling Force

We study the unfold and translocation of knotted protein, YibK and YbeA, through α-hemolysin nano-pore via a coarse grained computational model. We observe that knot of protein unfold in advance before the translocation take place. We also characterized the translocation mechanism by studying the thermodynamical and kinetic properties of the process. In particular, we study the average of translocation time, and the translocation probability as a function of pulling force F acting in the channel. In limit of low pulling inward constant force acting along the axis of the pore, the YibK knotted protein takes longer average translocation time as compare to YbeA knotted protein.

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