178 citations · 602 across the 8 of their papers we have counts for
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GLN -- a method to reveal unique properties of lasso type topology in proteins
Wanda Niemyska, Kenneth C. Millett, Joanna I. Sulkowska
Geometry and topology are the main factors that determine the functional properties of proteins. In this work, we show how to use the Gauss linking integral (GLN) in the form of a…
Jamming proteins with slipknots and their free energy landscape
Joanna I. Sułkowska, Piotr Sułkowski, José N. Onuchic
Theoretical studies of stretching proteins with slipknots reveal a surprising growth of their unfolding times when the stretching force crosses an intermediate threshold. This beha…
Dodging the crisis of folding proteins with knots
Joanna I. Sułkowska, Piotr Sułkowski, José N. Onuchic
Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is su…
Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots
Mateusz Sikora, Joanna I. Sułkowska, Marek Cieplak
A new theoretical survey of proteins' resistance to constant speed stretching is performed for a set of 17 134 proteins as described by a structure-based model. The proteins select…
How knots influence properties of proteins
Joanna I. Sułkowska, Piotr Sułkowski, P. Szymczak +1
Molecular dynamics studies within a coarse-grained structure based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects in the nati…
Tightening of knots in proteins
Joanna I. Sułkowska, Piotr Sułkowski, Piotr Szymczak +1
We perform theoretical studies of stretching of 20 proteins with knots within a coarse grained model. The knot's ends are found to jump to well defined sequential locations that ar…