J. I. Sulkowska

This paper analyzes 6-crossing protein knots using AlphaFold 2 predictions and a coarse-grained model, identifying two distinct folding mechanisms for the 63 knot.

This study elucidates the catalytic mechanism of Nep1 using molecular dynamics and quantum chemical calculations, revealing that water mediates proton transfer rather than a conserved serine residue.

The paper presents the first crystal structure of a double knotted protein TrmD-Tm1570 and shows it can be degraded by the ClpXP system, with simulations explaining degradation kinetics.

The paper analyzes SAM conformational space in free and bound states, identifying structural differences between knotted and unknotted methyltransferases.