58 citations · 139 across the 7 of their papers we have counts for
7 papers
Contact-based molecular dynamics of structured and disordered proteins in a coarse-grained model: fixed contacts, switchable contacts and those described by pseudo-improper-dihedral angles
Łukasz Mioduszewski, Jakub Bednarz, Mateusz Chwastyk +1
We present a coarse-grained C-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential…
The GōMartini approach: Revisiting the concept of contact maps and the modelling of protein complexes
Luis F. Cofas-Vargas, Rodrigo A. Moreira, Simón Poblete +2
We present a review of a series of contact maps for the determination of native interactions in proteins and nucleic acids based on a distance-threshold. Such contact maps are most…
Conformational Biases of α-Synuclein and Formation of Transient Knots
Mateusz Chwastyk, Marek Cieplak
We study local conformational biases in the dynamics of α-synuclein by using all-atom simulations with explicit and implicit solvents. The biases are related to the frequency of th…
Structural entanglements in protein complexes
Yani Zhao, Mateusz Chwastyk, Marek Cieplak
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behav…
Topological transformations in proteins: effects of heating and proximity of an interface
Yani Zhao, Mateusz Chwastyk, Marek Cieplak
Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding…
Cotranslational folding of deeply knotted proteins
Mateusz Chwastyk, Marek Cieplak
Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By e…
Multiple folding pathways of proteins with shallow knots and co-translational folding
Mateusz Chwastyk, Marek Cieplak
We study the folding process in the shallowly knotted protein MJ0366 within two variants of a structure-based model. We observe that the resulting topological pathways are much ric…