301 citations · 2.5k across the 73 of their papers we have counts for
40 papers · 1 filter
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…
Self-assembly of model proteins into virus capsids
Karol Wolek, Marek Cieplak
We consider self-assembly of proteins into a virus capsid by the methods of molecular dynamics. The capsid corresponds either to SPMV or CCMV and is studied with and without the RN…
Disordered peptide chains in an α-C-based coarse-grained model
Łukasz Mioduszewski, Marek Cieplak
We construct a one-bead-per-residue coarse-grained dynamical model to describe intrinsically disordered proteins at significantly longer timescales than in the all-atom models. In…
Proteins at air-water and oil-water interfaces in an all-atom model
Yani Zhao, Marek Cieplak
We study the behavior of five proteins at the air-water and oil-water interfaces by all-atom molecular dynamics. The proteins are found to get distorted when pinned to the interfac…
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…
Structural changes in barley protein LTP1 isoforms at air-water interfaces
Yani Zhao, Marek Cieplak
We use a coarse-grained model to study the conformational changes in two barley proteins, LTP1 and its ligand adduct isoform LTP1b, that result from their adsorption to the air-wat…
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…
Unfolding knots by proteasome-like systems: simulations of the behaviour of folded and neurotoxic proteins
Michał Wojciechowski, Àngel Gómez-Sicilia, Mariano Carrión-Vázquez +1
Knots in proteins have been proposed to resist proteasomal degradation. Ample evidence associates proteasomal degradation with neurodegeneration. One interesting possibility is tha…
Stiffness of the C-terminal disordered linker affects the geometry of the active site in endoglucanase Cel8A
Bartosz Rozycki, Marek Cieplak
Cellulosomes are complex multi-enzyme machineries which efficiently degrade plant cell-wall polysaccharides. The multiple domains of the cellulosome proteins are often tethered tog…
Criteria for folding in structure-based models of proteins
Karol Wołek, Marek Cieplak
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem…
Unbinding and unfolding of adhesion protein complexes through stretching: Interplay between shear and tensile mechanical clamps
Bartosz Rozycki, Lukasz Mioduszewski, Marek Cieplak
Using coarse-grained molecular dynamics simulations, we analyze mechanically induced dissociation and unfolding of the protein complex CD48-2B4. This heterodimer is an indispensabl…
Citrate synthase proteins in extremophilic organisms: Studies within a structure-based model
Bartosz Rozycki, Marek Cieplak
We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bact…
Aqueous Amino Acids and Proteins Near the Surface of Gold in Hydrophilic and Hydrophobic Force Fields
Grzegorz Nawrocki, Marek Cieplak
We calculate potentials of the mean force for twenty amino acids in the vicinity of the (111) surface of gold, for several dipeptides, and for some analogs of the side chains, usin…
Amino acids and proteins at ZnO-water interfaces in molecular dynamics simulations
Grzegorz Nawrocki, Marek Cieplak
We determine potentials of the mean force for interactions of amino acids with four common surfaces of ZnO in aqueous solutions. The method involves all-atom molecular dynamics sim…
Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations
Grzegorz Nawrocki, Marek Cieplak
The growing usage of nanoparticles of zinc sulfide as quantum dots and biosensors calls for a theoretical assessment of interactions of ZnS with biomolecules. We employ the molecul…
Formation of Cystine Slipknots in Dimeric Proteins
Mateusz Sikora, Marek Cieplak
We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some m…
Cystine plug and other novel mechanisms of large mechanical stability in dimeric proteins
Mateusz Sikora, Marek Cieplak
We identify three dimeric proteins whose mechanostability is anisotropic and should exceed 1 nN along some directions. They come with distinct mechanical clamps: shear-based, invol…
Molecular jamming - the cystine slipknot mechanical clamp in all-atom simulations
Lukasz Peplowski, Mateusz Sikora, Wieslaw Nowak +1
A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force-peaks in the range of 1 nN. Such high force peaks sho…
Nanoindentation of virus capsids in a molecular model
Marek Cieplak, Mark O. Robbins
A molecular-level model is used to study the mechanical response of empty cowpea chlorotic mottle virus (CCMV) and cowpea mosaic virus (CPMV) capsids. The model is based on the nat…
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…
Hydrodynamic Interactions in Protein Folding
Marek Cieplak, Szymon Niewieczerzał
We incorporate hydrodynamic interactions (HI) in a coarse-grained and structure-based model of proteins by employing the Rotne-Prager hydrodynamic tensor. We study several small pr…
Stretching and twisting of the DNA duplexes in coarse grained dynamical models
Szymon Niewieczerzał, Marek Cieplak
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The m…
Effects of confinement and crowding on folding of model proteins
M. Wojciechowski, Marek Cieplak
We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the…
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…