Publications

2022

K. Walczewska-Szewc, J. Rydzewski, A. Lewkowicz
Inhibition-mediated changes in prolyl oligopeptidase dynamics possibly related to α-synuclein aggregation
Phys Chem Chem Phys, 24, 4366-4373 (2022)
DOI

2021

K. Mikulska-Ruminska, T. Anthonymuthu, A. Levkina, I. Shrivastava, A. Kapralov, H. Bayır, V. Kagan, I. Bahar
NO● represses the oxygenation of arachidonoyl PE by 15LOX/PEBP1: Mechanism and role in ferroptosis
Inter. J. Mol. Sci. 22, 5253 (2021)

W. Sun, V. Tyurin, K. Mikulska-Ruminska, I. Shrivastava, … , I. Bahar, H. Bayır, Y. Tyurina, R. He, V. Kagan
Phospholipase iPLA2β averts ferroptosis by eliminating a redox lipid death signal
Nature Chem. Biol. 1, 12 (2021)

T. Anthonymuthu, Y. Tyurina, W. Sun, K. Mikulska-Ruminska, I. Shrivastava, V. Tyurin, F. Cinemre, H. Dar, A. VanDemark, T. Holman, Y. Sadovsky, B. Stockwell, R. He, I. Bahar, H. Bayır, V. Kagan
Resolving the paradox of ferroptotic cell death: Ferrostatin-1 binds to 15LOX/PEBP1 complex, suppresses generation of peroxidized ETE-PE, and protects against ferroptosis
Redox Biol. 38, 101744 (2021)

K. Walczewska-Szewc, W. Nowak
Photo-Switchable Sulfonylureas Binding to ATP-Sensitive Potassium Channel Reveal the Mechanism of Light-Controlled Insulin Release
J. Phys. Chem. B 125, 13111-13121 (2021)
DOI

J. Grzyb, K.Walczewska-Szewc, J. Sławski, M. Trojnar
Quantum dot clusters as self-assembled antennae with phycocyanine and phycobilisomes as energy acceptors
Phys Chem Chem Phys, 23, 24505-24517 (2021)
DOI

2020

J. Rydzewski, and O. Valsson
Multiscale reweighted stochastic embedding (MRSE): Deep learning of collective variables for enhanced sampling
Submitted (2020)
arXiv

J. Rydzewski
maze: Heterogeneous Ligand Unbinding along Transient Protein Tunnels
Comp. Phys. Commun. 247, 106865 (2020)
DOI arXiv Github plumID:19.056

K. Walczewska-Szewc, and W. Nowak
Structural Determinants of Insulin Release: Disordered N-Terminal Tail of Kir6. 2 Affects Potassium Channel Dynamics through Interactions with Sulfonylurea Binding Region in a SUR1 Partner
J. Phys. Chem. B 124, 6198 (2020)
DOI

A. Kapralov, Q. Yang, H. Dar, Y. Tyurina, T. Anthonymuthu, R. Kim, C. Croix, K. Mikulska-Ruminska, B. Liu, I. Shrivastava, V. Tyurin, H. Ting, Y. Gao, R. Domingues, D. Stoyanovsky, R. Mallampalli, I. Bahar, D. Gabrilovich, H. Bayir, V. Kagan
Redox Lipid Reprogramming Commands Susceptibility of Macrophages and Microglia to Ferroptotic Death
Nature Chem. Biol. 3, 278-290 (2020)

2019

J. Rydzewski
Machine Learning for Enhanced Sampling Methods (in Polish)
Głos Uczelni UMK 77, 7 (2019)
PDF

K. Walczewska-Szewc, and W. Nowak
Spacial models of malfunctioned protein complexes help to elucidate signal transduction critical for insulin release Biosystems 177, 48 (2019)
DOI

J. Rydzewski as part of The PLUMED Consortium
Promoting Transparency and Reproducibility in Enhanced Molecular Simulations
Nat. Methods 16, 670 (2019)
DOI

J. Rydzewski, and O. Valsson
Communication: Finding Multiple Reaction Pathways of Ligand Unbinding
J. Chem. Phys. 150, 221101 (2019)
DOI arXiv Github plumID:19.066

J. F. Carrascoza Mayén, J. Rydzewski, N. Szostak, J. Blazewicz, and W. Nowak
Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations
Life 9, 46 (2019)
Special Issue DOI

K. Mikulska-Ruminska, I. Shrivastava, J. Krieger, S. Zhang, H. Li, H. Bayır, S. Wenzel, A. VanDemark, V. Kagan, I. Bahar, Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members, J. Chem. Inf. Model., 59 (2019) 2496-2508.

2018

J. Rydzewski, R. Jakubowski, W. Nowak, and H. Grubmüller
Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways
J. Chem. Theory Comput. 14, 2843 (2018)
DOI Figshare plumID:19.067

J. Rydzewski, and W. Nowak
Photoinduced Transport in an H64Q Neuroglobin Antidote for Carbon Monoxide Poisoning
J. Chem. Phys. 148, 115101 (2018)
DOI

J. Rydzewski, R. Jakubowski, G. Nicosia, and W. Nowak
Conformational Sampling of a Biomolecular Rugged Energy Landscape
IEEE/ACM Trans. Comput. Biol. Bioinformatics 15, 732 (2018)
DOI

T. Anthonymuthu, E. Kenny, I. Shrivastava, Y. Tyurina, V. Tyurin, A. Nestorova, A. Amoscato, K. Mikulska-Ruminska, M. Conrad, et al., Empowerment of 15-LOX catalytic competence in selective oxidation of membrane AA-PE to ferroptotic death signals, HOO-AA-PE, JACS 140 (2018) 17835-17839.

H. Dar, Y. Tyurina, K. Mikulska-Ruminska, I. Shrivastava, et al., Pseudomonas aeruginosa utilizes host polyunsaturated phosphatidylethanolamines to trigger theft-ferroptosis in bronchial epithelium, J. Clin. Invest. 128 (2018) 4639-4653.

2017

J. Rydzewski, and W. Nowak
Rare-Event Sampling in Ligand Diffusion
Phys. Life Rev. 22-23, 85 (2017)
DOI

J. Rydzewski, and W. Nowak
Ligand Diffusion in Proteins via Enhanced Sampling in Molecular Dynamics
Phys. Life Rev. 22-23, 58 (2017)
DOI

J. Rydzewski, and W. Nowak
Thermodynamics of Camphor Migration in Cytochrome P450cam by Atomistic Simulations
Sci. Rep. 7, 7736 (2017)
DOI

S. Wenzel, Y. Tyurina, J. Zhao, C. Croix, G Mao, V. Tyurin, T. Anthonymuthu, A. Kapralov, K. Mikulska-Ruminska, I. Shrivastava, …, A. VanDemark, J. Kellum, Y. Minami, I. Bahar, H. Bayir, V. Kagan, PEBP1 Wardens Ferroptosis by Enabling Lipoxygenase Generation of Lipid Death Signals, CELL 171 (2017) 628-641.

2016

J. Rydzewski, and W. Nowak
Machine Learning Based Dimensionality Reduction Facilitates Ligand Diffusion Paths Assessment: A Case of Cytochrome P450cam
J. Chem. Theory Comput. 12, 2110 (2016)
DOI Figshare

J. Rydzewski, and W. Nowak
Molecular Dynamics Simulations of Large Systems in Electronic Excited States
Handbook of Computational Chemistry (Vol. I)
Second Edition (2016) (Editior: J. Leszczynski)
DOI

2015

J. Rydzewski, W. Nowak, and G. Nicosia
Inferring Pathological States in Cortical Neuron Microcircuits
J. Theor. Biol. 386, 34 (2015)
DOI

J. Rydzewski, R. Jakubowski, and W. Nowak
Communication: Entropic Measure to Prevent Energy Over-Minimization in Molecular Dynamics Simulations
J. Chem. Phys. 143, 171103 (2015)
DOI arXiv

J. Rydzewski, and W. Nowak
Memetic Algorithms for Ligand Expulsion from Protein Cavities
J. Chem. Phys. 143, 124101 (2015)
DOI arXiv

J. Rydzewski, W. Strzałka, and W. Nowak
Nanomechanics of PCNA: A Protein-Made DNA Sliding Clamp
Chem. Phys. Lett. 634, 236 (2015)
DOI