Publications by authors named "Stepan Timr"

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Can Macromolecular Crowding Help Regulate Glutamate Dehydrogenase Activity?
Genesis Rosario, Andrea Desrochers, Alec Robitaille, Emily Rundlett, Daniel Myšák, Štěpán Timr

ACS Omega· November 2025

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Multiscale Simulation of Phosphofructokinase-1 Assemblies: Capturing the Interplay between Specific and Transient Interactions.
Mehrnoosh Khodam Hazrati, Tom Miclot, Stepan Timr

J Phys Chem B· November 2025

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Cytoplasmic fluidity and the cold life: proteome stability is decoupled from viability in psychrophiles.
Beatrice Caviglia, Stepan Timr, Marianne Guiral, Marie-Thérèse Giudici-Orticoni, Tilo Seydel

Nat Commun· November 2025

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Purinosome Unmasked: Exploring the Molecular-Scale Structure of a Purinosome Complex In Silico.
Florencia Klein, Stepan Timr, Simon Ebbinghaus, Fabio Sterpone

J Phys Chem Lett· August 2025

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Structural basis for allosteric regulation of human phosphofructokinase-1.
Eric M Lynch, Heather Hansen, Lauren Salay, Madison Cooper, Stepan Timr

Nat Commun· August 2024

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Structural basis for allosteric regulation of human phosphofructokinase-1.
Eric M Lynch, Heather Hansen, Lauren Salay, Madison Cooper, Stepan Timr

bioRxiv· March 2024

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Decoding the Role of the Global Proteome Dynamics for Cellular Thermal Stability.
Beatrice Caviglia, Daniele Di Bari, Stepan Timr, Marianne Guiral, Marie-Thérèse Giudici-Orticoni

J Phys Chem Lett· February 2024

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Evolution of large Aβ16-22 aggregates at atomic details and potential of mean force associated to peptide unbinding and fragmentation events.
Antonio Iorio, Štěpán Timr, Letizia Chiodo, Philippe Derreumaux, Fabio Sterpone

Proteins· August 2023

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Optimized OPEP Force Field for Simulation of Crowded Protein Solutions.
Stepan Timr, Simone Melchionna, Philippe Derreumaux, Fabio Sterpone

J Phys Chem B· April 2023

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Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death.
Daniele Di Bari, Stepan Timr, Marianne Guiral, Marie-Thérèse Giudici-Orticoni, Tilo Seydel

ACS Cent Sci· January 2023

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Sequestration of Proteins in Stress Granules Relies on the In-Cell but Not the Folding Stability.
Nirnay Samanta, Sara S Ribeiro, Mailin Becker, Emeline Laborie, Roland Pollak, Stepan Timr

J Am Chem Soc· December 2021

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Computational Insights into the Unfolding of a Destabilized Superoxide Dismutase 1 Mutant.
Stepan Timr, Fabio Sterpone

Biology (Basel)· November 2021

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Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis.
Phuong H Nguyen, Ayyalusamy Ramamoorthy, Bikash R Sahoo, Jie Zheng, Peter Faller, Stepan Timr

Chem Rev· February 2021

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Stabilizing or Destabilizing: Simulations of Chymotrypsin Inhibitor 2 under Crowding Reveal Existence of a Crossover Temperature.
Stepan Timr, Fabio Sterpone

J Phys Chem Lett· February 2021

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Quantitative linear dichroism imaging of molecular processes in living cells made simple by open software tools.
Alexey Bondar, Olga Rybakova, Josef Melcr, Jan Dohnálek, Petro Khoroshyy, Štěpán Timr

Commun Biol· February 2021

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Protein thermal stability.
Stepan Timr, Dominique Madern, Fabio Sterpone

Prog Mol Biol Transl Sci· January 2021

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The Unfolding Journey of Superoxide Dismutase 1 Barrels under Crowding: Atomistic Simulations Shed Light on Intermediate States and Their Interactions with Crowders.
Stepan Timr, David Gnutt, Simon Ebbinghaus, Fabio Sterpone

J Phys Chem Lett· May 2020

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Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics.
Astrid F Brandner, Stepan Timr, Simone Melchionna, Philippe Derreumaux, Marc Baaden

Sci Rep· November 2019

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Stability Effect of Quinary Interactions Reversed by Single Point Mutations.
David Gnutt, Stepan Timr, Jonas Ahlers, Benedikt König, Emily Manderfeld

J Am Chem Soc· March 2019

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Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering.
Tomas Martinek, Elise Duboué-Dijon, Štěpán Timr, Philip E Mason, Katarina Baxová

J Chem Phys· June 2018

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Calcium Sensing by Recoverin: Effect of Protein Conformation on Ion Affinity.
Štěpán Timr, Jan Kadlec, Pavel Srb, O H Samuli Ollila, Pavel Jungwirth

J Phys Chem Lett· April 2018

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Membrane Binding of Recoverin: From Mechanistic Understanding to Biological Functionality.
Štěpán Timr, Roman Pleskot, Jan Kadlec, Miriam Kohagen, Aniket Magarkar

ACS Cent Sci· August 2017

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Transmembrane Potential Modeling: Comparison between Methods of Constant Electric Field and Ion Imbalance.
Josef Melcr, Daniel Bonhenry, Štěpán Timr, Pavel Jungwirth

J Chem Theory Comput· May 2016

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Nonlinear Optical Properties of Fluorescent Dyes Allow for Accurate Determination of Their Molecular Orientations in Phospholipid Membranes.
Štěpán Timr, Jiří Brabec, Alexey Bondar, Tomáš Ryba, Miloš Železný

J Phys Chem B· July 2015

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Oxidation of cholesterol does not alter significantly its uptake into high-density lipoprotein particles.
Topi Karilainen, Štěpán Timr, Ilpo Vattulainen, Pavel Jungwirth

J Phys Chem B· April 2015

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