Publications

JOURNAL ARTICLES

[16] Timr S, Sterpone F. Computational Insights into the Unfolding of a Destabilized Superoxide Dismutase 1 Mutant. Biology 10, 1240, 2021. link

[15] Samanta N, Ribeiro S S, Becker M, Laborie E, Pollak R, Timr S, Sterpone F, Ebbinghaus S. Sequestration of Proteins in Stress Granules Relies on the In-Cell but Not the In Vitro Folding Stability. Journal of the American Chemical Society 143, 47, 19909 – 19918, 2021. link

[14] Bondar A, Rybakova O, Melcr J, Dohnálek J, Khoroshyy P, Ticháček O, Timr S, Miclea P, Sakhi A, Marková V, Lazar J. Quantitative linear dichroism imaging of molecular processes in living cells made simple by open software tools. Communications Biology 4, 189, 2021. link

[13] Timr S, Sterpone F. Stabilizing or Destabilizing: Simulations of Chymotrypsin Inhibitor 2 under Crowding Reveal Existence of a Crossover Temperature. Journal of Physical Chemistry Letters 12, 1741 – 1746, 2021. link

[12] Timr S, Gnutt D, Ebbinghaus S, Sterpone F. The Unfolding Journey of Superoxide Dismutase 1 Barrels under Crowding: Atomistic Simulations Shed Light on Intermediate States and Their Interactions with Crowders. Journal of Physical Chemistry Letters 11, 4206 – 4212, 2020. link

[11] Brandner A F, Timr S, Melchionna S, Derreumaux P, Baaden M, Sterpone F. Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics. Scientific Reports 9, 16450, 2019. link

[10] Gnutt D, Timr S, Ahlers J, König B, Manderfeld E, Heyden M, Sterpone, F, Ebbinghaus, S. Stability Effect of Quinary Interactions Reversed by Single Point Mutations. Journal of the American Chemical Society 141, 4660 – 4669, 2019. link

[9] Timr S, Kadlec J, Srb P, Ollila O H S, Jungwirth P. Calcium Sensing by Recoverin: Effect of Protein Conformation on Ion Affinity. Journal of Physical Chemistry Letters 9, 1613 – 1619, 2018. link

[8] Martinek T, Duboue-Dijon E, Timr S, Mason P E, Baxova K, Fischer H E, Schmidt B, Pluharova E, Jungwirth P. Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering. Journal of Chemical Physics 148, 222813, 2018. link

[7] Timr S, Pleskot R, Kadlec J, Kohagen M, Magarkar A, Jungwirth P. Membrane Binding of Recoverin: From Mechanistic Understanding to Biological Functionality. ACS Central Science 3, 868 – 874, 2017. link

[6] Melcr J, Bonhenry D, Timr S, Jungwirth P. Transmembrane Potential Modeling: Comparison between Methods of Constant Electric Field and Ion Imbalance. Journal of Chemical Theory and Computation 12, 2418 – 2425, 2016. link

[5] Timr S, Brabec J, Bondar A, Ryba T, Zelezny M, Lazar J, Jungwirth P. Nonlinear Optical Properties of Fluorescent Dyes Allow for Accurate Determination of Their Molecular Orientations in Phospholipid Membranes. Journal of Physical Chemistry B 119, 9706 – 97162015. link

[4] Karilainen T, Timr S, Vattulainen I, Jungwirth P. Oxidation of Cholesterol Does Not Alter Significantly Its Uptake into High-Density Lipoprotein Particles. Journal of Physical Chemistry B 119, 4594 – 46002015. link

[3] Timr S, Bondar A, Cwiklik L, Stefl M, Hof M, Vazdar M, Lazar J, and Jungwirth P. Accurate Determination of the Orientational Distribution of a Fluorescent Molecule in a Phospholipid Membrane. Journal of Physical Chemistry B 118, 855 – 863, 2014. link

[2] Lazar J, Bondar A, Timr S, and Firestein SJ. Two-photon polarization microscopy reveals protein structure and function. Nature Methods 8, 684 – 690, 2011. link

[1] Levitner T, Timr S, and Stys D. Expertomica Cells: analysis of cell monolayer development. Bioinformatics 26, 278 – 279, 2010. link

BOOK CHAPTERS

[1] Timr S, Madern D, Sterpone F. Protein thermal stability. In: Computational approaches for understanding dynamical systems: Protein folding and assembly. Editors: Birgit Strodel Bogdan Barz. Progress in Molecular Biology and Translational Science 170,239 – 272, 2020. link

REVIEWS

[1] Nguyen P H, Ramamoorthy A, Sahoo B R, Zheng J, Faller P, Straub J E, Dominguez L, Shea J-E, Dokholyan N V, De Simone A, Ma B, Nussinov R, Najafi S, Ngo S T, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li M S, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig A J, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chemical Reviews, 2021. link