Dr Wojciech Kopec

Profile

Dr Wojciech Kopec is a Lecturer in Computational Pharmaceutical Chemistry at the Department of Chemistry, working on biophysical mechanisms and pharmacology of ion channels using computational approaches. Before joining QMUL in 2023, Wojciech worked for several years at the Max Planck Institute for Multidisciplinary Sciences in Goettingen, Germany, focusing on computational electrophysiology simulations. Wojciech enjoys integrating computational and experimental approaches in a truly interdisciplinary manner.

Dr Kopec got his bachelor and master degrees in Chemistry from the Jagiellonian University in Kraków, Poland, where he worked on the application of graph theory in chemistry and molecular modelling of polycation interactions with lipid membranes. For his doctoral studies, he moved to Odense, Denmark, where he worked at MEMPHYS - Centre for Biomembrane Physics, located at the University of Southern Denmark, where he focused on studying ion binding and selectivity of ion pumps. During his PhD, Dr Kopec visited the University of Chicago, working with prof. Benoit Roux on polarizable force fields. After obtaining his PhD degree, Dr Kopec moved to Germany, to work with prof. Bert de Groot at the Max Planck Institute for Multidisciplinary Sciences in Goettingen, on ion permeation and gating mechanisms of potassium channels. After working for a few years as a postdoc, Dr Kopec became a Project Group Leader at the same institute, continuing his work on ion channels. In August 2023, he moved to the Queen Mary University of London.

Teaching

Undergraduate courses

• CHE305, Computational Chemistry (since 2024)
• CHE100, Essential Skills for Chemists (since 2023)

Postgraduate courses

• CHE705P, Molecular Modelling for Drug Discovery (since 2024)

Research

Research Interests:

I use physics-based numerical models to understand the dynamic behavior, on the atomistic scale, of complex molecular machines - proteins, membranes and small molecules. In particular, I use Molecular Dynamics (MD) simulations and related methods to gain an unfiltered view into physics of processes happening at the interfaces of biological cells and their synthetic counterparts. Such an approach is often referred to as ‘computational microscope’, and I am using it to discover novel mechanisms governing biological processes, with an overarching goal of exploiting them in the future to solve major societal issues: in medicinal or environmental science.

I am currently focused on computational studies of transport phenomena across biological and synthetic membranes. In our bodies, these processes are controlled by specialized proteins - ion channels and transporters. Malfunctions of those proteins often lead to diseases, and it is estimated 15-20% of current drugs target ion channels. I aim to discover and characterize molecular mechanisms of action of these proteins, and exploit them for drug design and biotechnological applications.

Publications

Kopec W., Thomson A.S., de Groot B.L., Rothberg B.S., Interactions between selectivity filter and pore helix control filter gating in the MthK channel, Journal of General Physiology, 155(8), 2023.

Öster C., Mollevan, K.T., Goold B., Hendriks K., Lange S., Becker S., de Groot B.L., Kopec W., Andreas L.B., Lange A., Direct detection of bound ammonium ions in the selectivity filter of ion channels by solid-state NMR, Journal of American Chemical Society, 144(9): 4147-4157, 2022

Mironenko A., Zachariae U., de Groot B.L., Kopec W., The persistent question of potassium channel permeation mechanisms, Journal of Molecular Biology, 167002, 2021

Kopec W., Rothberg B.S., de Groot B.L., Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling, Nature Communications 10(1):5366, 2020

Kopec W., Köpfer D.A., Vickery O.N., Bondarenko A.S., Jansen T.L.C., de Groot B.L., Zachariae U., Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels, Nature Chemistry 10(8):813-820, 2018

• Mendez-Otalvaro E, Kopec W, de Groot BL (2024). Effect of two activators on the gating of a K2P channel. nameOfConference

  
  

  DOI: 10.1016/j.bpj.2024.08.006

  
  

  QMRO: https://qmro.qmul.ac.uk/xmlui/handle/123456789/100522
• Gapsys V, Kopec W, Matthes D et al. (2024). Biomolecular simulations at the exascale: From drug design to organelles and beyond. nameOfConference

  
  

  DOI: 10.1016/j.sbi.2024.102887

  
  

  QMRO: https://qmro.qmul.ac.uk/xmlui/handle/123456789/98445
• Mironenko A, de Groot BL, Kopec W (2024). Selectivity filter mutations shift ion permeation mechanism in potassium channels. nameOfConference

  
  

  DOI: 10.1093/pnasnexus/pgae272

  
  

  QMRO: https://qmro.qmul.ac.uk/xmlui/handle/123456789/97870
• Kopec W, Thomson AS, de Groot BL et al. (2023). Interactions between selectivity filter and pore helix control filter gating in the MthK channel. nameOfConference

  
  

  DOI: 10.1085/jgp.202213166

  
  

  QMRO: https://qmro.qmul.ac.uk/xmlui/handle/123456789/100544
• Hui C, Kopec W, de Groot BL (2023). Ab initio MD for K+ channel parameter optimization. nameOfConference

  
  

  DOI: 10.1016/j.bpj.2022.11.2764

  
  

  QMRO: qmroHref
• de Vries R, Kopec W, de Groot BL (2023). Gating transitions in the MthK potassium channel. nameOfConference

  
  

  DOI: 10.1016/j.bpj.2022.11.2122

  
  

  QMRO: qmroHref
• Otalvaro EFM, Kopec W, de Groot BL (2023). Pharmacological modulation of TREK-1 channel. nameOfConference

  
  

  DOI: 10.1016/j.bpj.2022.11.1481

  
  

  QMRO: qmroHref
• Shehata M, Kopec W, de Groot BL et al. (2023). The potassium-selective channel “NaK2K”: Why is it a potassium channel?. nameOfConference

  
  

  DOI: 10.1016/j.bpj.2022.11.1429

  
  

  QMRO: qmroHref
• Öster C, Movellan KT, Goold B et al. (2022). Direct Detection of Bound Ammonium Ions in the Selectivity Filter of Ion Channels by Solid-State NMR. nameOfConference

  
  

  DOI: 10.1021/jacs.1c13247

  
  

  QMRO: https://qmro.qmul.ac.uk/xmlui/handle/123456789/100545
• Mironenko A, Zachariae U, de Groot BL et al. (2021). The Persistent Question of Potassium Channel Permeation Mechanisms. nameOfConference

  
  

  DOI: 10.1016/j.jmb.2021.167002

  
  

  QMRO: qmroHref
• Roy RN, Hendriks K, Kopec W et al. (2021). Structural plasticity of the selectivity filter in a nonselective ion channel. nameOfConference

  
  

  DOI: 10.1107/s205225252100213x

  
  

  QMRO: https://qmro.qmul.ac.uk/xmlui/handle/123456789/100531
• Mironenko A, de Groot BL, Kopec W (2021). Conductance Mechanism of Mutant K+ Channels. nameOfConference

  
  

  DOI: 10.1016/j.bpj.2020.11.1131

  
  

  QMRO: qmroHref
• Kopec W, Mironenko A, Goold B et al. (2021). Current Regulation in Potassium Channels. nameOfConference

  
  

  DOI: 10.1016/j.bpj.2020.11.1582

  
  

  QMRO: qmroHref
• Schewe M, Riel EB, Rinné S et al. (2021). Structural Basis for Gating of the Two-Pore Domain K+ (K2P) Channels TASK-1 and TALK-2. nameOfConference

  
  

  DOI: 10.1016/j.bpj.2020.11.1850

  
  

  QMRO: qmroHref
• Kopec W, Żak A, Jamróz D et al. (2020). Polycation–Anionic Lipid Membrane Interactions. nameOfConference

  
  

  DOI: 10.1021/acs.langmuir.0c01062

  
  

  QMRO: https://qmro.qmul.ac.uk/xmlui/handle/123456789/100523
• Schubeis T, Le Marchand T, Daday C et al. (2020). A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL. nameOfConference

  
  

  DOI: 10.1073/pnas.2002598117

  
  

  QMRO: qmroHref
• Langan PS, Vandavasi VG, Kopec W et al. (2020). The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation. nameOfConference

  
  

  DOI: 10.1107/s2052252520008271

  
  

  QMRO: qmroHref
• Daday C, Kopec W, de Groot BL (2020). Simulating Streaming Potentials in Potassium Channels. nameOfConference

  
  

  DOI: 10.1016/j.bpj.2019.11.1029

  
  

  QMRO: qmroHref
• Kopec W, Rothberg BS, de Groot BL (publicationYear). Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling. nameOfConference

  
  

  DOI: 10.1038/s41467-019-13227-w

  
  

  QMRO: qmroHref
• Öster C, Hendriks K, Kopec W et al. (2019). The conduction pathway of potassium channels is water free under physiological conditions. nameOfConference

  
  

  DOI: 10.1126/sciadv.aaw6756

  
  

  QMRO: qmroHref
• Kopec W, de Groot BL (2019). Molecular Simulations of Ion Permeation, Gating and Selectivity in K+ Channels. nameOfConference

  
  

  DOI: 10.1016/j.bpj.2018.11.127

  
  

  QMRO: qmroHref
• Cordeiro S, Finol-Urdaneta RK, Köpfer D et al. (2019). Conotoxin κM-RIIIJ, a tool targeting asymmetric heteromeric Kv1 channels. nameOfConference

  
  

  DOI: 10.1073/pnas.1813161116

  
  

  QMRO: qmroHref
• Awasthi N, Kopec W, Wilkosz N et al. (2019). Molecular Mechanism of Polycation-Induced Pore Formation in Biomembranes. nameOfConference

  
  

  DOI: 10.1021/acsbiomaterials.8b01495

  
  

  QMRO: qmroHref
• Dubey V, Han M, Kopec W et al. (publicationYear). K+ binding and proton redistribution in the E2P state of the H+, K+-ATPase. nameOfConference

  
  

  DOI: 10.1038/s41598-018-30885-w

  
  

  QMRO: qmroHref
• Kopec W, Köpfer DA, Vickery ON et al. (2018). Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels. nameOfConference

  
  

  DOI: 10.1038/s41557-018-0105-9

  
  

  QMRO: qmroHref
• Heinz LP, Kopec W, de Groot BL et al. (publicationYear). In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways. nameOfConference

  
  

  DOI: 10.1038/s41598-018-25061-z

  
  

  QMRO: qmroHref
• Tranebjærg L, Strenzke N, Lindholm S et al. (2018). Correction to: The CAPOS mutation in ATP1A3 alters Na/K-ATPase function and results in auditory neuropathy which has implications for management. nameOfConference

  
  

  DOI: 10.1007/s00439-018-1870-7

  
  

  QMRO: qmroHref
• Tranebjærg L, Strenzke N, Lindholm S et al. (2018). The CAPOS mutation in ATP1A3 alters Na/K-ATPase function and results in auditory neuropathy which has implications for management. nameOfConference

  
  

  DOI: 10.1007/s00439-017-1862-z

  
  

  QMRO: qmroHref
• Kopec W, de Groot B (2017). Molecular Simulations of Ion Permeation in Potassium Channels. nameOfConference

  
  

  DOI: 10.1016/j.bpj.2016.11.898

  
  

  QMRO: qmroHref
• Han M, Kopec W, Solov’yov IA et al. (publicationYear). Glutamate Water Gates in the Ion Binding Pocket of Na+ Bound Na+, K+-ATPase. nameOfConference

  
  

  DOI: 10.1038/srep39829

  
  

  QMRO: qmroHref
• Hilbers F, Kopec W, Isaksen TJ et al. (publicationYear). Tuning of the Na,K-ATPase by the beta subunit. nameOfConference

  
  

  DOI: 10.1038/srep20442

  
  

  QMRO: qmroHref
• Sahoo SK, Shaikh SA, Sopariwala DH et al. (2016). The N-Termini of Sarcolipin and Phospholamban Play an Important Role in Distinct Regulation of Sarco-Endoplasmic Reticulum Ca2+ ATPase (SERCA) Function. nameOfConference

  
  

  DOI: 10.1016/j.bpj.2015.11.1980

  
  

  QMRO: qmroHref
• Garcia A, Eljack ND, Sani M-A et al. (2015). Membrane accessibility of glutathione. nameOfConference

  
  

  DOI: 10.1016/j.bbamem.2015.07.016

  
  

  QMRO: qmroHref
• Sahoo SK, Shaikh SA, Sopariwala DH et al. (2015). The N Terminus of Sarcolipin Plays an Important Role in Uncoupling Sarco-endoplasmic Reticulum Ca2+-ATPase (SERCA) ATP Hydrolysis from Ca2+ Transport*. nameOfConference

  
  

  DOI: 10.1074/jbc.m115.636738

  
  

  QMRO: qmroHref
• Mahmmoud YA, Kopec W, Khandelia H (2015). K+ Congeners That Do Not Compromise Na+ Activation of the Na+,K+-ATPase HYDRATION OF THE ION BINDING CAVITY LIKELY CONTROLS ION SELECTIVITY*. nameOfConference

  
  

  DOI: 10.1074/jbc.m114.577486

  
  

  QMRO: qmroHref
• Loubet B, Kopec W, Khandelia H (2014). Accelerating All-Atom MD Simulations of Lipids Using a Modified Virtual-Sites Technique. nameOfConference

  
  

  DOI: 10.1021/ct500100f

  
  

  QMRO: qmroHref
• Chaban VV, Nielsen MB, Kopec W et al. (2014). Insights into the role of cyclic ladderane lipids in bacteria from computer simulations. nameOfConference

  
  

  DOI: 10.1016/j.chemphyslip.2014.04.002

  
  

  QMRO: qmroHref
• Kopec W, Khandelia H (2014). Reinforcing the membrane-mediated mechanism of action of the anti-tuberculosis candidate drug thioridazine with molecular simulations. nameOfConference

  
  

  DOI: 10.1007/s10822-014-9737-z

  
  

  QMRO: qmroHref
• Kopec W, Loubet B, Poulsen H et al. (2014). Molecular Mechanism of Na+,K+‑ATPase Malfunction in Mutations Characteristic of Adrenal Hypertension. nameOfConference

  
  

  DOI: 10.1021/bi401425g

  
  

  QMRO: qmroHref
• Loubet B, Kopec W, Khandelia H (2014). Application of the Virtual Site Technique to Lipids in Gromacs, Hydrogens Degrees of Freedom Removal and Performance Increase. nameOfConference

  
  

  DOI: 10.1016/j.bpj.2013.11.146

  
  

  QMRO: qmroHref
• Kopec W, Loubet B, Khandelia H (2014). Glutathionylation of the Na K Pump. nameOfConference

  
  

  DOI: 10.1016/j.bpj.2013.11.3230

  
  

  QMRO: qmroHref
• Kopec W, Loubet B, Poulsen H et al. (2014). The Molecular Mechanism of Na+, K+-ATPase Malfunction in Mutations Characteristic for Adrenal Hypertension. nameOfConference

  
  

  DOI: 10.1016/j.bpj.2013.11.3229

  
  

  QMRO: qmroHref
• Hermetter A, Kopec W, Khandelia H (2013). Conformations of double-headed, triple-tailed phospholipid oxidation lipid products in model membranes. nameOfConference

  
  

  DOI: 10.1016/j.bbamem.2013.03.030

  
  

  QMRO: qmroHref