Dr Wojciech Kopec
Lecturer in Computational Pharmaceutical Chemistry
School of Physical and Chemical Sciences
Queen Mary University of London
Queen Mary University of London
Research
Molecular Dynamics, Ion Channels, Drug Design, Computational Electrophysiology, Membranes, Free Energy Calculations
Interests
I use physics-based numerical models to understand the dynamic behavior, on the atomistic scale, of complex molecular machines - proteins, membranes and synthetic 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 peek into and discover novel mechanisms governing biological processes, with an overarching goal of exploiting them in the future to solve major issues we are facing as a society - either 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. Moreover, a precise manipulation of such proteins by light or soundwaves, in approaches such as optogenetics and sonogenetics, can be exploited to control specific circuits in the brain.
Publications
2024
Mendez-Otalvaro E, Kopec W and de Groot BL (2024). Effect of two activators on the gating of a K2P channel. Biophysical Journal, Elsevier vol. 123 (19), 3408-3420. 19-08-2024
Gapsys V, Kopec W, Matthes D and de Groot BL (2024). Biomolecular simulations at the exascale: From drug design to organelles and beyond. Current Opinion in Structural Biology, Elsevier vol. 88 18-07-2024
Mironenko A, de Groot BL and Kopec W (2024). Selectivity filter mutations shift ion permeation mechanism in potassium channels. PNAS Nexus, Oxford University Press (OUP) vol. 3 (7) 28-06-2024
2023
Kopec W, Thomson AS, de Groot BL and Rothberg BS (2023). Interactions between selectivity filter and pore helix control filter gating in the MthK channel. The Journal of General Physiology, Rockefeller University Press vol. 155 (8) 15-06-2023
Hui C, Kopec W and de Groot BL (2023). Ab initio MD for K+ channel parameter optimization. Biophysical Journal, Elsevier vol. 122 (3) 01-02-2023
de Vries R, Kopec W and de Groot BL (2023). Gating transitions in the MthK potassium channel. Biophysical Journal, Elsevier vol. 122 (3) 01-02-2023
Otalvaro EFM, Kopec W and de Groot BL (2023). Pharmacological modulation of TREK-1 channel. Biophysical Journal, Elsevier vol. 122 (3) 01-02-2023
Shehata M, Kopec W, de Groot BL and Amaro RE (2023). The potassium-selective channel “NaK2K”: Why is it a potassium channel? Biophysical Journal, Elsevier vol. 122 (3) 01-02-2023
2022
Öster C, Movellan KT, Goold B, Hendriks K, Lange S, Becker S, de Groot BL, Kopec W, Andreas LB and Lange A (2022). Direct Detection of Bound Ammonium Ions in the Selectivity Filter of Ion Channels by Solid-State NMR. Journal of the American Chemical Society, American Chemical Society (ACS) vol. 144 (9), 4147-4157. 24-02-2022
2021
Mironenko A, Zachariae U, de Groot BL and Kopec W (2021). The Persistent Question of Potassium Channel Permeation Mechanisms. Journal of Molecular Biology, Elsevier vol. 433 (17) 20-04-2021
Roy RN, Hendriks K, Kopec W, Abdolvand S, Weiss KL, de Groot BL, Lange A, Sun H and Coates L (2021). Structural plasticity of the selectivity filter in a nonselective ion channel. IUCrJ, International Union of Crystallography (IUCr) vol. 8 (Pt 3), 421-430. 02-04-2021
Schewe M, Riel EB, Rinné S, Kopec W, Langer J, Lindemann P, Jürs BC, Nazaré M, de Groot BL, Decher N and Baukrowitz T (2021). Structural Basis for Gating of the Two-Pore Domain K+ (K2P) Channels TASK-1 and TALK-2. Biophysical Journal, Elsevier vol. 120 (3) 01-02-2021
Kopec W, Mironenko A, Goold B and de Groot BL (2021). Current Regulation in Potassium Channels. Biophysical Journal, Elsevier vol. 120 (3) 01-02-2021
Mironenko A, de Groot BL and Kopec W (2021). Conductance Mechanism of Mutant K+ Channels. Biophysical Journal, Elsevier vol. 120 (3) 01-02-2021
2020
Kopec W, Żak A, Jamróz D, Nakahata R, Yusa S-I, Gapsys V and Kepczynski M (2020). Polycation–Anionic Lipid Membrane Interactions. Langmuir, American Chemical Society (ACS) vol. 36 (42), 12435-12450. 15-10-2020
Schubeis T, Le Marchand T, Daday C, Kopec W, Tekwani Movellan K, Stanek J, Schwarzer TS, Castiglione K, de Groot BL, Pintacuda G and Andreas LB (2020). A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL. Proceedings of the National Academy of Sciences of the United States of America, Proceedings of the National Academy of Sciences vol. 117 (35), 21014-21021. 19-08-2020
Langan PS, Vandavasi VG, Kopec W, Sullivan B, Afonne PV, Weiss KL, de Groot BL and Coates L (2020). The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation. IUCrJ, International Union of Crystallography (IUCr) vol. 7 (Pt 5), 835-843. 25-07-2020
Daday C, Kopec W and de Groot BL (2020). Simulating Streaming Potentials in Potassium Channels. Biophysical Journal, Elsevier vol. 118 (3) 01-02-2020
2019
Kopec W, Rothberg BS and de Groot BL (2019). Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling. Nature Communications, Springer Nature vol. 10 (1) 26-11-2019
Öster C, Hendriks K, Kopec W, Chevelkov V, Shi C, Michl D, Lange S, Sun H, de Groot BL and Lange A (2019). The conduction pathway of potassium channels is water free under physiological conditions. Science Advances, American Association for the Advancement of Science (AAAS) vol. 5 (7) 05-07-2019
Kopec W and de Groot BL (2019). Molecular Simulations of Ion Permeation, Gating and Selectivity in K+ Channels. Biophysical Journal, Elsevier vol. 116 (3) 01-02-2019
2018
Cordeiro S, Finol-Urdaneta RK, Köpfer D, Markushina A, Song J, French RJ, Kopec W, de Groot BL, Giacobassi MJ, Leavitt LS, Raghuraman S, Teichert RW, Olivera BM and Terlau H (2018). Conotoxin κM-RIIIJ, a tool targeting asymmetric heteromeric Kv1 channels. Proceedings of the National Academy of Sciences of the United States of America, Proceedings of the National Academy of Sciences vol. 116 (3), 1059-1064. 28-12-2018
Awasthi N, Kopec W, Wilkosz N, Jamróz D, Hub JS, Zatorska M, Petka R, Nowakowska M and Kepczynski M (2018). Molecular Mechanism of Polycation-Induced Pore Formation in Biomembranes. ACS Biomaterials Science & Engineering, American Chemical Society (ACS) vol. 5 (2), 780-794. 03-12-2018
Dubey V, Han M, Kopec W, Solov’yov IA, Abe K and Khandelia H (2018). K+ binding and proton redistribution in the E2P state of the H+, K+-ATPase. Scientific Reports, Springer Nature vol. 8 (1) 24-08-2018
Kopec W, Köpfer DA, Vickery ON, Bondarenko AS, Jansen TLC, de Groot BL and Zachariae U (2018). Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels. Nature Chemistry, Springer Nature vol. 10 (8), 813-820. 20-07-2018
Heinz LP, Kopec W, de Groot BL and Fink RHA (2018). In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways. Scientific Reports, Springer Nature vol. 8 (1) 02-05-2018
Tranebjærg L, Strenzke N, Lindholm S, Rendtorff ND, Poulsen H, Khandelia H, Kopec W, Lyngbye TJB, Hamel C, Delettre C, Bocquet B, Bille M, Owen HH, Bek T, Jensen H, Østergaard K, Möller C, Luxon L, Carr L, Wilson L, 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. Human Genetics, Springer Nature vol. 137 (3), 279-280. 12-02-2018
Tranebjærg L, Strenzke N, Lindholm S, Rendtorff ND, Poulsen H, Khandelia H, Kopec W, Lyngbye TJB, Hamel C, Delettre C, Bocquet B, Bille M, Owen HH, Bek T, Jensen H, Østergaard K, Möller C, Luxon L, Carr L, Wilson L, et al. (2018). The CAPOS mutation in ATP1A3 alters Na/K-ATPase function and results in auditory neuropathy which has implications for management. Human Genetics, Springer Nature vol. 137 (2), 111-127. 05-01-2018
2017
Wilkosz N, Jamróz D, Kopeć W, Nakai K, Yusa S-I, Wytrwal-Sarna M, Bednar J, Nowakowska M and Kepczynski M (2017). Effect of Polycation Structure on Interaction with Lipid Membranes. The Journal of Physical Chemistry B, American Chemical Society (ACS) vol. 121 (30), 7318-7326. 19-07-2017
Kopec W and de Groot B (2017). Molecular Simulations of Ion Permeation in Potassium Channels. Biophysical Journal, Elsevier vol. 112 (3) 01-02-2017
Han M, Kopeć W, Solov’yov IA and Khandelia H (2017). Protonation Dependent Water Permeation of Ion Binding Pocket of Na+ Bound Na+, K+-ATPase. Biophysical Journal, Elsevier vol. 112 (3) 01-02-2017
Han M, Kopec W, Solov’yov IA and Khandelia H (2017). Glutamate Water Gates in the Ion Binding Pocket of Na+ Bound Na+, K+-ATPase. Scientific Reports, Springer Nature vol. 7 (1) 13-01-2017
2016
Hilbers F, Kopec W, Isaksen TJ, Holm TH, Lykke-Hartmann K, Nissen P, Khandelia H and Poulsen H (2016). Tuning of the Na,K-ATPase by the beta subunit. Scientific Reports, Springer Nature vol. 6 (1) 05-02-2016
Sahoo SK, Shaikh SA, Sopariwala DH, Bal NC, Bruhn DS, Kopec W, Khandelia H and Periasamy M (2016). The N-Termini of Sarcolipin and Phospholamban Play an Important Role in Distinct Regulation of Sarco-Endoplasmic Reticulum Ca2+ ATPase (SERCA) Function. Biophysical Journal, Elsevier vol. 110 (3), 367a-368a. 01-02-2016
2015
Garcia A, Eljack ND, Sani M-A, Separovic F, Rasmussen HH, Kopec W, Khandelia H, Cornelius F and Clarke RJ (2015). Membrane accessibility of glutathione. Biochimica et Biophysica Acta, Elsevier vol. 1848 (10), 2430-2436. 30-07-2015
Sahoo SK, Shaikh SA, Sopariwala DH, Bal NC, Bruhn DS, Kopec W, Khandelia H and Periasamy M (2015). The N Terminus of Sarcolipin Plays an Important Role in Uncoupling Sarco-endoplasmic Reticulum Ca2+-ATPase (SERCA) ATP Hydrolysis from Ca2+ Transport*. Journal of Biological Chemistry, Elsevier vol. 290 (22), 14057-14067. 16-04-2015
2014
Mahmmoud YA, Kopec W and Khandelia H (2014). K+ Congeners That Do Not Compromise Na+ Activation of the Na+,K+-ATPase HYDRATION OF THE ION BINDING CAVITY LIKELY CONTROLS ION SELECTIVITY*. Journal of Biological Chemistry, Elsevier vol. 290 (6), 3720-3731. 22-12-2014
Loubet B, Kopec W and Khandelia H (2014). Accelerating All-Atom MD Simulations of Lipids Using a Modified Virtual-Sites Technique. Journal of Chemical Theory and Computation, American Chemical Society (ACS) vol. 10 (12), 5690-5695. 07-11-2014
Chaban VV, Nielsen MB, Kopec W and Khandelia H (2014). Insights into the role of cyclic ladderane lipids in bacteria from computer simulations. Chemistry and Physics of Lipids, Elsevier vol. 181, 76-82. 13-04-2014
Kopec W and Khandelia H (2014). Reinforcing the membrane-mediated mechanism of action of the anti-tuberculosis candidate drug thioridazine with molecular simulations. Journal of Computer-Aided Molecular Design, Springer Nature vol. 28 (2), 123-134. 01-02-2014
Kopec W, Loubet B, Poulsen H and Khandelia H (2014). Molecular Mechanism of Na+,K+‑ATPase Malfunction in Mutations Characteristic of Adrenal Hypertension. Biochemistry, American Chemical Society (ACS) vol. 53 (4), 746-754. 24-01-2014
Kopec W, Loubet B and Khandelia H (2014). Glutathionylation of the Na K Pump. Biophysical Journal, Elsevier vol. 106 (2) 01-01-2014
Kopec W, Loubet B, Poulsen H and Khandelia H (2014). The Molecular Mechanism of Na+, K+-ATPase Malfunction in Mutations Characteristic for Adrenal Hypertension. Biophysical Journal, Elsevier vol. 106 (2), 582a-583a. 01-01-2014
Loubet B, Kopec W and Khandelia H (2014). Application of the Virtual Site Technique to Lipids in Gromacs, Hydrogens Degrees of Freedom Removal and Performance Increase. Biophysical Journal, Elsevier vol. 106 (2) 01-01-2014
2013
Kopeć W, Telenius J and Khandelia H (2013). Molecular dynamics simulations of the interactions of medicinal plant extracts and drugs with lipid bilayer membranes. The FEBS Journal, Wiley vol. 280 (12), 2785-2805. 16-05-2013
Hermetter A, Kopec W and Khandelia H (2013). Conformations of double-headed, triple-tailed phospholipid oxidation lipid products in model membranes. Biochimica et Biophysica Acta, Elsevier vol. 1828 (8), 1700-1706. 06-04-2013
Grants
Grants of specific relevance to the Centre for Chemical ResearchBBSRC AIDD CTP CASE Award: Ivan ManozaWojciech Kopec
£18,000 Janssen Pharmaceutica (Belg) (01-10-2024 - 30-09-2028)
Unraveling the fundamental mechanisms of neuromodulation by focused ultrasoundWojciech Kopec
£27,574 Human Frontier Science Program (HFSP) (01-01-2024 - 31-12-2024)