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
Effect of two activators on the gating of a K2P channelMendez-Otalvaro E, Kopec W and de Groot BL
Biophysical Journal, Elsevier vol. 123 (19), 3408-3420.
19-08-2024
Biomolecular simulations at the exascale: From drug design to organelles and beyondGapsys V, Kopec W, Matthes D and de Groot BL
Current Opinion in Structural Biology, Elsevier vol. 88
18-07-2024
Selectivity filter mutations shift ion permeation mechanism in potassium channelsMironenko A, de Groot BL and Kopec W
Pnas Nexus, Oxford University Press (Oup) vol. 3 (7)
28-06-2024
2023
Interactions between selectivity filter and pore helix control filter gating in the MthK channelKopec W, Thomson AS, de Groot BL and Rothberg BS
The Journal of General Physiology, Rockefeller University Press vol. 155 (8)
15-06-2023
Ab initio MD for K+ channel parameter optimizationHui C, Kopec W and de Groot BL
Biophysical Journal, Elsevier vol. 122 (3)
01-02-2023
Gating transitions in the MthK potassium channelde Vries R, Kopec W and de Groot BL
Biophysical Journal, Elsevier vol. 122 (3)
01-02-2023
Pharmacological modulation of TREK-1 channelOtalvaro EFM, Kopec W and de Groot BL
Biophysical Journal, Elsevier vol. 122 (3)
01-02-2023
The potassium-selective channel “NaK2K”: Why is it a potassium channel?Shehata M, Kopec W, de Groot BL and Amaro RE
Biophysical Journal, Elsevier vol. 122 (3)
01-02-2023
2022
Direct Detection of Bound Ammonium Ions in the Selectivity Filter of Ion Channels by Solid-State NMRÖster C, Movellan KT, Goold B, Hendriks K, Lange S, Becker S, de Groot BL, Kopec W, Andreas LB and Lange A
Journal of The American Chemical Society, American Chemical Society (Acs) vol. 144 (9), 4147-4157.
24-02-2022
2021
The Persistent Question of Potassium Channel Permeation MechanismsMironenko A, Zachariae U, de Groot BL and Kopec W
Journal of Molecular Biology, Elsevier vol. 433 (17)
20-04-2021
Structural plasticity of the selectivity filter in a nonselective ion channelRoy RN, Hendriks K, Kopec W, Abdolvand S, Weiss KL, de Groot BL, Lange A, Sun H and Coates L
Iucrj, International Union of Crystallography (Iucr) vol. 8 (Pt 3), 421-430.
02-04-2021
Structural Basis for Gating of the Two-Pore Domain K+ (K2P) Channels TASK-1 and TALK-2Schewe M, Riel EB, Rinné S, Kopec W, Langer J, Lindemann P, Jürs BC, Nazaré M, de Groot BL, Decher N and Baukrowitz T
Biophysical Journal, Elsevier vol. 120 (3)
01-02-2021
Current Regulation in Potassium ChannelsKopec W, Mironenko A, Goold B and de Groot BL
Biophysical Journal, Elsevier vol. 120 (3)
01-02-2021
Conductance Mechanism of Mutant K+ ChannelsMironenko A, de Groot BL and Kopec W
Biophysical Journal, Elsevier vol. 120 (3)
01-02-2021
2020
Polycation–Anionic Lipid Membrane InteractionsKopec W, Żak A, Jamróz D, Nakahata R, Yusa S-I, Gapsys V and Kepczynski M
Langmuir, American Chemical Society (Acs) vol. 36 (42), 12435-12450.
15-10-2020
A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkLSchubeis 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
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
The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeationLangan PS, Vandavasi VG, Kopec W, Sullivan B, Afonne PV, Weiss KL, de Groot BL and Coates L
Iucrj, International Union of Crystallography (Iucr) vol. 7 (Pt 5), 835-843.
25-07-2020
Simulating Streaming Potentials in Potassium ChannelsDaday C, Kopec W and de Groot BL
Biophysical Journal, Elsevier vol. 118 (3)
01-02-2020
2019
Molecular mechanism of a potassium channel gating through activation gate-selectivity filter couplingKopec W, Rothberg BS and de Groot BL
Nature Communications, Springer Nature vol. 10 (1)
26-11-2019
The conduction pathway of potassium channels is water free under physiological conditionsÖster C, Hendriks K, Kopec W, Chevelkov V, Shi C, Michl D, Lange S, Sun H, de Groot BL and Lange A
Science Advances, American Association For The Advancement of Science (Aaas) vol. 5 (7)
05-07-2019
Molecular Simulations of Ion Permeation, Gating and Selectivity in K+ ChannelsKopec W and de Groot BL
Biophysical Journal, Elsevier vol. 116 (3)
01-02-2019
2018
Conotoxin κM-RIIIJ, a tool targeting asymmetric heteromeric Kv1 channelsCordeiro 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
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
Molecular Mechanism of Polycation-Induced Pore Formation in BiomembranesAwasthi N, Kopec W, Wilkosz N, Jamróz D, Hub JS, Zatorska M, Petka R, Nowakowska M and Kepczynski M
Acs Biomaterials Science & Engineering, American Chemical Society (Acs) vol. 5 (2), 780-794.
03-12-2018
K+ binding and proton redistribution in the E2P state of the H+, K+-ATPaseDubey V, Han M, Kopec W, Solov’yov IA, Abe K and Khandelia H
Scientific Reports, Springer Nature vol. 8 (1)
24-08-2018
Direct knock-on of desolvated ions governs strict ion selectivity in K+ channelsKopec W, Köpfer DA, Vickery ON, Bondarenko AS, Jansen TLC, de Groot BL and Zachariae U
Nature Chemistry, Springer Nature vol. 10 (8), 813-820.
20-07-2018
In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathwaysHeinz LP, Kopec W, de Groot BL and Fink RHA
Scientific Reports, Springer Nature vol. 8 (1)
02-05-2018
Correction to: The CAPOS mutation in ATP1A3 alters Na/K-ATPase function and results in auditory neuropathy which has implications for managementTranebjærg 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.
Human Genetics, Springer Nature vol. 137 (3), 279-280.
12-02-2018
The CAPOS mutation in ATP1A3 alters Na/K-ATPase function and results in auditory neuropathy which has implications for managementTranebjærg 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.
Human Genetics, Springer Nature vol. 137 (2), 111-127.
05-01-2018
2017
Effect of Polycation Structure on Interaction with Lipid MembranesWilkosz N, Jamróz D, Kopeć W, Nakai K, Yusa S-I, Wytrwal-Sarna M, Bednar J, Nowakowska M and Kepczynski M
The Journal of Physical Chemistry B, American Chemical Society (Acs) vol. 121 (30), 7318-7326.
19-07-2017
Molecular Simulations of Ion Permeation in Potassium ChannelsKopec W and de Groot B
Biophysical Journal, Elsevier vol. 112 (3)
01-02-2017
Protonation Dependent Water Permeation of Ion Binding Pocket of Na+ Bound Na+, K+-ATPaseHan M, Kopeć W, Solov’yov IA and Khandelia H
Biophysical Journal, Elsevier vol. 112 (3)
01-02-2017
Glutamate Water Gates in the Ion Binding Pocket of Na+ Bound Na+, K+-ATPaseHan M, Kopec W, Solov’yov IA and Khandelia H
Scientific Reports, Springer Nature vol. 7 (1)
13-01-2017
2016
Tuning of the Na,K-ATPase by the beta subunitHilbers F, Kopec W, Isaksen TJ, Holm TH, Lykke-Hartmann K, Nissen P, Khandelia H and Poulsen H
Scientific Reports, Springer Nature vol. 6 (1)
05-02-2016
The N-Termini of Sarcolipin and Phospholamban Play an Important Role in Distinct Regulation of Sarco-Endoplasmic Reticulum Ca2+ ATPase (SERCA) FunctionSahoo SK, Shaikh SA, Sopariwala DH, Bal NC, Bruhn DS, Kopec W, Khandelia H and Periasamy M
Biophysical Journal, Elsevier vol. 110 (3), 367a-368a.
01-02-2016
2015
Membrane accessibility of glutathioneGarcia A, Eljack ND, Sani M-A, Separovic F, Rasmussen HH, Kopec W, Khandelia H, Cornelius F and Clarke RJ
Biochimica Et Biophysica Acta, Elsevier vol. 1848 (10), 2430-2436.
30-07-2015
The N Terminus of Sarcolipin Plays an Important Role in Uncoupling Sarco-endoplasmic Reticulum Ca2+-ATPase (SERCA) ATP Hydrolysis from Ca2+ Transport*Sahoo SK, Shaikh SA, Sopariwala DH, Bal NC, Bruhn DS, Kopec W, Khandelia H and Periasamy M
Journal of Biological Chemistry, Elsevier vol. 290 (22), 14057-14067.
16-04-2015
2014
K+ Congeners That Do Not Compromise Na+ Activation of the Na+,K+-ATPase HYDRATION OF THE ION BINDING CAVITY LIKELY CONTROLS ION SELECTIVITY*Mahmmoud YA, Kopec W and Khandelia H
Journal of Biological Chemistry, Elsevier vol. 290 (6), 3720-3731.
22-12-2014
Accelerating All-Atom MD Simulations of Lipids Using a Modified Virtual-Sites TechniqueLoubet B, Kopec W and Khandelia H
Journal of Chemical Theory and Computation, American Chemical Society (Acs) vol. 10 (12), 5690-5695.
07-11-2014
Insights into the role of cyclic ladderane lipids in bacteria from computer simulationsChaban VV, Nielsen MB, Kopec W and Khandelia H
Chemistry and Physics of Lipids, Elsevier vol. 181, 76-82.
13-04-2014
Reinforcing the membrane-mediated mechanism of action of the anti-tuberculosis candidate drug thioridazine with molecular simulationsKopec W and Khandelia H
Journal of Computer-Aided Molecular Design, Springer Nature vol. 28 (2), 123-134.
01-02-2014
Molecular Mechanism of Na+,K+‑ATPase Malfunction in Mutations Characteristic of Adrenal HypertensionKopec W, Loubet B, Poulsen H and Khandelia H
Biochemistry, American Chemical Society (Acs) vol. 53 (4), 746-754.
24-01-2014
Glutathionylation of the Na K PumpKopec W, Loubet B and Khandelia H
Biophysical Journal, Elsevier vol. 106 (2)
01-01-2014
The Molecular Mechanism of Na+, K+-ATPase Malfunction in Mutations Characteristic for Adrenal HypertensionKopec W, Loubet B, Poulsen H and Khandelia H
Biophysical Journal, Elsevier vol. 106 (2), 582a-583a.
01-01-2014
Application of the Virtual Site Technique to Lipids in Gromacs, Hydrogens Degrees of Freedom Removal and Performance IncreaseLoubet B, Kopec W and Khandelia H
Biophysical Journal, Elsevier vol. 106 (2)
01-01-2014
2013
Molecular dynamics simulations of the interactions of medicinal plant extracts and drugs with lipid bilayer membranesKopeć W, Telenius J and Khandelia H
The Febs Journal, Wiley vol. 280 (12), 2785-2805.
16-05-2013
Conformations of double-headed, triple-tailed phospholipid oxidation lipid products in model membranesHermetter A, Kopec W and Khandelia H
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