Kurnikova Research Group

The Biomolecular Modeling Group

Publications

  1. Active Learning-Guided Hit Optimization for the Leucine-Rich Repeat Kinase 2 WDR Domain Based on In Silico Ligand-Binding Affinities Gusev Filipp, Gutkin Evgeny, Gentile Francesco, Ban Fuqiang, Koby S. Benjamin, Li Fengling, Chau Irene, Ackloo Suzanne, Arrowsmith Cheryl H., Bolotokova Albina, Ghiabi, Pegah, Gibson, Elisa, Halabelian Levon, Houliston Scott, Harding Rachel J., Hutchinson Ashley, Loppnau Peter, Perveen Sumera, Seitova Almagul, Zeng Hong, Schapira Matthieu, Cherkasov Artem, Isayev Olexandr, Kurnikova Maria G. J. Chem. Inf. Model. 65, 11, 5706–5717 (2025)
  2. Automated On-the-Fly Optimization of Resource Allocation for Efficient Free Energy Simulations S. Benjamin Koby, Evgeny Gutkin, Shree Patel, Maria G. Kurnikova J. Chem. Inf. Model. 65, 10, 4932–4951 (2025)
  3. Trapping of spermine, Kukoamine A, and polyamine toxin blockers in GluK2 kainate receptor channels Gangwar SP, Yelshanskaya MV, Aktolun M, Yen LY, Newton TP, Strømgaard K, Kurnikova MG, Sobolevsky AI. Nat Commun 15, 10257 (2024)
  4. CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson’s Disease Associated Protein Fengling Li, Suzanne Ackloo, Cheryl H. Arrowsmith, Fuqiang Ban, Christopher J. Barden, Hartmut Beck, Jan Beránek, Francois Berenger, Albina Bolotokova, Guillaume Bret, Marko Breznik, Emanuele Carosati, Irene Chau, Yu Chen, Artem Cherkasov, Dennis Della Corte, Katrin Denzinger, Aiping Dong, Sorin Draga, Ian Dunn, Kristina Edfeldt, Aled Edwards, Merveille Eguida, Paul Eisenhuth, Lukas Friedrich, Alexander Fuerll, Spencer S Gardiner, Francesco Gentile, Pegah Ghiabi, Elisa Gibson, Marta Glavatskikh, Christoph Gorgulla, Judith Guenther, Anders Gunnarsson, Filipp Gusev, Evgeny Gutkin, Levon Halabelian, Rachel J. Harding, Alexander Hillisch, Laurent Hoffer, Anders Hogner, Scott Houliston, John J Irwin, Olexandr Isayev, Aleksandra Ivanova, Celien Jacquemard, Austin J Jarrett, Jan H. Jensen, Dmitri Kireev, Julian Kleber, S. Benjamin Koby, David Koes, Ashutosh Kumar, Maria G. Kurnikova, Alina Kutlushina, Uta Lessel, Fabian Liessmann, Sijie Liu, Wei Lu, Jens Meiler, Akhila Mettu, Guzel Minibaeva, Rocco Moretti, Connor J Morris, Chamali Narangoda, Theresa Noonan, Leon Obendorf, Szymon Pach, Amit Pandit, Sumera Perveen, Gennady Poda, Pavel Polishchuk, Kristina Puls, Vera Pütter, Didier Rognan, Dylan Roskams-Edris, Christina Schindler, François Sindt, VojtečhSpiwok,CasperSteinmann,RickL.Stevens,ValerijTalagayev,DamonTingey,OanhVu, W. Patrick Walters, Xiaowen Wang, Zhenyu Wang, Gerhard Wolber, Clemens Alexander Wolf, Lars Wortmann, Hong Zeng, Carlos A. Zepeda, Kam Y. J. Zhang, Jixian Zhang, Shuangjia Zheng, and Matthieu Schapira J. Chem. Inf. Model. 64, 8521−8536 (2024)
  5. Kainate receptor channel opening and gating mechanism. Gangwar, S.P., Yelshanskaya, M.V., Nadezhdin, K.D., Yen L.Y., Newton Th.P., Aktolun M., Kurnikova M.G., Sobolevsky A.I. Nature (2024)
  6. Structural basis of selective TRPM7 inhibition by the anticancer agent CCT128930 Nadezhdin K.D., Correia L., Shalygin A., Aktolun M., Neuberger A., Gudermann Th., Kurnikova M.G., Chubanov V., Sobolevsky A.I. Cell Reports 43(4), 114108 (2024)
  7. In silico screening of LRRK2 WDR domain inhibitors using deep docking and free energy simulations Gutkin E., Gusev F., Gentile F., Ban F., Koby S.B., Narangoda C., Isayev O., Cherkasov A., Kurnikova M.G. Chem. Sci. (2024)
  8. Chapter Nine - Spectroscopic and computational studies of a bifunctional iron- and 2-oxoglutarate dependent enzyme, AsqJ Shan Xue, Yijie Tang, Igor V. Kurnikov, Hsuan-Jen Liao, Jikun Li, Nei-Li Chan, Maria G. Kurnikova, Wei-chen Chang, Yisong Guo, Methods in Enzymology Volume 704, (2024)
  9. A community effort in SARS-CoV-2 drug discovery Schimunek J., Seidl P., Elez K., Hempel T., Le T., Noé F., Olsson S., Raich L., Winter R., Gokcan H., Gusev F., Gutkin E.M., Isayev O., Kurnikova M.G., Narangoda C.H., Zubatyuk R., et al. Mol. Inform. (2023)
  10. Combining Force Fields and Neural Networks for an Accurate Representation of Chemically Diverse Molecular Interactions Illarionov A., Sakipov S., Pereyaslavets L., Kurnikov I.V., Kamath G., Butin O., Voronina E., Ivahnenko I., Leontyev I., Nawrocki G., Darkhovskiy M., Olevanov M., Cherniavskyi Y.K., Lock C., Greenslade S., Sankaranarayanan S.K., Kurnikova M.G., Potoff J., Kornberg R.D., Levitt M., Fain B. J. Am. Chem. Soc. 145(43), 23620–23629 (2023)
  11. Structural mechanisms of TRPM7 activation and inhibition Nadezhdin K.D., Correia L., Narangoda C., Patel D.S., Neuberger A., Gudermann Th., Kurnikova M.G., Chubanov V., Sobolevsky A.I. Nat. Commun. 14, 2639 (2023)
  12. Active Learning Guided Drug Design Lead Optimization Based on Relative Binding Free Energy Modeling Gusev F., Gutkin E., Kurnikova M.G., Isayev O. J. Chem. Inf. Model. 63(2), 583–594 (2023)
  13. Protein-Ligand Binding Free-Energy Calculations with ARROW─A purely first-principles parameterized polarizable force field Nawrocki G., Leontyev I., Sakipov S., Darkhovskiy M., Kurnikov I., Pereyaslavets L., Kamath G., Voronina E., Butin O., Illarionov A., Olevanov M., Kostikov A., Ivahnenko I., Patel D.S., Sankaranarayanan S.K.R.S., Kurnikova M.G., Lock C., Crooks G.E., Levitt M., Kornberg R.D., Fain B. J. Chem. Theory Comput. 18(12), 7751–7763 (2022)
  14. Inhibition of NMDA receptors through a membrane-to-channel path Wilcox M.R., Nigam A., Glasgow N.G., Narangoda C., Phillips M.B., Patel D.S., Mesbahi-Vasey S., Turcu A.L., Vázquez S., Kurnikova M.G., Johnson J.W. Nat. Commun. 13(1), 4114 (2022)
  15. Design, synthesis, and in vitro and in vivo characterization of new memantine analogs for Alzheimer's disease Turcu A.L., Companys-Alemany J., Phillips M.B., Patel D.S., Griñán-Ferré C., Loza M.I., Brea J.M., Pérez B., Soto D., Sureda F.X., Kurnikova M.G., Johnson J.W., Pallàs M., Vázquez S. Eur. J. Med. Chem. 236, 114354 (2022)
  16. Opening of glutamate receptor channel to subconductance levels Yelshanskaya M.V., Patel D.S., Kottke C.M., Kurnikova M.G., Sobolevsky A.I. Nature 605(7908), 172–178 (2022)
  17. Structural mechanism of TRPM7 channel regulation by intracellular magnesium Schmidt E., Narangoda C., Nörenberg W., Egawa M., Rössig A., Leonhardt M., Schaefer M., Zierler S., Kurnikova M.G., Gudermann T., Chubanov V. Cell Mol Life Sci. 79(5), 225 (2022)
  18. Accurate determination of solvation free energies of neutral organic compounds from first principles Pereyaslavets L., Kamath G., Butin O., Illarionov A., Olevanov M., Kurnikov I., Sakipov S., Leontyev I., Voronina E., Gannon T., Nawrocki G., Darkhovskiy M., Ivahnenko I., Kostikov A., Scaranto J., Kurnikova M.G., Banik S., Chan H., Sternberg M.G., Sankaranarayanan S.K.R.S., Crawford B., Potoff J., Levitt M., Kornberg R.D., Fain B. Nat. Commun. 13(1), 414 (2022)
  19. Structural basis of AMPA receptor inhibition by trans-4-butylcyclohexane carboxylic acid Yelshanskaya M.V., Singh A.K., Narangoda C., Williams R.S.B., Kurnikova M.G., Sobolevsky A.I. Br J Pharmacol. 179(14), 3628–3644 (2022)
  20. Baseline Comparisons of Complementary sampling methods for assembly driven by short-ranged pair potentials toward fast and flexible hybridization Ozkan A., Sitharam M., Flores-Canales J.C., Prabhu R., Kurnikova M.G. J. Chem. Theory Comput. 17(3), 1967–1987 (2021)
  21. Structure and function of the calcium-selective TRP channel TRPV6 Yelshanskaya M.V., Nadezhdin K.D., Kurnikova M.G., Sobolevsky A.I. J. Physiol. 599(10), 2673–2697 (2021)
  22. Harnessing the substrate promiscuity of dioxygenase AsqJ and developing efficient chemoenzymatic synthesis for quinolones Tang H., Tang Y., Kurnikov I.V., Liao H.J., Chan N.L., Kurnikova M.G., Guo Y., Chang W.C. ACS Catal. 11(12), 7186–7192 (2021)
  23. Epoxidation catalyzed by the nonheme iron(II)- and 2-oxoglutarate-dependent oxygenase, AsqJ: Mechanistic elucidation of oxygen atom transfer by a ferryl intermediate Li J., Liao H.J., Tang Y., Huang J.L., Cha L., Lin T.S., Lee J.L., Kurnikov I.V., Kurnikova M.G., Chang W.C., Chan N.L., Guo Y. J. Am. Chem. Soc. 142(13), 6268–6284 (2020)
  24. AMPA receptor noncompetitive inhibitors occupy a promiscuous binding site Narangoda C., Sakipov S.N., Kurnikova M.G. ACS Chem. Neurosci. 10(11), 4511–4521 (2019)
  25. A Hierarchical Approach to Predict Conformation Dependent Histidine Protonation States in Stable and Flexible Proteins Sakipov S.N., Flores-Canales J.C., Kurnikova M.G. J. Phys. Chem. B 123(24), 5024–5034 (2019)
  26. Microsecond Molecular Dynamics Simulations of Diphtheria Toxin Translocation T-Domain pH-Dependent Unfolding in Solution Flores-Canales J.C., Simakov N.A., Kurnikova M.G. bioRxiv 572040 (2018)
  27. Ion Permeation Mechanism in Epithelial Calcium Channel TRPV6 Sakipov S., Sobolevsky A.I., Kurnikova M.G. Sci Rep. 8(1), 5715 (2018)
  28. Insights into the Desaturation of Cyclopeptin and its C3 Epimer Catalyzed by a non-Heme Iron Enzyme: Structural Characterization and Mechanism Elucidation Liao H.J., Li J., Huang J.L., Davidson M., Kurnikov I., Lin T.S., Lee J.L., Kurnikova M., Guo Y., Chan N.L., Chang W.C. Angew Chem Int Ed Engl. 57(7), 1831–1835 (2018)
  29. Membrane Position Dependency of the pKa and Conductivity of the Protein Ion Channel Simakov N.A., Kurnikova M.G. J. Membr. Biol. (2018)
  30. Protein stability and dynamics influenced by ligands in extremophilic complexes – a molecular dynamics investigation Khan S., Farooq U., Kurnikova M. Mol Biosyst. 13(9), 1874–1887 (2017)
  31. Role of the Ion Channel Extracellular Collar in AMPA Receptor Gating Yelshanskaya M.V., Mesbahi-Vasey S., Kurnikova M.G., Sobolevsky A.I. Sci Rep. 7(1), 1050 (2017)
  32. All atom NMDA receptor transmembrane domain model development and simulations in lipid bilayers and water Mesbahi-Vasey S., Veras L., Yonkunas M., Johnson J.W., Kurnikova M.G. PLoS One 12(6), e0177686 (2017)
  33. Configurational preference of the glutamate receptor ligand binding domain dimers Yonkunas M., Buddhadev M., Flores-Canales J.C., Kurnikova M.G. Biophys. J. 112(11), 2291–2300 (2017)
  34. Molecular mechanisms of bio-catalysis of heme extraction from hemoglobin Sakipov S., Rafikova O., Kurnikova M.G., Rafikov R. Redox Biology 11, 516–523 (2017)
  35. Structural Bases of Noncompetitive Inhibition of AMPA-Subtype Ionotropic Glutamate Receptors by Antiepileptic Drugs Yelshanskaya M.V., Singh A.K., Sampson J.M., Narangoda C., Kurnikova M., Sobolevsky A.I. Neuron 91(6), 1305–1315 (2016)
  36. Exploring Protein Stability by Comparative Molecular Dynamics Simulations of Homologous Hyperthermophilic, Mesophilic, and Psychrophilic Proteins Khan S., Farooq U., Kurnikova M. J. Chem. Inf. Model. 56(11), 2129–2139 (2016)
  37. Microsecond simulations of the diphtheria toxin translocation domain in association with anionic lipid bilayers Flores-Canales J., Kurnikova M. J. Phys. Chem. B 119(36), 12074–12085 (2015)
  38. The hydrophobic effect contributes to the closed state of a simplified ion channel through a conserved hydrophobic patch at the pore-helix crossing Yonkunas M., Kurnikova M. Front Pharmacol. 6, 284 (2015)
  39. Modeling electronic polarizability changes in the course of water ligand exchange around magnesium Kurnikov I., Kurnikova M. J. Phys. Chem. B 119(32), 10275–10286 (2015)
  40. Role of Acidic Residues in Helices TH8-TH9 in Membrane Interactions of the Diphtheria Toxin T domain Ghatak C., Rodnin M.V., Vargas-Uribe M., McCluskey A.J., Flores-Canales J.C., Kurnikova M., Ladokhin A.S. Toxins 7(4), 1303–1323 (2015)
  41. Membrane Association of the Diphtheria Toxin Translocation Domain Studied by Coarse-Grained Simulations and Experiment Flores-Canales J., Vargas M., Ladokhin A., Kurnikova M. J. Membr. Biol. 248(3), 529–543 (2015)
  42. Targeting Direct-Space Intra-Solute Electrostatic Interactions in Accelerated Molecular Dynamics with Application to Protein Partial Unfolding Flores-Canales J., Kurnikova M. J. Chem. Theory Comput. 11(6), 2550–2559 (2015)
  43. Crosslinking constraints and computational models as complementary tools in modeling the extracellular domain of the glycine receptor Liu Z., Szarecka A., Yonkunas M., Speranskiy K., Kurnikova M., Cascio M. PLoS One 9(7), e102571 (2014)
  44. Graphical Processing Unit accelerated Poisson equation solver and its application for calculation of single ion potential in ion-channels Simakov N.A., Kurnikova M.G. Molecular Based Mathematical Biology 1, 151–163 (2013)
  45. pH-Triggered Conformational Switching of the Diphtheria Toxin T-Domain: The Roles of N-Terminal Histidines Kurnikov I.V., Kyrychenko A., Flores-Canales J.C., Rodnin M.V., Simakov N., Vargas-Uribe M., Posokhov Y.O., Kurnikova M., Ladokhin A.S. J. Mol. Biol. 425(15), 2752–2764 (2013)
  46. Stability and rigidity/flexibility—Two sides of the same coin? Mamonova T., Glyakina A.V., Galzitskaya O.V., Kurnikova M.G. Biochim. Biophys. Acta 1834, 854–866 (2013)
  47. Structural Basis for NHERF1 PDZ Domain Binding Mamonova T., Kurnikova M., Friedman P.A. Biochemistry 51(14), 3110–3120 (2012)
  48. Characterizing the Energetic States of the GluR2 Ligand Binding Domain Core-Dimer Yonkunas M., Kurnikova M. Biophys. J. 100(2), L5–L7 (2011)
  49. Soft Wall Ion Channel in Continuum Representation with Application to Modeling Ion Currents in α-Hemolysin Simakov N., Kurnikova K. J. Phys. Chem. B 114(46), 15180–15190 (2010)
  50. Flexibility and Mobility in Mesophilic and Thermophilic Homologous Proteins from Molecular Dynamics and FoldUnfold Method Mamonova T.B., Glyakina A.V., Kurnikova M.G., Galzitskaya O.G. J. Bioinform. Comput. Biol. 8(3), 377–394 (2010)
  51. An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations Ramanathan A., Agarwal P.K., Kurnikova M., Langmead C.J. J. Comput. Biol. 17(3), 309–324 (2010)
  52. An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations Ramanathan A., Agarwal P.K., Kurnikova M., Langmead C.J. Proc. 13th Annual RECOMB, 138–154 (2009)
  53. Biologically Relevant Motions of HIV-1 Reverse Transcriptase Investigated by Long-scale Molecular Dynamics Ramanathan A., Mamonova T., Madrid M., Kurnikova M. Proc. 3rd Annual TeraGrid Conference (2009)
  54. Modeling of peptides connecting the ligand-binding and transmembrane domains in the GluR2 glutamate receptor Speranskiy K., Kurnikova M. Proteins 76(2), 271–280 (2009)
  55. Overexpression and functional characterization of the extracellular domain of the human α1 glycine receptor Liu Z., Ramanoudjame G., Fox R., Jayaraman V., Kurnikova M., Cascio M. Biochemistry 47, 9803–9810 (2008)
  56. Energetics of the cleft closing transition and glutamate binding in the Glutamate Receptor ligand Binding Domain Mamonova T., Yonkunas M., Kurnikova M. Biochemistry 47(42), 11077–11085 (2008)
  57. Ion Channels, Computation of Kurnikova M. In Wiley Encyclopedia of Chemical Biology, ed. T.P. Begley, Wiley (2008)
  58. Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds Cheng M.H., Coalson R.D., Cascio M., Kurnikova M. J. Comput. Aided Mol. Des. 22, 563–570 (2008)
  59. Interplay between structural rigidity and electrostatic interactions in the ligand binding domain of GluR2 Mamonova T., Speranskiy K., Kurnikova M. Proteins 73(3), 656–671 (2008)
  60. Replica Exchange Molecular Dynamics Simulation of Poly(alkylthiophenes) Widge A., Matsuoka Y., Kurnikova M. J. Mol. Graph. Comput. 27, 34–44 (2008)
  61. Computational Modeling of Poly(alkylthiophene) Conductive Polymer Insertion Into Phospholipid Bilayers Widge A., Matsuoka Y., Kurnikova M. Langmuir 23, 10672–10681 (2007)
  62. Homology modeling and molecular dynamics simulations of the glycine receptor ligand binding domain Speranskiy K., Cascio M., Kurnikova M. Proteins 67(4), 950–960 (2007)
  63. Poisson-Nernst-Planck theory of ion permeation through biological channels Coalson R.D., Kurnikova M.G. In: Biological Membrane Ion Channels, Springer (2006)
  64. Diffusion constant of K+ inside Gramicidin A: a comparative study of four computational methods Mamonov A., Kurnikova M., Coalson R. Biophys. Chem. 124(3), 268–278 (2006)
  65. Structure and energetics of channel-forming protein–polysaccharide complexes inferred via computational statistical thermodynamics Mamonova T., Kurnikova M., J. Phys. Chem. B 110(49), 25091–25100 (2006)
  66. Spontaneous field potentials in the glomeruli of the olfactory bulb: The leading role of juxtaglomerular cells Karnup S.V., Hayar A., Shipley M.T., Kurnikova M.G. Neuroscience 142(1), 203–221 (2006)
  67. Protein Flexibility using Constraints from Molecular Dynamics Simulations Mamonova T., Hespenheide B., Straub R., Thorpe M., Kurnikova M. Phys. Biol. 2, S137–S147 (2005)
  68. Investigation of the glutamate ligand binding to the Glutamate Receptor by theoretical methodologies Speranskiy K., Kurnikova M. Biochemistry 44(34), 11508–11517 (2005)
  69. Poisson-Nernst-Planck theory approach to the calculation of current through biological ion channels Coalson R.D., Kurnikova M.G. IEEE Trans. NanoBioscience 4(1), 81–93 (2005)
  70. Accurate theoretical prediction of vibrational frequencies in an inhomogeneous dynamic environment: a case study of a glutamate molecule in water solution and in a protein-bound form Speranskiy K., Kurnikova M. J. Chem. Phys. 121, 1516–1524 (2004)
  71. Comparison of dynamic lattice Monte Carlo simulations and the dielectric self-energy Poisson-Nernst-Planck continuum theory for model ion channels Graf P., Kurnikova M.G., Coalson R.D., Nitzan A. J. Phys. Chem. B 108, 2006–2015 (2004)
  72. Energetics and dynamics of a cyclic oligosaccharide molecule in a confined protein pore environment: A molecular dynamics study Shilov I., Kurnikova M. J. Phys. Chem. B 107(29), 7108–7201 (2003)
  73. The role of the dielectric barrier in narrow biological channels: a novel composite approach to modeling single channel currents Mamonov A., Coalson R., Nitzan A., Kurnikova M. Biophys. J. 84(6), 3646–3661 (2003)
  74. A dynamic lattice Monte-Carlo model of ion transport in inhomogeneous dielectric environments: method and implementation Graf P., Nitzan A., Kurnikova M.G., Coalson R.D. J. Phys. Chem. B 104, 12324–12338 (2000)
  75. 3D Poisson-Nernst-Planck theory studies of the influence of membrane electrostatics on Gramicidin A channel conductance Cardenas A., Kurnikova M., Coalson R. Biophys. J. 79, 80–93 (2000)
  76. A lattice relaxation algorithm for 3D Poisson-Nernst-Planck theory with application to ion transport through the Gramicidin A channel Kurnikova M.G., Coalson R.D., Graf P., Nitzan A. Biophys. J. 76, 642–656 (1999)
  77. Rotational diffusion of organic solutes: the role of dielectric friction in polar solvents and electrolyte solutions Balabai N., Sukharevsky A., Read I., Strazisar B., Kurnikova M., Hartman R.S., Coalson R.D., Waldeck D.H. J. Mol. Liq. 77, 37–60 (1998)
  78. Rotational relaxation of ionic molecules in electrolyte solutions. Anisotropy relaxation and molecular dynamics study Balabai N., Kurnikova M.G., Coalson R.D., Waldeck D.H. J. Am. Chem. Soc. 120(31), 7944–7951 (1998)
  79. Rotational relaxation in polar solvents. Molecular dynamics study of solute-solvent interactions Kurnikova M.G., Balabai N., Waldeck D.H., Coalson R.D. J. Am. Chem. Soc. 120(24), 6121–6130 (1998)
  80. Structural fluctuations, spin, reorganization energy, and tunneling energy control of intramolecular electron transfer: The surprising case of electron transfer in a d8-d8 bimetallic system Kurnikov I.V., Zusman L.D., Kurnikova M.G., Farid R.S., Beratan D.N. J. Am. Chem. Soc. 119(24), 5690–5700 (1997)
  81. A Molecular dynamics study of photothermal compression of colloidal crystals Zahorchak J.C., Kurnikova M.G., Coalson R.D. J. Chem. Phys. 105(23), 628–638 (1996)
  82. A Molecular dynamics study of dielectric friction Kurnikova M.G., Waldeck D.H., Coalson R.D. J. Chem. Phys. 105(2), 628–638 (1996)
  83. Structural analysis of the EEG data. Software package for the personal computer Iskra Bacharev B.V., Kurnikova M.G. Russian Academy of Science, Pushchino (1991)