Publications


1. Khan S, Farooq U, Kurnikova M. Protein stability and dynamics influenced by ligands in extremophilic complexes - a molecular dynamics investigation. Mol Biosyst. 13(9):1874-1887. doi: 10.1039/c7mb00210f. (2017)

2. Yelshanskaya MV, Mesbahi-Vasey S, Kurnikova MG, Sobolevsky AI. Role of the Ion Channel Extracellular Collar in AMPA Receptor Gating. Sci Rep. 7(1):1050. doi: 10.1038/s41598-017- 01146-z. PubMed PMID: 28432359; (2017

3. Mesbahi-Vasey S, Veras L, Yonkunas M, Johnson JW, Kurnikova MG. All atom NMDA receptor transmembrane domain model development and simulations in lipid bilayers and water. PLoS One. 12(6):e0177686. doi: 10.1371/journal.pone.0177686. PubMed PMID: 28582391; (2017)

4. M. Yonkunas, M. Buddhadev,J. C. Flores Canales, M. G. Kurnikova, Configurational preference of the glutamate receptor ligand binding domain dimers, Biophys. J., 112(11):2291-2300. http://dx.doi.org/10.1016/ j.bpj.2017.04.042 , PubMed PMID: 28591602; (2017)

5. Sakipov, S; Rafikova, O; Kurnikova, MG; Rafikov, R. Molecular mechanisms of bio-catalysis of heme extraction from hemoglobinRedox Biology (imp. fact. 6.35), 11, 516-523 doi: 10.1016/j.redox.2017.01.004. Epub 2017 Jan 7. PubMed PMID: 28088643; (2017)

6. M. V. Yelshanskaya, A. K. Singh, J. M. Sampson, C. Narangoda, M. Kurnikova, A. I. Sobolevsky, Structural Bases of Noncompetitive Inhibition of AMPA-Subtype Ionotropic Glutamate Receptors by Antiepileptic Drugs, Neuron (imp.fact. 15), 91(6), pp. 1305–1315 (2016)

7. Khan S, Farooq U, Kurnikova M. Exploring Protein Stability by Comparative Molecular Dynamics Simulations of Homologous Hyperthermophilic, Mesophilic, and Psychrophilic Proteins. J Chem Inf Model. 56(11):2129-2139. Epub 2016 Oct 14. (2016)

8. J. Flores-Canales and M. Kurnikova, Microsecond simulations of the diphtheria toxin translocation domain in association with anionic lipid bilayersJ. Phys. Chem B, 119(36), pp 12074-12085 (2015) 

9. M. Yonkunas and M. Kurnikova, The hydrophobic effect contributes to the closed state of a simplified ion channel through a conserved hydrophobic patch at the pore-helix crossing. Frontiers of Pharmacology (Front Pharmacol), 6, pp 284 (2015)

10. I. Kurnikov and M. Kurnikova, Modeling electronic polarizability changes in the course of water ligand exchange around magnesium. J. Phys. Chem B, Vol 119 (32), pp 10275- 10286 (2015)

11. C. Gathak, M.V. Rodnin, M. Vargas-Uribe, A.J. McCluskey, J.C. Flores-Canales, M. Kurnikova, A.S. Ladokhin, Role of Acidic Residues in Helices TH8-TH9 in Membrane Interactions of the Diphtheria Toxin T domain, Toxins, Vol 7 (4), pp 1303-1323 (2015)

12. J. Flores-Canales, M. Vargas, A. Ladokhin and M. Kurnikova, Membrane Association of the Diphtheria Toxin Translocation Domain Studied by Coarse-Grained Simulations and Experiment, J. Membr. Biol., 248 (3), pp 529-543 (2015)

13. J. Flores-Canales and M. Kurnikova, Targeting Direct-Space Intra-Solute Electrostatic Interactions in Accelerated Molecular Dynamics with Application to Protein Partial Unfolding. Journal of Theoretical and Computational Chemistry (JTCT), 11 (6), pp 2550-2559 (2015)

14. A. Ozkan J. Flores-Canales, M. Sitharam, and M. Kurnikova, Fast and Flexible Geometric Method For Enhancing MC Sampling of Compact Configurations For Protein Docking Problem. pre-published at arXiv:1408.2481 (2014)

15. Liu Z, Szarecka A, Yonkunas M, Speranskiy K, Kurnikova M, Cascio M., Crosslinking constraints and computational models as complementary tools in modeling the extracellular domain of the glycine receptor. PLoS One.9(7):e102571. doi: 10.1371 (2014)

16. N.A. Simakov, M.G. Kurnikova, Graphical Processing Unit accelerated Poisson equation solver and its application for calculation of single ion potential in ion-channels. Molecular Based Mathematical Biology Vol 1, pp 151-163 (2013)

17. I.V. Kurnikov, A. Kyrychenko, J.C. Flores-Canales, M.V. Rodnin, N. Simakov, M. Vargas- Uribe, Y.O. Posokhov, M. Kurnikova, and A.S. Ladokhin, pH-Triggered Conformational Switching of the Diphtheria Toxin T-Domain: The Roles of N-Terminal Histidines. J. Molecular Biology Vol 425 (15), pp2752-64 (2013)

18. T. Mamonova, A. V. Glyakina, O. V. Galzitskaya, M. G. Kurnikova, Stability and rigidity/flexibility—Two sides of the same coin? Biochimica et Biophysica Acta, 1834 (2013), 854–866 (2013)

19. T. Mamonova, M. Kurnikova, and P. A. Friedman, Structural Basis for NHERF1 PDZ Domain Binding. Biochemistry, 51 (14), 3110–3120 (2012)

20. M. Yonkunas and M. Kurnikova, Characterizing the Energetic States of the GluR2 Ligand Binding Domain Core-Dimer. Biophys. J., 100(2), L5-L7 (2011)

21. N. Simakov and K. Kurnikova, Soft Wall Ion Channel in Continuum Representation with Application to Modeling Ion Currents in α-Hemolysin. J. Phys. Chem. B, 114(46), 15180-15190 (2010)

22. T. B. Mamonova, A.V. Glyakina, M. G. Kurnikova and O. G. Galzitskaya, Flexibility and Mobility in Mesophilic and Thermophilic Homologous Proteins from Molecular Dynamics and FoldUnfold Method. J. Bioinform. and Comp. Biol., 8(3), 377-394 (2010)

23. A. Ramanathan, P. K. Agarwal, M. Kurnikova, C. J. Langmead An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations J. Comp. Biol., 17 (3), 309-324 (2010) (invited submission)