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Overexpression and functional characterization
of the extracellular domain of the human α1 glycine receptor
Z. Liu, G. Ramanoudjame, R. Fox, V. Jayaraman, M. Kurnikova and M. Cascio
Biochemistry (2008) in press
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Energetics of the cleft closing transition and
glutamate binding in the Glutamate Receptor ligand Binding Domain
T. Mamonova, M. Yonkunas, and M. Kurnikova
Biochemistry (2008) in press
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Theoretical Study of the Glutamate Receptor Ligand Binding Domain Flexibility and Conformational Reorganization
T. Mamonova, K. Speranskiy, and M. Kurnikova
Prot.: Struct., Func., Bioinf., Vol. 73 (3), pp 656-671 (2008)
doi:10.1002/prot.22090
[PDF]
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Computational Prediction of Ion Permeation Characteristics in the Clycine Receptor Modifid by Photo-Sensitive Compounds
M. H. Cheng, R. D. Coalson, M. Cascio, and M. Kurnikova
J. Comput. Aided Mol. Des., Vol. 22, pp.563-570 (2008) [PDF]
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Replica Exchange Molecular Dynamics Simulation of
Poly(alkylthiophenes)
A. Widge, Y. Matsuoka, M. Kurnikova
J. Mol. Graph. Model. Vol. 27, pp 34 (2008)
doi:10.1016/j.jmgm.2008.02.005
[PDF]
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Computational Modeling of Poly(alkylthiophene)
Conductive Polymer Insertion Into Phospholipid Bilayers
A. Widge, Y. Matsuoka, M. Kurnikova
Langmuir, Vol. 23, pp. 10672-10681 (2007) [PDF]
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Homology Model and Molecular Dynamics Simulations of the Glycine Receptor Ligand Binding Domain
K. Sperankiy, M. Casio, M. Kurnikova
Prot.: Struct., Func., Bioinf. Vol 67, pp. 950-960 (2007) [PDF]
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Poisson-Nernst-Planck theory of ion permeation through biological channels
R. Coalson, M. Kurnikova
In Book: Biological Membrane Ion
Channels. Dynamics, Structure, and Applications (2007)
Ed. S-H Chung, O. Andersen, and V. Krishnamurthy
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Diffusion constant of K+ inside Gramicidin A: a comparative study of four computational methods
A. Mamonov, M. Kurnikova, and R. Coalson
Biophys. Chem., Vol. 124, Iss. 3, pp. 268-278 (2006) [PDF]
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Spontaneous field potentials in the glomeruli of the olfactory bulb: The leading role of juxtaglomerular cells
S. V. Karnup, A. Hayar, M. T. Shipley, Kurnikova, M. G.
Neuroscience, Vol. 142, Iss. 1, pp. 203-221 (2006) [PDF]
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Structure and energetics of channel-forming protein-polysaccharide complexes inferred via computational statistical thermodynamics
T. Mamonova, M. G. Kurnikova
J. Phys. Chem., Vol. 110, Iss. 49, pp. 25091-25100 (2006) [PDF]
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Protein Flexibility using Constraints from Molecular Dynamics Simulations
T. Mamonova, B. Hespenheide, R. Straub, M. F. Thorpe, M. G.
Kurnikova
Physical Biology, Vol. 2, S137-S147 (2005)[PDF]
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On the Binding Determinants of the Glutamate Agonist with the Glutamate Receptor Ligand Binding Domain
K. Speranskiy, M. G. Kurnikova
Biochemistry Vol. 44, pp. 11208-11517 (2005) [ PDF]
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Poisson-Nernst-Planck theory approach to the
calculation of current through biological ion channels
R. Coalson, M. G. Kurnikova
IEEE Transaction on NanoBioscience Vol. 4, pp. 81-93 (2005) [PDF]
- Comparison of Dynamic Lattice Monte Carlo Simulations and the Dielectric Self-Energy Poisson-Nernst-Planck Continuum Theory for Model Ion Channels.
P. Graf, M. G. Kurnikova, R. Coalson, and A. Nitzan,
J. Phys. Chem. B, Vol. 108, p. 02006 (2004) [PDF]
- Theoretical Prediction of Vibrational Frequencies in a Realistic Dynamic Environment: A Case Study of Glutamate in Water Solution and in a Protein-Bound Form
K. Speranskiy, M. Kurnikova
J. Chem. Phys., Vol. 121, p. 1516 (2004) [ PDF]
- Role of the Dielectric Barrier in Narrow Biological Channels: A Novel Composite Approach to Modeling Single-Channel Currents.
A. B. Mamonov, R. D. Coalson, A. Nitzan, and M. G. Kurnikova
Biophys. J., Vol. 84, Issue 6, pp. 3646-3661 (2003) [PDF]
- Energetics and Dynamics of a Cyclic Oligosaccharide Molecule in a Confined Protein Pore Environment. A Molecular Dynamics Study
I. V. Shilov and M. G. Kurnikova
J. Phys. Chem. B, Vol. 107, Issue 29, pp. 7189-7201 (2003) [PDF]
- Three-Dimensional Poisson-Nernst-Planck Theory Studies: Influence of Membrane Electrostatics on Gramicidin A Channel Conductance
A. E. Cardenas, R. D. Coalson, and M. G. Kurnikova
Biophys. J., Vol. 79, pp. 80-93 (2000) [PDF]
- A Dynamic Lattice Monte Carlo Model of Ion Transport in Inhomogeneous Dielectric Environments: Method and Implementation
P. Graf, A. Nitzan, M. G. Kurnikova, and R. D. Coalson
J. Phys. Chem. B, Vol. 104, Iss. 51, pp. 12324-12338 (2000) [PDF]
- A Lattice Relaxation Algorithm for Three-Dimensional Poisson- Nernst-Planck Theory With Application to Ion Transport Through the Gramicidin A Channel
M. G. Kurnikova, R. D. Coalson, P. Graf, and A. Nitzan
Biophys. J., Vol. 76, Iss. 2, pp. 642-656 (1999) [PDF]
- Rotational Relaxation in Polar Solvents. Molecular Dynamics Study of Solute-Solvent Interaction
M. G. Kurnikova, N. Balabai, D. H. Waldeck, and R. D. Coalson
J. Am. Chem. Soc., Vol. 120, Iss. 24, pp. 6121-6130 (1998) [PDF]
- Rotational Relaxation of Ionic Molecules in Electrolyte Solutions. Anisotropy Relaxation and Molecular Dynamics Study
N. Balabai, M. G. Kurnikova, R. D. Coalson, and D. H. Waldeck
J. Am. Chem. Soc., Vol. 120, Iss. 31, pp. 7944-7951 (1998) [PDF]
- Rotational Diffusion of Organic Solutes: The Role of Dielectric Friction in Polar Solvents and Electrolyte Solutions
N. Balabai, A. Sukharevsky, I. Read, B. Strazisar, M. G. Kurnikova, R. S. Hartman, R. D. Coalson, and D. H. Waldeck
J. Mol. Liquids, Vol. 77, Iss. 1-3, pp. 37-60 (1998) [PDF]
- Structural Fluctuations, Spin, Reorganization Energy, and Tunneling Energy Control of Intramolecular Electron Transfer: The Surprising Case of Electron Transfer in a D(8)-d(8) Bimetallic System
I. Kurnikov, L. V. Zusman, M. G. Kurnikova, R. S. Farid, and D. Beratan
J. Am. Chem. Soc., Vol. 119, Iss. 24, pp. 5690-5700 (1997) [PDF]
- A Molecular Dynamics Study of Photothermal Compression of Colloidal Crystals
J. C. Zahorchak, M. G. Kurnikova, and R. D. Coalson
J. Chem. Phys., Vol. 106, Iss. 4, pp. 1585-1592 (1997) [PDF]
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Molecular Dynamics Study of Dielectric Friction
M. G. Kurnikova, D. H. Waldeck, and R. D. Coalson
J. Chem. Phys., Vol. 105, Iss. 2, pp. 628-638 (1996) [PDF]
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