Carnegie Mellon University

Maria Kurnikova

Maria Kurnikova

Associate Professor, Chemistry

  • Mellon Institute 503
  • 412-268-9772


1998     Ph.D., Theoretical Chemistry, University of Pittsburgh


My research is in the area of computational chemistry and biophysics.

Theory,computational chemistry, biophysical, molecular modeling, continuum electrostatics, drift-diffusion models, ion channels, membrane receptors, signal transduction, membrane protein structure-function relations, flexibility and rigidity in protein dynamics.


Membrane Proteins and Ion Channels

I am interested in understanding the work of membrane proteins, such as receptors, signal transduction proteins, toxins and ion channels. The goal is to model and predict structure-function relationships in these proteins associated with ligand binding, gating of channels and mechanisms of selectivity and mobility in the confined environment of the channel. The systems I am interested specifically include Glutamate Receptors (AMPA and NMDA types), alpha-Hemolysin, Diphteria Toxin t-domain, Gramicidin A, PDZ-domain — ligand interaction of the NHERF1 protein.

Protein Flexibility/Rigidity

In many protein systems and complexes protein flexibility and rigidity play important role in inducing functionally important movements and conformational transitions. In other cases small fluctuations of protein atoms, due to thermal noise, create a conducive environment for initiation of functionally significant rearrangements of atoms. We apply a range of methods and models of computational chemistry and biology to characterize dynamics of proteins in a wide spatial and temporal scale


The approach my research group is taking includes a combination of physics-based computational methodologies, such as molecular dynamics simulations, continuum electrostatics and quantum chemistry. The name of the game in this field is Statistical Mechanics, which is the corner-stone theory for understanding behavior of large molecular ensembles. Huge computational resources are needed to obtain correct statistics in biomolecular modeling, thus, we are active users of the national super-computer facilities sponsored by NSF and NIH, such as for example Pittsburgh Super Computer Center. Another challenge in this field is to develop models of intermolecular interactions that account for the properties of the system on a quantitative level, yet are simple enough computationally to be evaluated effectively. Finding a right balance between the complexity of the model and an effectiveness of it in the simulation — is a significant and yet unsolved intellectual challenge for many biologically important systems and processes. The educational background and interests needed to succeed in this field is physical chemistry, soft condensed matter physics and biophysics.


Role of the Ion Channel Extracellular Collar in AMPA Receptor Gating
Yelshanskaya MV, Mesbahi-Vasey S, Kurnikova MG, Sobolevsky AI, Scientific Reports 7(1):1050. (2017)

All atom NMDA receptor transmembrane domain model development and simulations in lipid bilayers and water
Mesbahi-Vasey S, Veras L, Yonkunas M, Johnson JW, Kurnikova MG, PLoS One 12(6):e0177686. (2017)

Configurational preference of the glutamate receptor ligand binding domain dimers
M. Yonkunas, M. Buddhadev, J. C. Flores Canales, M. G. Kurnikova,  Biophys. J., 112(11):2291–2300 (2017)

Molecular mechanisms of bio-catalysis of heme extraction from hemoglobin
Sakipov S., Rafikova O., Kurnikova MG. , Rafikov R., Redox Biology, 11, 516–523 (2017)

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

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

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

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

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

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

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

pH-Triggered Conformational Switching of the Diphtheria Toxin T-Domain: The Roles of N-Terminal Histidines
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, J. Molecular Biology, 425 (15), 2752–64 (2013)

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


2011 Visiting Fellow, Princeton University
2009–present Associate Professor of Chemistry, Carnegie Mellon University
2005 Visiting Researcher, Arizona State University
2003–2009 Assistant Professor of Chemistry, Carnegie Mellon University
2002 Visiting Researcher, Michigan State University
2001–2003 Assistant Professor, Marquette University
1999–2001 Research Associate, University of Pittsburgh
1999–2000 Guest Researcher, National Institute of Standards and Technology (NIST)
1998–1999 Postdoctoral Fellow, University of Tel-Aviv, Israel

Awards and Distinctions

2002 Research Corporation, Research Innovation Award