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1

Four novel ELANE mutations in patients with congenital neutropenia

Maria Kurnikova, Michael Maschan, Evgeniya Dinova, Irina Shagina, Natalia Finogenova, Elena Mamedova, Tatyana Polovtseva, Dmitry Shagin, Anna Shcherbina

Journal:

Pediatric Blood & Cancer

Year:

2011

Language:

english

File:

PDF, 65 KB

english, 2011

2

Stability and rigidity/flexibility—Two sides of the same coin?

Mamonova, Tatyana B., Glyakina, Anna V., Galzitskaya, Oxana V., Kurnikova, Maria G.

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2013

Language:

english

File:

PDF, 2.58 MB

english, 2013

3

Comparison of Dynamic Lattice Monte Carlo Simulations and the Dielectric Self-Energy Poisson−Nernst−Planck Continuum Theory for Model Ion Channels

Graf, Peter, Kurnikova, Maria G., Coalson, Rob D., Nitzan, Abraham

Journal:

Journal of Physical Chemistry B

Year:

2004

Language:

english

File:

PDF, 140 KB

english, 2004

4

Insights into desaturation of cyclopeptin and its C3-epimer catalyzed by a non-heme iron enzyme: structural characterization and mechanism elucidation

CHANG, WEI-CHEN, Liao, Hsuan-Jen, Li, Jikun, Huang, Jhih-Liang, Davidson, Madison, Kurnikov, Igor, Lin, Te-Sheng, Lee, Justin L., Kurnikova, Maria, Guo, Yisong, Chan, Nei-Li

Journal:

Angewandte Chemie International Edition

Year:

2018

Language:

english

File:

PDF, 1.09 MB

english, 2018

5

Alu-mediated recombination in the HAX1 gene as the molecular basis of severe congenital neutropenia

Maria Kurnikova, Evgeniya Dinova, Irina Shagina, Dmitriy Shagin

Journal:

American Journal of Medical Genetics Part A

Year:

2011

Language:

english

File:

PDF, 58 KB

english, 2011

6

Development and initial testing of an empirical forcefield for simulation of poly(alkylthiophenes)

Alik S. Widge, Yoky Matsuoka, Maria Kurnikova

Journal:

Journal of Molecular Graphics and Modelling

Year:

2008

Language:

english

File:

PDF, 801 KB

english, 2008

7

Identification of a novel mutation in DKC1 in dyskeratosis congenita

Maria Kurnikova, Irina Shagina, Lilia Khachatryan, Olga Schagina, Mikchail Maschan, Dmitriy Shagin

Journal:

Pediatric Blood & Cancer

Year:

2009

Language:

english

File:

PDF, 112 KB

english, 2009

8

Homology modeling and molecular dynamics simulations of the glycine receptor ligand binding domain

Kirill Speranskiy, Michael Cascio, Maria Kurnikova

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 704 KB

english, 2007

9

Interplay between structural rigidity and electrostatic interactions in the ligand binding domain of GluR2

Tatyana Mamonova, Kirill Speranskiy, Maria Kurnikova

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.40 MB

english, 2008

10

Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds

Mary Hongying Cheng, Rob D. Coalson, Michael Cascio, Maria Kurnikova

Journal:

Journal of Computer-Aided Molecular Design

Year:

2008

Language:

english

File:

PDF, 376 KB

english, 2008

11

Diffusion constant of K+ inside Gramicidin A: A comparative study of four computational methods

Artem B. Mamonov, Maria G. Kurnikova, Rob D. Coalson

Journal:

Biophysical Chemistry

Year:

2006

Language:

english

File:

PDF, 360 KB

english, 2006

12

Three-Dimensional Poisson-Nernst-Planck Theory Studies: Influence of Membrane Electrostatics on Gramicidin A Channel Conductance

Cárdenas, Alfredo E., Coalson, Rob D., Kurnikova, Maria G.

Journal:

Biophysical Journal

Year:

2000

Language:

english

File:

PDF, 355 KB

english, 2000

13

The Role of the Dielectric Barrier in Narrow Biological Channels: A Novel Composite Approach to Modeling Single-Channel Currents

Mamonov, Artem B., Coalson, Rob D., Nitzan, Abraham, Kurnikova, Maria G.

Journal:

Biophysical Journal

Year:

2003

Language:

english

File:

PDF, 447 KB

english, 2003

14

Modeling and Mutation of NHERF1 Dimerization Domains

Mamonova, Tatyana, Wang, Bin, Kurnikova, Maria, Friedman, Peter A.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 33 KB

english, 2010

15

Characterizing the Energetic States of the GluR2 Ligand Binding Domain Core-Dimer

Yonkunas, Michael, Kurnikova, Maria

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 226 KB

english, 2011

16

A Hydrophobic Bundle Crossing Found in Glutamate Receptor and K+ channel Pore Helices Dominates the Conformational Free Energy Landscape

Yonkunas, Michael J., Kurnikova, Maria

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 39 KB

english, 2011

17

A Lattice Relaxation Algorithm for Three-Dimensional Poisson-Nernst-Planck Theory with Application to Ion Transport through the Gramicidin A Channel

Kurnikova, Maria G., Coalson, Rob D., Graf, Peter, Nitzan, Abraham

Journal:

Biophysical Journal

Year:

1999

Language:

english

File:

PDF, 511 KB

english, 1999

18

A Dynamic Lattice Monte Carlo Model of Ion Transport in Inhomogeneous Dielectric Environments: Method and Implementation

Graf, Peter, Nitzan, Abraham, Kurnikova, Maria G., Coalson, Rob D.

Journal:

Journal of Physical Chemistry B

Year:

2000

Language:

english

File:

PDF, 147 KB

english, 2000

19

Glutamate Receptor Model and Atomistic Simulations; AMPA and NMDA

Abroshan, Hadi, Yonkunas, Mike, Johnson, Jon W., Kurnikova, Maria

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 41 KB

english, 2013

20

pH-Triggered Conformational Switching of the Diphtheria Toxin T-Domain: The Roles of N-Terminal Histidines

Kurnikov, Igor V., Kyrychenko, Alexander, Flores-Canales, Jose C., Rodnin, Mykola V., Simakov, Nikolay, Vargas-Uribe, Mauricio, Posokhov, Yevgen O., Kurnikova, Maria, Ladokhin, Alexey S.

Journal:

Journal of Molecular Biology

Year:

2013

Language:

english

File:

PDF, 2.59 MB

english, 2013

21

FLEXIBILITY AND MOBILITY IN MESOPHILIC AND THERMOPHILIC HOMOLOGOUS PROTEINS FROM MOLECULAR DYNAMICS AND FOLDUNFOLD METHOD

MAMONOVA, TATYANA B., GLYAKINA, ANNA V., KURNIKOVA, MARIA G., GALZITSKAYA, OXANA V.

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2010

Language:

english

File:

PDF, 2.04 MB

english, 2010

22

On the Binding Determinants of the Glutamate Agonist with the Glutamate Receptor Ligand Binding Domain

Speranskiy, Kirill, Kurnikova, Maria

Journal:

Year:

2005

Language:

english

File:

PDF, 355 KB

english, 2005

23

Membrane Association of Diphtheria Toxin T-Domain Characterized by Coarse-Grained and Atomistic Molecular Dynamics Simulations and Experiments

Flores-Canales, Jose C., Vargas-Uribe, Mauricio, Ladokhin, Alexey S., Kurnikova, Maria

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 42 KB

english, 2013

24

Computational Studies of the Molecular Mechanisms Responsible for Ca2+ Permeation and Mg2+ Block of NMDA Receptors

Veras, Lea, Kurnikov, Igor, Johnson, Jon W., Kurnikova, Maria

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 51 KB

english, 2012

25

Energetics of the Cleft Closing Transition and the Role of Electrostatic Interactions in Conformational Rearrangements of the Glutamate Receptor Ligand Binding Domain

Yonkunas, Michael J., Mamonova, Tatyana, Kurnikova, Maria

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 38 KB

english, 2009

26

Multiscale Simulations of Diphtheria Toxin T-Domain Membrane Association

Flores-Canales, Jose C., Ladokhin, Alexey S., Kurnikova, Maria

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 43 KB

english, 2014

27

Calculation of Current-Voltage properties of Biological Ion Channel, using Poisson-Nernst-Planck (PNP) Theory

Simakov, Nikolay A., Kurnikova, Maria G.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 34 KB

english, 2009

28

Mechanism of the pH-Triggered Formation of Membrane-Competent State of the Diphtheria Toxin Translocation Domain Revealed by Simulations and Experiment

Flores-Canales, Jose C., Kurnikov, Igor, Simakov, Nikolay, Kyrychenko, Alexander, Rodnin, Mykola V., Ladokhin, Alexey S., Kurnikova, Maria

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 38 KB

english, 2011

29

Theoretical Investigation of Structure and Gating Mechanisms in Glutamate Receptor Ion Channels

Yonkunas, Michael J., Kurnikova, Maria

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 32 KB

english, 2010

30

Molecular Mechanisms of Ca2+ Selectivity and Mg2+ Block of NMDA Receptors

Veras, Lea, Younkunas, Michael, Hwang, Jane, Kallenbach, Erik, Kurnikov, Igor, Johnson, Jon W., Kurnikova, Maria

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 37 KB

english, 2011

31

An Empirical Scoring Function for the Transmembrane Helical Protein Assembly

Flores, Jose C., Kurnikov, Igor, Kurnikova, Maria

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 36 KB

english, 2012

32

Characterizing the Energetic States of a Glutamate Receptor using Umbrella Sampling and Microsecond Molecular Dynamics Simulations

Yonkunas, Michael, Buddhadev, Maiti, Kurnikova, Maria

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 40 KB

english, 2014

33

Extension of Poisson-Nernst Planck Theory of Ion Conductivity with Soft-Repulsion Potential between Ions and Protein. Sensitivity of I-V Properties of α-Hemolysin Channel on its Penetration Depth into Membrane

Simakov, Nikolay A., Kurnikova, Maria G.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 37 KB

english, 2010

34

Generating Pathways for Free Energy Calculations in Proteins Using Constraint-Based Conformational Sampling

Farrell, Daniel W., Mamonova, Tatyana, Kurnikova, Maria, Thorpe, Michael F.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 35 KB

english, 2009

35

Protein flexibility using constraints from molecular dynamics simulations

Mamonova, Tatyana, Hespenheide, Brandon, Straub, Rachel, Thorpe, M F, Kurnikova, Maria

Journal:

Physical Biology

Year:

2005

Language:

english

File:

PDF, 1.15 MB

english, 2005

36

Energetics of the Cleft Closing Transition and the Role of Electrostatic Interactions in Conformational Rearrangements of the Glutamate Receptor Ligand Binding Domain †

Mamonova, Tatyana, Yonkunas, Michael J., Kurnikova, Maria G.

Journal:

Year:

2008

Language:

english

File:

PDF, 2.13 MB

english, 2008

37

Structure and Energetics of Channel-Forming Protein−Polysaccharide Complexes Inferred via Computational Statistical Thermodynamics

Mamonova, Tatyana, Kurnikova, Maria

Journal:

Journal of Physical Chemistry B

Year:

2006

Language:

english

File:

PDF, 479 KB

english, 2006

38

Computational Modeling of Poly(alkylthiophene) Conductive Polymer Insertion into Phospholipid Bilayers

Widge, Alik S., Matsuoka, Yoky, Kurnikova, Maria

Journal:

Year:

2007

Language:

english

File:

PDF, 1.98 MB

english, 2007

39

Structural Basis for NHERF1 PDZ Domain Binding

Mamonova, Tatyana, Kurnikova, Maria, Friedman, Peter A.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.60 MB

english, 2012

40

Soft Wall Ion Channel in Continuum Representation with Application to Modeling Ion Currents in α-Hemolysin

Simakov, Nikolay A., Kurnikova, Maria G.

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 2.33 MB

english, 2010

41

Overexpression and Functional Characterization of the Extracellular Domain of the Human α1 Glycine Receptor †‡

Liu, Zhenyu, Ramanoudjame, Gomathi, Liu, Deqian, Fox, Robert O., Jayaraman, Vasanthi, Kurnikova, Maria, Cascio, Michael

Journal:

Year:

2008

Language:

english

File:

PDF, 2.13 MB

english, 2008

42

Energetics and Dynamics of a Cyclic Oligosaccharide Molecule in a Confined Protein Pore Environment. A Molecular Dynamics Study

Shilov, Ignat Yu., Kurnikova, Maria G.

Journal:

Journal of Physical Chemistry B

Year:

2003

Language:

english

File:

PDF, 793 KB

english, 2003

43

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, Kirill, Kurnikova, Maria

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 751 KB

english, 2004

44

A molecular dynamics study of photothermal compression of colloidal crystals

Zahorchak, James C., Kurnikova, Maria G., Coalson, Rob D.

Journal:

The Journal of Chemical Physics

Year:

1997

Language:

english

File:

PDF, 366 KB

english, 1997

45

An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations

Ramanathan, Arvind, Agarwal, Pratul K., Kurnikova, Maria, Langmead, Christopher J.

Journal:

Journal of Computational Biology

Year:

2010

Language:

english

File:

PDF, 6.92 MB

english, 2010

46

Membrane Association of the Diphtheria Toxin Translocation Domain Studied by Coarse-Grained Simulations and Experiment

Flores-Canales, Jose C., Vargas-Uribe, Mauricio, Ladokhin, Alexey S., Kurnikova, Maria

Journal:

Journal of Membrane Biology

Year:

2015

Language:

english

File:

PDF, 2.72 MB

english, 2015

47

Targeting Electrostatic Interactions in Accelerated Molecular Dynamics with Application to Protein Partial Unfolding

Flores-Canales, Jose C., Kurnikova, Maria

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.19 MB

english, 2015

48

Role of Acidic Residues in Helices TH8–TH9 in Membrane Interactions of the Diphtheria Toxin T Domain

Ghatak, Chiranjib, Rodnin, Mykola, Vargas-Uribe, Mauricio, McCluskey, Andrew, Flores-Canales, Jose, Kurnikova, Maria, Ladokhin, Alexey

Journal:

Year:

2015

Language:

english

File:

PDF, 3.21 MB

english, 2015

49

Microsecond Simulations of the Diphtheria Toxin Translocation Domain in Association with Anionic Lipid Bilayers

Flores-Canales, Jose C., Kurnikova, Maria

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 2.23 MB

english, 2015

50

Modeling Electronic Polarizability Changes in the Course of a Magnesium Ion Water Ligand Exchange Process

Kurnikov, Igor V., Kurnikova, Maria

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 1.50 MB

english, 2015