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1

Improving the Design of the Triple-Decker Motif in Red Fluorescent Proteins

Khrenova, Maria G., Polyakov, Igor V., Grigorenko, Bella L, Krylov, Anna I., Nemukhin, Alexander V.

Journal:

Journal of Physical Chemistry B

Year:

2017

Language:

english

File:

PDF, 2.15 MB

english, 2017

2

Testing the ability of rhodanine and 2, 4-thiazolidinedione to interact with the human pancreatic alpha-amylase: electron-density descriptors complement molecular docking, QM, and QM/MM dynamics calculations

Devi, Rajendran Niranjana, Khrenova, Maria G., Israel, Samuel, Anzline, Chellam, Astakhov, Andrey A., Tsirelson, Vladimir G.

Journal:

Journal of Molecular Modeling

Year:

2017

Language:

english

File:

PDF, 4.95 MB

english, 2017

3

Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes

Nemukhin, Alexander V., Grigorenko, Bella L, Khrenova, Maria G., Krylov, Anna I.

Journal:

Journal of Physical Chemistry B

Year:

2019

Language:

english

File:

PDF, 3.02 MB

english, 2019

4

Towards first-principles calculation of electronic excitations in the ring of the protein-bound bacteriochlorophylls

Polyakov, Igor V., Khrenova, Maria G., Moskovsky, Alexander A., Shabanov, Boris M., Nemukhin, Alexander V.

Journal:

Chemical Physics

Year:

2018

Language:

english

File:

PDF, 2.26 MB

english, 2018

5

Monomerization of the photoconvertible fluorescent protein SAASoti by rational mutagenesis of single amino acids

Solovyev, Ilya D., Gavshina, Alexandra V., Katti, Aditya S., Chizhik, Alexey I., Vinokurov, Leonid M., Lapshin, Grigory D., Ivashina, Tatiana V., Khrenova, Maria G., Kireev, Igor I., Gregor, Ingo, End

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 3.47 MB

english, 2018

6

Competition between two cysteines in covalent binding of biliverdin to phytochrome domains

Khrenova, Maria G., Kulakova, Anna M., Nemukhin, Alexander V.

Journal:

Organic & Biomolecular Chemistry

Year:

2018

Language:

english

File:

PDF, 1.98 MB

english, 2018

7

A Light-Induced Reaction with Oxygen Leads to Chromophore Decomposition and Irreversible Photobleaching in GFP-Type Proteins

Grigorenko, Bella L., Nemukhin, Alexander V., Polyakov, Igor V., Khrenova, Maria G., Krylov, Anna I.

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 1.56 MB

english, 2015

8

Reaction Mechanism of Guanosine Triphosphate Hydrolysis by the Vision-Related Protein Complex Arl3–RP2

Khrenova, Maria G., Kots, Ekaterina D., Nemukhin, Alexander V.

Journal:

Journal of Physical Chemistry B

Year:

2016

Language:

english

File:

PDF, 4.66 MB

english, 2016

9

Computational characterization of the chemical step in the GTP hydrolysis by Ras-GAP for the wild-type and G13V mutated Ras

Mironov, Vladimir A., Khrenova, Maria G., Lychko, Leonora A., Nemukhin, Alexander V

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2015

Language:

english

File:

PDF, 1.33 MB

english, 2015

10

Why does mutation of Gln61 in Ras by the nitro analog NGln maintain activity of Ras-GAP in hydrolysis of guanosine triphosphate?

Khrenova, Maria G., Grigorenko, Bella L., Mironov, Vladimir A., Nemukhin, Alexander V.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2015

Language:

english

File:

PDF, 735 KB

english, 2015

11

Molecular mechanism of the dark-state recovery in BLUF photoreceptors

Khrenova, Maria G., Domratcheva, Tatiana, Nemukhin, Alexander V.

Journal:

Chemical Physics Letters

Year:

2017

Language:

english

File:

PDF, 1.21 MB

english, 2017

12

Amide-imide tautomerization in the glutamine side chain in enzymatic and photochemical reactions in proteins

Grigorenko, Bella L, Khrenova, Maria, Nemukhin, Alexander

Journal:

Physical Chemistry Chemical Physics

Year:

2018

Language:

english

File:

PDF, 1.55 MB

english, 2018

13

Allosteric Control of N-Acetyl-Aspartate Hydrolysis by the Y231C and F295S Mutants of Human Aspartoacylase

Kots, Ekaterina D, Khrenova, Maria G., Nemukhin, Alexander V.

Journal:

Journal of Chemical Information and Modeling

Year:

2018

Language:

english

File:

PDF, 2.07 MB

english, 2018

14

Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase

Tikhonova, Tamara V., Sorokin, Dimitry Y., Hagen, Wilfred R., Khrenova, Maria G., Muyzer, Gerard, Rakitina, Tatiana V., Shabalin, Ivan G., Trofimov, Anton A., Tsallagov, Stanislav I., Popov, Vladimir

Journal:

Proceedings of the National Academy of Sciences

Year:

2020

Language:

english

File:

PDF, 1.43 MB

english, 2020

15

Revealing electronic features governing hydrolysis of cephalosporins in the active site of the L1 metallo-Î²-lactamase

Levina, Elena O., Khrenova, Maria G., Astakhov, Andrey A., Tsirelson, Vladimir G.

Journal:

Year:

2020

File:

PDF, 1.32 MB

2020

16

Quantum chemistry in studies of fluorescent and photosensing proteins

Nemukhin, Alexander, Topol, Igor, Collins, Jack, Khrenova, Maria

Journal:

International Journal of Quantum Chemistry

Year:

2013

Language:

english

File:

PDF, 417 KB

english, 2013

17

Catalytic Cycle of Penicillin Acylase from Escherichia coli : QM/MM Modeling of Chemical Transformations in the Enzyme Active Site upon Penicillin G Hydrolysis

Grigorenko, Bella L., Khrenova, Maria G., Nilov, Dmitry K., Nemukhin, Alexander V., Švedas, Vytas K.

Journal:

Year:

2014

Language:

english

File:

PDF, 2.66 MB

english, 2014

18

The N···H hydrogen bond strength in the transition state at the limiting step determines the reactivity of cephalosporins in the active site of L1 metallo-β-lactamase

Khrenova, Maria G., Tsirelson, Vladimir G.

Journal:

Mendeleev Communications

Year:

2019

Language:

english

File:

PDF, 460 KB

english, 2019

19

Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme

Khrenova, Maria G., Grigorenko, Bella L., Kolomeisky, Anatoly B., Nemukhin, Alexander V.

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 1.79 MB

english, 2015

20

Theoretical vibrational spectroscopy of intermediates and the reaction mechanism of the guanosine triphosphate hydrolysis by the protein complex Ras-GAP

Khrenova, Maria G., Grigorenko, Bella L., Nemukhin, Alexander V.

Journal:

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy

Year:

2016

Language:

english

File:

PDF, 1.28 MB

english, 2016

21

Benchmark studies of hydrogen bond governing reactivity of cephalosporins in L1 metalloâÎ²âlactamase: Efficient and reliable QSPR equations

Khrenova, Maria G., Levina, Elena O., Tsirelson, Vladimir G.

Journal:

International Journal of Quantum Chemistry

Year:

2020

File:

PDF, 3.99 MB

2020

22

Coupling between the BLUF and EAL domains in the blue light-regulated phosphodiesterase BlrP1

Maria Khrenova, Tatiana Domratcheva, Bella Grigorenko, Alexander Nemukhin

Journal:

Journal of Molecular Modeling

Year:

2011

Language:

english

File:

PDF, 477 KB

english, 2011

23

Exploration of the Zinc Finger Motif in Controlling Activity of Matrix Metalloproteinases

Khrenova, Maria G., Savitsky, Alexander P., Topol, Igor A., Nemukhin, Alexander V.

Journal:

Journal of Physical Chemistry B

Year:

2014

Language:

english

File:

PDF, 1.91 MB

english, 2014

24

Modeling the Complete Catalytic Cycle of Aspartoacylase

Kots, Ekaterina D., Khrenova, Maria G., Lushchekina, Sofya V., Varfolomeev, Sergei D., Grigorenko, Bella L., Nemukhin, Alexander V.

Journal:

Journal of Physical Chemistry B

Year:

2016

Language:

english

File:

PDF, 6.00 MB

english, 2016

25

Molecular mechanism of interactions between MMP-2 and its oligopeptide-based inhibitors

Khrenova, Maria G., Solovyev, Ilya D., Lapshin, Grigory D., Savitsky, Alexander P.

Journal:

Mendeleev Communications

Year:

2017

Language:

english

File:

PDF, 511 KB

english, 2017

26

Proof of concept for poor inhibitor binding and efficient formation of covalent adducts of KRAS G12C and ARS compounds

Khrenova, Maria G., Kulakova, Anna M., Nemukhin, Alexander V.

Journal:

Organic & Biomolecular Chemistry

Year:

2020

Language:

english

File:

PDF, 4.67 MB

english, 2020

27

Thermal Isomerization of the Chromoprotein asFP595 and Its Kindling Mutant A143G: QM/MM Molecular Dynamics Simulations

Mironov, Vladimir A., Khrenova, Maria G., Grigorenko, Bella L., Savitsky, Alexander P., Nemukhin, Alexander V.

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 1.58 MB

english, 2013

28

Origin of the π-stacking induced shifts in absorption spectral bands of the green fluorescent protein chromophore

Khrenova, Maria G., Nemukhin, Alexander V., Tsirelson, Vladimir G.

Journal:

Chemical Physics

Year:

2019

Language:

english

File:

PDF, 1.78 MB

english, 2019

29

Minimum energy reaction profiles for the hydrolysis reaction of the cyclic guanosine monophosphate in water: Comparison of the results of two QM/MM approaches

Dmitry Morozov, Maria Khrenova, Natalya Andrijchenko, Bella Grigorenko, Alexander Nemukhin

Journal:

Computational and Theoretical Chemistry

Year:

2012

Language:

english

File:

PDF, 775 KB

english, 2012

30

SPIE Proceedings [SPIE SPIE BiOS - San Francisco, California, USA (Saturday 2 February 2013)] Single Molecule Spectroscopy and Superresolution Imaging VI - Molecular modeling of the Förster resonance energy transfer between FusionRed and Dedushka(eqFP670) fluorescent proteins

Khrenova, Maria G., Goryashchenko, Alexander S., Nemukhin, Alexander V., Savitsky, Alexander P., Enderlein, Jörg, Gregor, Ingo, Gryczynski, Zygmunt K., Erdmann, Rainer, Koberling, Felix

Year:

2013

Language:

english

File:

PDF, 2.22 MB

english, 2013

31

Estimating Orientation Factors in the FRET Theory of Fluorescent Proteins: The TagRFP-KFP Pair and Beyond

Khrenova, Maria, Topol, Igor, Collins, Jack, Nemukhin, Alexander

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 1.05 MB

english, 2015

32

Dynamical properties of enzyme-substrate complexes disclose substrate specificity of the SARS-CoV-2 main protease as characterized by the electron density descriptors

Khrenova, Maria, Tsirelson, Vladimir G., Nemukhin, Alexander

Journal:

Physical Chemistry Chemical Physics

Year:

2020

File:

PDF, 4.26 MB

2020

33

All-atom structures and calcium binding sites of the bacterial photosynthetic LH1-RC core complex fromThermochromatium tepidum

Khrenova, Maria G., Nemukhin, Alexander V., Grigorenko, Bella L., Wang, Peng, Zhang, Jian-Ping

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 1.27 MB

english, 2014

34

Computational Characterization of Ketone–Ketal Transformations at the Active Site of Matrix Metalloproteinases

Khrenova, Maria G., Nemukhin, Alexander V., Savitsky, Alexander P.

Journal:

Journal of Physical Chemistry B

Year:

2014

Language:

english

File:

PDF, 1.85 MB

english, 2014

35

Effect of solvation water shells on enzyme active sites in zinc-dependent hydrolases

Kapusta, Dmitry P., Firsov, Denis A., Khrenova, Maria G., Grigorenko, Bella L., Nemukhin, Alexander V.

Journal:

Structural Chemistry

Year:

2018

Language:

english

File:

PDF, 1.70 MB

english, 2018

36

Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling

Vasilevskaya, Tatiana, Khrenova, Maria G., Nemukhin, Alexander V., Thiel, Walter

Journal:

Journal of Computational Chemistry

Year:

2015

Language:

english

File:

PDF, 831 KB

english, 2015

37

Discrimination of enzymeâsubstrate complexes by reactivity using the electron density analysis: peptide bond hydrolysis by the matrix metalloproteinase-2

Khrenova, Maria G., Nemukhin, Alexander V., Tsirelson, Vladimir G.

Journal:

Mendeleev Communications

Year:

2020

File:

PDF, 418 KB

2020

38

Effect of Protein Environment on Electronically Excited and Ionized States of the Green Fluorescent Protein Chromophore

Bravaya, Ksenia B., Khrenova, Maria G., Grigorenko, Bella L., Nemukhin, Alexander V., Krylov, Anna I.

Journal:

Journal of Physical Chemistry B

Year:

2011

Language:

english

File:

PDF, 858 KB

english, 2011

39

Conjugates of natural chlorins with cyclen as chelators of transition metals

Grin, Mikhail A., Brusov, Sergey S., Shchepelina, Ekaterina Yu., Ponomarev, Philipp V., Khrenova, Maria K., Smirnov, Alexander S., Lebedeva, Victoria S., Mironov, Andrey F.

Journal:

Mendeleev Communications

Year:

2017

Language:

english

File:

PDF, 355 KB

english, 2017

40

Mutants of the Flavoprotein iLOV as Prospective Red-Shifted Fluorescent Markers

Khrenova, Maria G., Meteleshko, Yulia I., Nemukhin, Alexander V.

Journal:

Journal of Physical Chemistry B

Year:

2017

Language:

english

File:

PDF, 2.54 MB

english, 2017

41

Genetically Encoded FRET-Sensor Based on Terbium Chelate and Red Fluorescent Protein for Detection of Caspase-3 Activity

Goryashchenko, Alexander, Khrenova, Maria, Bochkova, Anna, Ivashina, Tatiana, Vinokurov, Leonid, Savitsky, Alexander

Journal:

International Journal of Molecular Sciences

Year:

2015

Language:

english

File:

PDF, 1.48 MB

english, 2015

42

Theoretical Characterization of the Flavin-Based Fluorescent Protein iLOV and its Q489K Mutant

Khrenova, Maria G., Nemukhin, Alexander V., Domratcheva, Tatiana

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 2.23 MB

english, 2015

43

Modeling the Transient Kinetics of the L1 Metallo-β-Lactamase

Khrenova, Maria G., Nemukhin, Alexander V.

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 1.01 MB

english, 2018

44

Ionic Liquids Plasticize and Bring Ion-Sensing Ability to Polymer Membranes of Selective Electrodes

Natalia V. Shvedene, Denis V. Chernyshov, Maria G. Khrenova, Andrey A. Formanovsky, Vladimir E. Baulin, Igor V. Pletnev

Journal:

Electroanalysis

Year:

2006

Language:

english

File:

PDF, 309 KB

english, 2006

45

Screen-printed ion-selective electrodes covered with membranes containing ionic liquids

Denis V. Chernyshov, Maria G. Khrenova, Igor V. Pletnev, Natalia V. Shvedene

Journal:

Mendeleev Communications

Year:

2008

Language:

english

File:

PDF, 224 KB

english, 2008

46

Computational Characterization of Reaction Intermediates in the Photocycle of the Sensory Domain of the AppA Blue Light Photoreceptor

Maria G. Khrenova, Tatiana Domratcheva, Ilme Schlichting, Bella L. Grigorenko, Alexander V. Nemukhin

Journal:

Photochemistry and Photobiology

Year:

2011

Language:

english

File:

PDF, 833 KB

english, 2011

47

FLIM-FRET Imaging of Caspase-3 Activity in Live Cells Using Pair of Red Fluorescent Proteins

Savitsky, Alexander P., Rusanov, Alexander L., Zherdeva, Victoria V., Gorodnicheva, Tatiana V., Khrenova, Maria G., Nemukhin, Alexander V.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.20 MB

english, 2012

48

Modeling the Role of G12V and G13V Ras Mutations in the Ras-GAP-Catalyzed Hydrolysis Reaction of Guanosine Triphosphate

Khrenova, Maria G., Mironov, Vladimir A., Grigorenko, Bella L., Nemukhin, Alexander V.

Journal:

Year:

2014

Language:

english

File:

PDF, 980 KB

english, 2014

49

Oxoethylene derivative of the natural substrate as an inhibitor of matrix metalloproteinase MMP-2

Khrenova, Maria G., Solovyev, Ilya D., Azev, Viatcheslav N., Lapshin, Grigory D., Savitsky, Alexander P.

Journal:

Mendeleev Communications

Year:

2016

Language:

english

File:

PDF, 164 KB

english, 2016

50

Methodological aspects of QM/MM calculations: A case study on matrix metalloproteinase-2

Vasilevskaya, Tatiana, Khrenova, Maria G., Nemukhin, Alexander V., Thiel, Walter

Journal:

Journal of Computational Chemistry

Year:

2016

Language:

english

File:

PDF, 584 KB

english, 2016

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