M. Khrenova

发表

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

Alexander P. Savitsky, Maria G. Khrenova, Alexander V. Nemukhin, 2012, Theranostics.

Effect of protein environment on electronically excited and ionized states of the green fluorescent protein chromophore.

A. Krylov, B. Grigorenko, K. Bravaya, 2011, The journal of physical chemistry. B.

The photoreaction mechanism in the bacterial blue light receptor BLUF according to metadynamics modeling

A. Nemukhin, M. Khrenova, V. Mironov, 2014, Moscow University Chemistry Bulletin.

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

I. Polyakov, A. Krylov, B. Grigorenko, 2017, The journal of physical chemistry. B.

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

V. Tsirelson, A. Nemukhin, M. Khrenova, 2020, Physical chemistry chemical physics : PCCP.

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

A. Krylov, B. Grigorenko, A. Nemukhin, 2019, The journal of physical chemistry. B.

The common trends for the halogen, chalcogen, and pnictogen bonds via sorting principles and local bonding properties

V. Tsirelson, M. Khrenova, E. Bartashevich, 2020, Theoretical Chemistry Accounts.

Influence of the leaving group on the mechanism of hydrolysis of organophosphorus compounds by phosphotriesterase from bacterium Pseudomonas diminuta

M. Khrenova, A. M. Kulakova, A. V. Nemukhin, 2022, Russian Chemical Bulletin.

The QM/MM-QTAIM approach reveals the nature of the different reactivity of cephalosporins in the active site of L1 metallo-β-lactamase

V. Tsirelson, M. Khrenova, A. V. Krivitskaya, 2019, New Journal of Chemistry.

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

A. Savitsky, M. Khrenova, Grigory D. Lapshin, 2017 .

Modeling the Interplay of Poor Inhibitor Binding and Efficient Formation of a Covalent Adduct upon the Interaction of ARS Compounds with KRASᴳ¹²ᶜ

A. Nemukhin, M. Khrenova, A. M. Kulakova, 2019 .

Molecular Mechanism of Light-Induced Acceleration of the Adenosine Triphosphate Conversion to the Cyclic Adenosine Monophosphate Catalyzed by the Photoactivated Adenylyl Cyclase bPAC

A. Nemukhin, M. Khrenova, A. M. Kulakova, 2020 .

Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation

A. Nemukhin, M. Khrenova, F. Mulashkin, 2021, J. Chem. Inf. Model..

Modeling the Complete Catalytic Cycle of Aspartoacylase.

B. Grigorenko, A. Nemukhin, M. Khrenova, 2016, The journal of physical chemistry. B.

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

I. Polyakov, A. Krylov, B. Grigorenko, 2015, The journal of physical chemistry. B.

Nanopore Sequencing for De Novo Bacterial Genome Assembly and Search for Single-Nucleotide Polymorphism

I. Osterman, M. Khrenova, V. Rodin, 2022, International journal of molecular sciences.

Dipole Moment Variation Clears Up Electronic Excitations in the π-Stacked Complexes of Fluorescent Protein Chromophores

A. Nemukhin, M. Khrenova, F. Mulashkin, 2020, J. Chem. Inf. Model..

First biphotochromic fluorescent protein moxSAASoti stabilized for oxidizing environment

A. P. Savitsky, M. Khrenova, I. Solovyev, 2021, Scientific Reports.

Influence of the Active Site Flexibility on the Efficiency of Substrate Activation in the Active Sites of Bi-Zinc Metallo-β-Lactamases

M. Khrenova, A. V. Krivitskaya, 2022, Molecules.

Methodological aspects of the calculation of the free energy profile of guanosine triphosphate hydrolysis by Ras-GAP protein complex

M. Khrenova, V. Mironov, L. A. Lychko, 2016, Moscow University Chemistry Bulletin.

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

V. Tsirelson, A. Nemukhin, M. Khrenova, 2019, Chemical Physics.

Interplay between the Enamine and Imine Forms of the Hydrolyzed Imipenem in the Active Sites of Metallo-β-lactamases and in Water Solution

M. Khrenova, A. V. Krivitskaya, 2022, J. Chem. Inf. Model..

Extracellular Fe(III) reductase structure reveals a modular organization enabling S-layer insertion and electron transfer to insoluble substrates.

F. Robb, K. Boyko, V. Popov, 2022, Structure.

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

B. Grigorenko, A. Nemukhin, M. Khrenova, 2018, Physical chemistry chemical physics : PCCP.

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

V. Tsirelson, M. Khrenova, S. Israel, 2017, Journal of Molecular Modeling.

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

B. Grigorenko, A. Nemukhin, M. Khrenova, 2015, Proteins.

Applications of High Performance Computing: Born-Oppenheimer Molecular Dynamics of Complex Formation in Aqueous Solutions

Maria G. Khrenova, Dmitry P. Kapusta, Ilya V. Babchuk, 2018, Supercomput. Front. Innov..

The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme

E. Y. Bezsudnova, K. Boyko, M. Khrenova, 2021, Molecules.

State-of-the-art of computational green chemistry in leading universities in Russia

V. Tsirelson, M. Khrenova, E. Lokteva, 2022, Green Chemistry and Computational Chemistry.

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

V. Svedas, B. Grigorenko, A. Nemukhin, 2014 .

Photoinduced electron transfer facilitates tautomerization of the conserved signaling glutamine side chain in BLUF protein light sensors.

A. Nemukhin, M. Khrenova, A V Nemukhin, 2013, The journal of physical chemistry. B.

Drug Repurposing of the Unithiol: Inhibition of Metallo-β-Lactamases for the Treatment of Carbapenem-Resistant Gram-Negative Bacterial Infections

M. Khrenova, V. Grigorenko, A. Egorov, 2022, International journal of molecular sciences.

Modeling reaction routes from rhodopsin to bathorhodopsin

A. Nemukhin, M. Khrenova, A. Bochenkova, 2010, Proteins.

Studies on the conformational state of the chromophore group (11-cis-retinal) in rhodopsin by computer molecular simulation methods

A. Nemukhin, M. Khrenova, M. Ostrovsky, 2009, Biofizika.

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

A. Nemukhin, M. Khrenova, E. Kots, 2016, The journal of physical chemistry. B.

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

A. Kolomeisky, B. Grigorenko, A. Nemukhin, 2015, The journal of physical chemistry. B.

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

Maria G Khrenova, Alexander V Nemukhin, A. Nemukhin, 2015, Proteins.

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

Maria G. Khrenova, Alexander V. Nemukhin, Bella L. Grigorenko, 2012 .

Modeling the role of G12V and G13V Ras mutations in the Ras-GAP-catalyzed hydrolysis reaction of guanosine triphosphate.

Maria G Khrenova, Alexander V Nemukhin, B. Grigorenko, 2014, Biochemistry.

Proof of concept for poor inhibitor binding and efficient formation of covalent adducts of KRASG12C and ARS compounds.

A. Nemukhin, M. Khrenova, A. M. Kulakova, 2020, Organic & biomolecular chemistry.

Molecular Modeling Reveals the Mechanism of Ran-RanGAP-Catalyzed Guanosine Triphosphate Hydrolysis without an Arginine Finger

B. Grigorenko, A. Nemukhin, M. Khrenova, 2021, ACS Catalysis.

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

B. Grigorenko, A. Nemukhin, M. Khrenova, 2016, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.

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

A. Nemukhin, M. Khrenova, 2018, The journal of physical chemistry. B.

To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense

E. Y. Bezsudnova, K. Boyko, M. Khrenova, 2023, Molecules.

LSSmScarlet, dCyRFP2s, dCyOFP2s and CRISPRed2s, Genetically Encoded Red Fluorescent Proteins with a Large Stokes Shift

Kiryl D Piatkevich, P. Dorovatovskii, K. Boyko, 2021, International journal of molecular sciences.

Intermediates of the Autocatalytic Reaction of the Formation of a Chromophore in a Green Fluorescent Protein

B. Grigorenko, A. Nemukhin, M. Khrenova, 2020, Russian Journal of Physical Chemistry B.

Evolution of Ceftriaxone Resistance of Penicillin-Binding Proteins 2 Revealed by Molecular Modeling

M. Khrenova, A. V. Krivitskaya, 2022, International journal of molecular sciences.

Boronic Acids as Prospective Inhibitors of Metallo-β-Lactamases: Efficient Chemical Reaction in the Enzymatic Active Site Revealed by Molecular Modeling

M. Khrenova, A. V. Krivitskaya, 2021, Molecules.

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

B. Grigorenko, A. Nemukhin, M. Khrenova, 2011, Journal of molecular modeling.

Metallo-β-Lactamases: Influence of the Active Site Structure on the Mechanisms of Antibiotic Resistance and Inhibition

M. Khrenova, E. Levina, 2021, Biochemistry (Moscow).

Mechanism of Guanosine Triphosphate Hydrolysis by the Visual Proteins Arl3-RP2: Free Energy Reaction Profiles Computed with Ab Initio Type QM/MM Potentials

A. Nemukhin, M. Khrenova, F. Mulashkin, 2021, Molecules.

Complex of HIV-1 Integrase with Cellular Ku Protein: Interaction Interface and Search for Inhibitors

M. Gottikh, M. Khrenova, M. Serebryakova, 2022, International journal of molecular sciences.

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

A. Nemukhin, A. Savitsky, M. Khrenova, 2014, The journal of physical chemistry. B.

Keto‐enol tautomerism from the electron delocalization perspective

V. Tsirelson, M. Khrenova, A. A. Astakhov, 2022, J. Comput. Chem..

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

V. Tsirelson, M. Khrenova, A. A. Astakhov, 2020, RSC advances.

Keto‐enol tautomerism of the 4,5‐dimethyl‐2‐(2′‐hydroxyphenyl)imidazole in water solution: Modeling equilibrium between neutral forms and accurate assignment of the absorption bands

M. Khrenova, F. Mulashkin, D. Kapusta, 2020 .

Computational characterization of the all-atom structure and the calcium binding sites of the LH1-RC core complex from Thermochromatium tepidum

B. Grigorenko, A. Nemukhin, M. Khrenova, 2016 .

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

B. Grigorenko, A. Nemukhin, M. Khrenova, 2014, Journal of Molecular Modeling.

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

A. Nemukhin, M. Khrenova, T. Domratcheva, 2015, The journal of physical chemistry. B.

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

Yulia I. Meteleshko, A. Nemukhin, M. Khrenova, 2017, The journal of physical chemistry. B.

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

Walter Thiel, Tatiana Vasilevskaya, Maria G. Khrenova, 2016, J. Comput. Chem..

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

Walter Thiel, Tatiana Vasilevskaya, Maria G. Khrenova, 2015, J. Comput. Chem..

Three Faces of N-Acetylaspartate: Activator, Substrate, and Inhibitor of Human Aspartoacylase.

Ekaterina D Kots, Maria G Khrenova, Alexander V Nemukhin, 2017, The journal of physical chemistry. B.

Estimating orientation factors in the FRET theory of fluorescent proteins: the TagRFP-KFP pair and beyond.

J. Collins, A. Nemukhin, M. Khrenova, 2015, Biophysical journal.

Detection of protease activity by fluorescent protein FRET sensors: from computer simulation to live cells

A. Savitsky, M. Khrenova, A. S. Goryashchenko, 2018, Methods and applications in fluorescence.

The explicit role of electron exchange in the hydrogen bonded molecular complexes

Maria G. Khrenova, Elena O. Levina, Vladimir G. Tsirelson, 2021, J. Comput. Chem..

The role of cysteine residues in the allosteric modulation of the chromophore phototransformations of biphotochromic fluorescent protein SAASoti

A. P. Savitsky, M. Khrenova, I. Solovyev, 2021, Scientific Reports.

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

Igor V. Pletnev, Maria G. Khrenova, D. Chernyshov, 2006 .

Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms

A. Krylov, B. Grigorenko, A. Nemukhin, 2023, Journal of the American Chemical Society.

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

Ekaterina D Kots, Maria G Khrenova, Alexander V Nemukhin, 2018, J. Chem. Inf. Model..

Light-Induced Change of Arginine Conformation Modulates the Rate of Adenosine Triphosphate to Cyclic Adenosine Monophosphate Conversion in the Optogenetic System Containing Photoactivated Adenylyl Cyclase

Maria G. Khrenova, Alexander V. Nemukhin, Anna M. Kulakova, 2021, J. Chem. Inf. Model..

Combined Structural and Computational Study of the mRubyFT Fluorescent Timer Locked in Its Blue Form

P. Dorovatovskii, K. Boyko, F. Subach, 2023, International journal of molecular sciences.

Molecular Dynamics of Enzyme-Substrate Complexes in Guanosine Trifosphate-Binding Proteins

I. Polyakov, M. Khrenova, A. Nemukhin, 2022, Russian Journal of Physical Chemistry B.

Two Sides of Quantum-Based Modeling of Enzyme-Catalyzed Reactions: Mechanistic and Electronic Structure Aspects of the Hydrolysis by Glutamate Carboxypeptidase

A. Nemukhin, M. Khrenova, A. V. Krivitskaya, 2021, Molecules.

Molecular mechanism of the cesium and rubidium selective binding to the calix[4]arene revealed by Born–Oppenheimer molecular dynamics simulation and electron density analysis

M. Khrenova, A. Kulakova, 2021 .

Pyrrolo[2,3-e]indazole as a novel chemotype for both influenza A virus and pneumococcal neuraminidase inhibitors

M. Khrenova, M. Schmidtke, A. Egorova, 2023, RSC advances.

MODELING STRUCTURE AND SPECTRA OF PROTEIN COMPLEXES BY USING MOLECULAR DYNAMICS AND QUANTUM CHEMISTRY METHODS : FROM SIMPLE TWO-DOMAIN UNITS TO PHOTOSYNTHETIC AGGREGATES

A. Nemukhin, M. Khrenova, 2012 .

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

A. Nemukhin, M. Khrenova, A. Kulakova, 2018, Organic & biomolecular chemistry.

The O to S substitution in urea brings inhibition activity against thiocyanate dehydrogenase

V. Popov, M. Khrenova, T. Tikhonova, 2021, Mendeleev Communications.

Molecular mechanism of the dark-state recovery in BLUF photoreceptors

Maria G. Khrenova, Alexander V. Nemukhin, Tatiana Domratcheva, 2017 .

Computational characterization of ketone-ketal transformations at the active site of matrix metalloproteinases.

A. Nemukhin, A. Savitsky, M. Khrenova, 2014, The journal of physical chemistry. B.

Reaction mechanism of matrix metalloproteinases with a catalytically active zinc ion studied by the QM(DFTB)/MM simulations

W. Thiel, T. Vasilevskaya, A. Nemukhin, 2016 .

Thermal isomerization of the chromoprotein asFP595 and its kindling mutant A143G: QM/MM molecular dynamics simulations.

B. Grigorenko, A. Nemukhin, A. Savitsky, 2013, The journal of physical chemistry. B.

Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase

G. Muyzer, V. Popov, W. Hagen, 2020, Proceedings of the National Academy of Sciences.

Computational Characterization of the Substrate Activation in the Active Site of SARS-CoV-2 Main Protease

Maria G. Khrenova, Alexander V. Nemukhin, Vladimir G. Tsirelson, 2020, Supercomput. Front. Innov..

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

Maria G Khrenova, Alexander V Nemukhin, Ilme Schlichting, 2011, Photochemistry and photobiology.

Effect of Substituents in Hydrolyzed Cephalosporins on Intramolecular O–H···N Bond

V. Tsirelson, M. Khrenova, E. Levina, 2020, Russian Journal of Physical Chemistry A.

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

L. Vinokurov, A. Savitsky, M. Khrenova, 2015, International journal of molecular sciences.

Full Structure Modeling of Three-Domains Monooxygenase CYP102A1 ВМ3 from Bacillus megaterium

V. Urlacher, M. Khrenova, P. D. Parshin, 2020, Moscow University Chemistry Bulletin.

Aspartoacylase: a central nervous system enzyme. Structure, catalytic activity and regulation mechanisms

A. Nemukhin, M. Khrenova, S. Varfolomeev, 2019, Russian Chemical Reviews.

Ionic liquid based on a quaternary phosphonium cation as a plasticizer and an electrode-active component of ion-selective electrode membranes

M. Khrenova, N. V. Shvedene, V. Baulin, 2007 .

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

B. Grigorenko, A. Nemukhin, M. Khrenova, 2018, Structural Chemistry.

Reconstructing the Electron Density of Intermediates of the Hydrolysis of N-Acetylaspartate by Aspartoacylase

A. Nemukhin, M. Khrenova, E. Kots, 2019, Russian Journal of Physical Chemistry A.

Quantum Chemistry Calculations Provide Support to the Mechanism of the Light-Induced Structural Changes in the Flavin-Binding Photoreceptor Proteins.

B. Grigorenko, A. Nemukhin, M. Khrenova, 2010, Journal of chemical theory and computation.

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

A. Kolomeisky, B. Grigorenko, A. Nemukhin, 2015, Journal of Physical Chemistry B.

Electronic Steric Factors in the Active Site of Metallo-β-Lactamase and Reactivity of Cephalosporin Antibiotics

V. Tsirelson, M. Khrenova, A. V. Tomilko, 2019, Moscow University Chemistry Bulletin.

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

A. Nemukhin, M. Khrenova, E. Kots, 2016, The journal of physical chemistry. B.

Structural framework for the understanding spectroscopic and functional signatures of the cyanobacterial Orange Carotenoid Protein families

K. Boyko, M. Khrenova, Baosheng Ge, 2023, bioRxiv.

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

A. Nemukhin, M. Khrenova, A. Moskovsky, 2018 .

In search for structural targets for engineering D-amino acid transaminase: modulation of pH optimum and substrate specificity.

E. Y. Bezsudnova, K. Boyko, M. Khrenova, 2023, The Biochemical journal.

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

W. Thiel, T. Vasilevskaya, A. Nemukhin, 2015, J. Comput. Chem..

Benchmark studies of hydrogen bond governing reactivity of cephalosporins in L1 metallo‐β‐lactamase: Efficient and reliable QSPR equations

V. Tsirelson, M. Khrenova, E. Levina, 2020 .

QM/MM Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms

A. Krylov, B. Grigorenko, A. Nemukhin, 2023 .

Quantum Chemistry in Studies of Fluorescent and Photosensing Proteins

J. Collins, A. Nemukhin, M. Khrenova, 2013 .