List of works - Alexander V. Nemukhin

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

scientific article

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

scientific article published on 23 May 2014

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

scientific article published on 20 November 2018

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

scientific article published on 11 September 2018

An opsin shift in rhodopsin: retinal S0-S1 excitation in protein, in solution, and in the gas phase.

scientific article published on 9 October 2007

Analysis of proton wires in the enzyme active site suggests a mechanism of c-di-GMP hydrolysis by the EAL domain phosphodiesterases.

scientific article published in August 2016

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

scientific article published in 2014

Characterization of a complete cycle of acetylcholinesterase catalysis by ab initio QM/MM modeling

scientific article

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

article

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

scientific article published on 10 May 2019

Computational Modeling Reveals the Mechanism of Fluorescent State Recovery in the Reversibly Photoswitchable Protein Dreiklang

scientific article published on 14 October 2019

Computational Modeling Reveals the Mechanism of Fluorescent State Recovery in the Reversibly Photoswitchable Protein Dreiklang

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

scientific article published on 11 April 2014

Computational characterization of reaction intermediates in the photocycle of the sensory domain of the AppA blue light photoreceptor.

scientific article published on 13 December 2010

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

scientific article published on 08 April 2015

Computational strategy for tuning spectral properties of red fluorescent proteins.

scientific article published on 27 May 2011

Computational study of a transition state analog of phosphoryl transfer in the Ras-RasGAP complex: AlF(x) versus MgF3-.

scientific article published on 29 July 2005

Computer-designed active human butyrylcholinesterase double mutant with a new catalytic triad

scientific article published on 19 April 2019

Conformation dependence of pKa's of the chromophores from the purple asFP595 and yellow zFP538 fluorescent proteins.

scientific article published on August 2008

Conformation-dependent chemical reaction of formic acid with an oxygen atom.

scientific article published in July 2009

Conformational partitioning in pH-induced fluorescence of the kindling fluorescent protein (KFP).

scientific article published on 5 July 2011

Correlation between the substrate structure and the rate of acetylcholinesterase hydrolysis modeled with the combined quantum mechanical/molecular mechanical studies.

scientific article published on 14 April 2010

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

scientific article published on 14 September 2010

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

scientific article published on 18 November 2020

Diversity of mechanisms in Ras-GAP catalysis of guanosine triphosphate hydrolysis revealed by molecular modeling

scientific article published on 01 May 2019

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

scientific article published on 19 August 2020

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

scientific article

Electronic Excitations of the Chromophore from the Fluorescent Protein asFP595 in Solutions.

scientific article published in March 2006

Emission of SH radicals in solid krypton: mixed quantum-classical molecular dynamics simulations

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

scientific article

Exploration of the zinc finger motif in controlling activity of matrix metalloproteinases.

scientific article

Exploring Structural and Optical Properties of Fluorescent Proteins by Squeezing: Modeling High-Pressure Effects on the mStrawberry and mCherry Red Fluorescent Proteins ⬇️

scientific article published on October 5, 2012

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

scientific article published on 15 February 2012

First-principles characterization of the energy landscape and optical spectra of green fluorescent protein along the A→I→B proton transfer route

scientific article published on 25 July 2013

Free Energy Barriers for the N-Terminal Asparagine to Succinimide Conversion: Quantum Molecular Dynamics Simulations for the Fully Solvated Model

scientific article published on 01 January 2010

Frontiers in Multiscale Modelling of Photoreceptor Proteins

scientific article published on 28 December 2020

Gas phase absorption studies of photoactive yellow protein chromophore derivatives.

scientific article published on 30 July 2009

Ground-state structures and vertical excitations for the kindling fluorescent protein asFP595.

scientific article published in September 2006

Hindered rotation of HArF in solid argon: Infrared spectroscopy and a theoretical model

scholarly article in Physical Review B, vol. 77 no. 9, March 2008

How Reproducible Are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur

scientific article published on 07 July 2022

Hybrid diatomics-in-molecules-based quantum mechanical/molecular mechanical approach applied to the modeling of structures and spectra of mixed molecular clusters Arn(HCl)m and Arn(HF)m.

scientific article published in February 2004

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

scientific article published on 15 September 2015

Impact of pyrophosphate and O-ethyl-substituted pyrophosphate groups on DNA structure

scientific article published on 01 January 2007

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

scientific article published in November 2017

Interaction of aromatic compounds with xenon: spectroscopic and computational characterization for the cases of p-cresol and toluene

scientific article

Interaction of phenol with xenon and nitrogen: spectroscopic and computational characterization.

scientific article published in October 2012

Interactions of Azodicarbonamide (ADA) Species with the Model Zinc Finger Site: Theoretical Support of the Zinc Finger Domain Destruction in the HIV-1 Nucleocapsid Protein (NCp7) by ADA

article

Intermolecular complexes of HXeOH with water: stabilization and destabilization effects

scientific article published in September 2002

Interplay between Locally Excited and Charge Transfer States Governs the Photoswitching Mechanism in the Fluorescent Protein Dreiklang

scientific article published on 07 January 2021

Matrix-isolation study of the phenol–water complex and phenol dimer

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

scientific article

Mechanism of the chemical step for the guanosine triphosphate (GTP) hydrolysis catalyzed by elongation factor Tu

scientific article published on 16 August 2008

Mechanism of the myosin catalyzed hydrolysis of ATP as rationalized by molecular modeling

scholarly article

Mechanism of triphosphate hydrolysis in aqueous solution: QM/MM simulations in water clusters

scientific article published in March 2006

Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires

scientific article published on 09 January 2020

Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires

Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations

scientific article published on 01 February 2007

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

scientific article published on 03 May 2016

Minimum energy reaction profiles for ATP hydrolysis in myosin

scientific article published on 23 July 2011

Modeling Structure and Absorption Spectra of the Bacteriophytochrome-Based Fluorescent Protein IFP1.4

Modeling negative ion defect migration through the gramicidin A channel

scientific article published on 7 February 2009

Modeling photoabsorption of the asFP595 chromophore.

scientific article published on 27 August 2008

Modeling reactivation of the phosphorylated human butyrylcholinesterase by QM(DFTB)/MM calculations

Modeling spectral tuning in monomeric teal fluorescent protein mTFP1

scientific article

Modeling the Complete Catalytic Cycle of Aspartoacylase.

scientific article published on 19 April 2016

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

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

scientific article published on 3 January 2018

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

scientific article

Molecular Dynamics of Surface-Moving Thermally Driven Nanocars

scientific article published on 01 April 2008

Molecular Modeling Clarifies the Mechanism of Chromophore Maturation in the Green Fluorescent Protein.

scientific article published on 5 July 2017

Molecular Modeling the Reaction Mechanism of Serine-Carboxyl Peptidases.

scientific article

Molecular modeling evidence for His438 flip in the mechanism of butyrylcholinesterase hysteretic behavior.

scientific article

Molecular models predict light-induced glutamine tautomerization in BLUF photoreceptors

scientific article published on 8 February 2008

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

scientific article

Novel flavin-based fluorescent proteins with red-shifted emission bands: a computational study

scientific article published on 07 November 2018

On photoabsorption of the neutral form of the green fluorescent protein chromophore

scientific article published on 14 August 2009

On quantum mechanical – molecular mechanical (QM/MM) approaches to model hydrolysis of acetylcholine by acetylcholinesterase

scientific article published on 13 September 2012

Opening the Arg-Glu salt bridge in myosin: computational study.

scientific article

Optimization of Cholinesterase-Based Catalytic Bioscavengers Against Organophosphorus Agents.

scientific article published on 13 March 2018

Performance of the Spin-Flip and Multireference Methods for Bond Breaking in Hydrocarbons: A Benchmark Study

scientific article published on 16 November 2007

Photochemical Synthesis of H2O2from the H2O···O(3P) van der Waals Complex: Experimental Observations in Solid Krypton and Theoretical Modeling

scientific article published on 19 October 2007

Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing?

scientific article

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

scientific article published on 13 February 2013

Potential Energy Landscape of the Electronic States of the GFP Chromophore in Different Protonation Forms: Electronic Transition Energies and Conical Intersections.

scientific article

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

scientific article published on 26 February 2020

QM/MM modeling the Ras-GAP catalyzed hydrolysis of guanosine triphosphate.

scientific article published in August 2005

Quantum Chemical Benchmark Studies of the Electronic Properties of the Green Fluorescent Protein Chromophore. 1. Electronically Excited and Ionized States of the Anionic Chromophore in the Gas Phase

scientific article published on 25 June 2009

Quantum Chemical Benchmark Studies of the Electronic Properties of the Green Fluorescent Protein Chromophore: 2. Cis-Trans Isomerization in Water.

scientific article published in July 2009

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

scientific article published on August 2010

Quantum chemical modeling of reaction mechanism for 2-oxoglutarate dependent enzymes: effect of substitution of iron by nickel and cobalt

scientific article published on 01 March 2006

Quantum chemical modeling of the GTP hydrolysis by the RAS-GAP protein complex

scientific article

Quantum chemical modelling in the research of molecular mechanisms of enzymatic catalysis

Quantum chemistry behind bioimaging: insights from ab initio studies of fluorescent proteins and their chromophores.

scientific article published in September 2011

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

scientific article published on 4 April 2016

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

Rigid-Body Molecular Dynamics of Fullerene-Based Nanocars on Metallic Surfaces

scientific article published on 01 September 2010

Role of Protein Dimeric Interface in Allosteric Inhibition of N-Acetyl-Aspartate Hydrolysis by Human Aspartoacylase

scientific article

Role of zwitterions in kindling fluorescent protein photochemistry.

scientific article published on 17 November 2014

Simulated 18O kinetic isotope effects in enzymatic hydrolysis of guanosine triphosphate.

scientific article published in September 2009

Structure of the Brain N-Acetylaspartate Biosynthetic Enzyme NAT8L Revealed by Computer Modeling

scientific article published on 08 July 2020

The effect of oxidation on the electronic structure of the green fluorescent protein chromophore.

scientific article published in March 2010

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

scientific article published on 9 April 2015

Theoretical characterization of the photochemical reaction CO2 + O(3P) → CO + O2 related to experiments in solid krypton

scientific article

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

scientific article

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

scientific article

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

scientific article published on 13 September 2017

Toward Molecular-Level Characterization of Photoinduced Decarboxylation of the Green Fluorescent Protein: Accessibility of the Charge-Transfer States

scientific article published on 30 April 2012

Toward molecular mechanism of xenon anesthesia: a link to studies of xenon complexes with small aromatic molecules.

scientific article published on 15 October 2014

Triple-Decker Motif for Red-Shifted Fluorescent Protein Mutants.

scientific article published on 9 May 2013

Tuning Electrostatic Gating of Semiconducting Carbon Nanotubes by Controlling Protein Orientation in Biosensing Devices

scientific article

Understanding the non-catalytic behavior of human butyrylcholinesterase silent variants: Comparison of wild-type enzyme, catalytically active Ala328Cys mutant, and silent Ala328Asp variant.

scientific article published on 7 April 2016

Unusual emitting states of the kindling fluorescent protein: appearance of the cationic chromophore in the GFP family.

scientific article published on 6 June 2013

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

scientific article published on 29 September 2015

List of works by Alexander V. Nemukhin

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

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

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

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

An opsin shift in rhodopsin: retinal S0-S1 excitation in protein, in solution, and in the gas phase.

Analysis of proton wires in the enzyme active site suggests a mechanism of c-di-GMP hydrolysis by the EAL domain phosphodiesterases.

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

Characterization of a complete cycle of acetylcholinesterase catalysis by ab initio QM/MM modeling

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

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

Computational Modeling Reveals the Mechanism of Fluorescent State Recovery in the Reversibly Photoswitchable Protein Dreiklang

Computational Modeling Reveals the Mechanism of Fluorescent State Recovery in the Reversibly Photoswitchable Protein Dreiklang

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

Computational characterization of reaction intermediates in the photocycle of the sensory domain of the AppA blue light photoreceptor.

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

Computational strategy for tuning spectral properties of red fluorescent proteins.

Computational study of a transition state analog of phosphoryl transfer in the Ras-RasGAP complex: AlF(x) versus MgF3-.

Computer-designed active human butyrylcholinesterase double mutant with a new catalytic triad

Conformation dependence of pKa's of the chromophores from the purple asFP595 and yellow zFP538 fluorescent proteins.

Conformation-dependent chemical reaction of formic acid with an oxygen atom.

Conformational partitioning in pH-induced fluorescence of the kindling fluorescent protein (KFP).

Correlation between the substrate structure and the rate of acetylcholinesterase hydrolysis modeled with the combined quantum mechanical/molecular mechanical studies.

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

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

Diversity of mechanisms in Ras-GAP catalysis of guanosine triphosphate hydrolysis revealed by molecular modeling

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

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

Electronic Excitations of the Chromophore from the Fluorescent Protein asFP595 in Solutions.

Emission of SH radicals in solid krypton: mixed quantum-classical molecular dynamics simulations

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

Exploration of the zinc finger motif in controlling activity of matrix metalloproteinases.

Exploring Structural and Optical Properties of Fluorescent Proteins by Squeezing: Modeling High-Pressure Effects on the mStrawberry and mCherry Red Fluorescent Proteins ⬇️

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

First-principles characterization of the energy landscape and optical spectra of green fluorescent protein along the A→I→B proton transfer route

Free Energy Barriers for the N-Terminal Asparagine to Succinimide Conversion: Quantum Molecular Dynamics Simulations for the Fully Solvated Model

Frontiers in Multiscale Modelling of Photoreceptor Proteins

Gas phase absorption studies of photoactive yellow protein chromophore derivatives.

Ground-state structures and vertical excitations for the kindling fluorescent protein asFP595.

Hindered rotation of HArF in solid argon: Infrared spectroscopy and a theoretical model

How Reproducible Are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur

Hybrid diatomics-in-molecules-based quantum mechanical/molecular mechanical approach applied to the modeling of structures and spectra of mixed molecular clusters Arn(HCl)m and Arn(HF)m.

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

Impact of pyrophosphate and O-ethyl-substituted pyrophosphate groups on DNA structure

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

Interaction of aromatic compounds with xenon: spectroscopic and computational characterization for the cases of p-cresol and toluene

Interaction of phenol with xenon and nitrogen: spectroscopic and computational characterization.

Interactions of Azodicarbonamide (ADA) Species with the Model Zinc Finger Site: Theoretical Support of the Zinc Finger Domain Destruction in the HIV-1 Nucleocapsid Protein (NCp7) by ADA

Intermolecular complexes of HXeOH with water: stabilization and destabilization effects

Interplay between Locally Excited and Charge Transfer States Governs the Photoswitching Mechanism in the Fluorescent Protein Dreiklang

Matrix-isolation study of the phenol–water complex and phenol dimer

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

Mechanism of the chemical step for the guanosine triphosphate (GTP) hydrolysis catalyzed by elongation factor Tu

Mechanism of the myosin catalyzed hydrolysis of ATP as rationalized by molecular modeling

Mechanism of triphosphate hydrolysis in aqueous solution: QM/MM simulations in water clusters

Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires

Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires

Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations

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

Minimum energy reaction profiles for ATP hydrolysis in myosin

Modeling Structure and Absorption Spectra of the Bacteriophytochrome-Based Fluorescent Protein IFP1.4

Modeling negative ion defect migration through the gramicidin A channel

Modeling photoabsorption of the asFP595 chromophore.

Modeling reactivation of the phosphorylated human butyrylcholinesterase by QM(DFTB)/MM calculations

Modeling spectral tuning in monomeric teal fluorescent protein mTFP1

Modeling the Complete Catalytic Cycle of Aspartoacylase.

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

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

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

Molecular Dynamics of Surface-Moving Thermally Driven Nanocars

Molecular Modeling Clarifies the Mechanism of Chromophore Maturation in the Green Fluorescent Protein.

Molecular Modeling the Reaction Mechanism of Serine-Carboxyl Peptidases.

Molecular modeling evidence for His438 flip in the mechanism of butyrylcholinesterase hysteretic behavior.

Molecular models predict light-induced glutamine tautomerization in BLUF photoreceptors

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

Novel flavin-based fluorescent proteins with red-shifted emission bands: a computational study

On photoabsorption of the neutral form of the green fluorescent protein chromophore

On quantum mechanical – molecular mechanical (QM/MM) approaches to model hydrolysis of acetylcholine by acetylcholinesterase

Opening the Arg-Glu salt bridge in myosin: computational study.

Optimization of Cholinesterase-Based Catalytic Bioscavengers Against Organophosphorus Agents.