Alexander V. Nemukhin - Publications

Affiliations: 
Chemistry Moscow State 

64 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Khrenova MG, Tsirelson VG, Nemukhin AV. Dynamical properties of enzyme-substrate complexes disclose substrate specificity of the SARS-CoV-2 main protease as characterized by the electron density descriptors. Physical Chemistry Chemical Physics : Pccp. 22: 19069-19079. PMID 32812956 DOI: 10.1039/d0cp03560b  0.6
2020 Polyakov IV, Kniga AE, Grigorenko BL, Nemukhin AV. Structure of the Brain -Acetylaspartate Biosynthetic Enzyme NAT8L Revealed by Computer Modeling. Acs Chemical Neuroscience. 11: 2296-2302. PMID 32639720 DOI: 10.1021/acschemneuro.0c00250  0.76
2020 Khrenova MG, Kulakova AM, Nemukhin AV. Proof of concept for poor inhibitor binding and efficient formation of covalent adducts of KRAS and ARS compounds. Organic & Biomolecular Chemistry. 18: 3069-3081. PMID 32101243 DOI: 10.1039/d0ob00071j  0.6
2019 Grigorenko BL, Polyakov IV, Krylov AI, Nemukhin AV. Computational Modeling Reveals the Mechanism of Fluorescent State Recovery in the Reversibly Photoswitchable Protein Dreiklang. The Journal of Physical Chemistry. B. PMID 31574224 DOI: 10.1021/acs.jpcb.9b06988  0.76
2019 Nemukhin AV, Grigorenko BL, Khrenova MG, Krylov AI. Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes. The Journal of Physical Chemistry. B. PMID 31042385 DOI: 10.1021/acs.jpcb.9b00591  0.76
2019 Grigorenko BL, Kots ED, Nemukhin AV. Diversity of mechanisms in Ras-GAP catalysis of guanosine triphosphate hydrolysis revealed by molecular modeling. Organic & Biomolecular Chemistry. 17: 4879-4891. PMID 31041977 DOI: 10.1039/c9ob00463g  0.76
2019 Grigorenko BL, Novichkova DA, Lushchekina SV, Zueva IV, Schopfer LM, Nemukhin AV, Varfolomeev SD, Lockridge O, Masson P. Computer-designed active human butyrylcholinesterase double mutant with a new catalytic triad. Chemico-Biological Interactions. PMID 31009643 DOI: 10.1016/j.cbi.2019.04.019  0.76
2019 Kots ED, Khrenova MG, Nemukhin AV. Allosteric Control of N-Acetyl-Aspartate Hydrolysis by the Y231C and F295S Mutants of Human Aspartoacylase. Journal of Chemical Information and Modeling. 59: 2299-2308. PMID 30431265 DOI: 10.1021/acs.jcim.8b00666  0.6
2019 Meteleshko YI, Nemukhin AV, Khrenova MG. Novel flavin-based fluorescent proteins with red-shifted emission bands: a computational study. Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society For Photobiology. 18: 177-189. PMID 30403258 DOI: 10.1039/c8pp00361k  0.6
2018 Khrenova MG, Kulakova AM, Nemukhin AV. Competition between two cysteines in covalent binding of biliverdin to phytochrome domains. Organic & Biomolecular Chemistry. 16: 7518-7529. PMID 30276392 DOI: 10.1039/c8ob02262c  0.6
2018 Grigorenko BL, Khrenova MG, Nemukhin AV. Amide-imide tautomerization in the glutamine side chain in enzymatic and photochemical reactions in proteins. Physical Chemistry Chemical Physics : Pccp. 20: 23827-23836. PMID 30202846 DOI: 10.1039/c8cp04817g  0.76
2018 Lushchekina SV, Schopfer LM, Grigorenko BL, Nemukhin AV, Varfolomeev SD, Lockridge O, Masson P. Optimization of Cholinesterase-Based Catalytic Bioscavengers Against Organophosphorus Agents. Frontiers in Pharmacology. 9: 211. PMID 29593539 DOI: 10.3389/fphar.2018.00211  0.76
2018 Khrenova MG, Nemukhin AV. Modeling the Transient Kinetics of the L1 Metallo-β-Lactamase. The Journal of Physical Chemistry. B. 122: 1378-1386. PMID 29298481 DOI: 10.1021/acs.jpcb.7b10188  0.6
2017 Khrenova MG, Polyakov IV, Grigorenko BL, Krylov AI, Nemukhin AV. Improving the Design of the Triple-Decker Motif in Red Fluorescent Proteins. The Journal of Physical Chemistry. B. PMID 29090574 DOI: 10.1021/acs.jpcb.7b07517  0.76
2017 Khrenova MG, Meteleshko YI, Nemukhin AV. Mutants of the Flavoprotein iLOV as Prospective Red-Shifted Fluorescent Markers. The Journal of Physical Chemistry. B. 121: 10018-10025. PMID 28992704 DOI: 10.1021/acs.jpcb.7b07533  0.6
2017 Khrenova MG, Kots ED, Varfolomeev SD, Lushchekina SV, Nemukhin AV. Three Faces of N-Acetylaspartate: Activator, Substrate, and Inhibitor of Human Aspartoacylase. The Journal of Physical Chemistry. B. 121: 9389-9397. PMID 28903559 DOI: 10.1021/acs.jpcb.7b08759  0.6
2017 Grigorenko BL, Krylov AI, Nemukhin AV. Molecular modeling clarifies the mechanism of chromophore maturation in the green fluorescent protein. Journal of the American Chemical Society. PMID 28675933 DOI: 10.1021/jacs.7b00676  0.76
2016 Acharya A, Bogdanov AM, Grigorenko BL, Bravaya KB, Nemukhin AV, Lukyanov KA, Krylov AI. Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing? Chemical Reviews. PMID 27754659 DOI: 10.1021/acs.chemrev.6b00238  0.76
2016 Grigorenko BL, Knyazeva MA, Nemukhin AV. Analysis of proton wires in the enzyme active site suggests a mechanism of c-di-GMP hydrolysis by the EAL domain phosphodiesterases. Proteins. 84: 1670-1680. PMID 27479508 DOI: 10.1002/prot.25108  0.76
2016 Khrenova MG, Grigorenko BL, Nemukhin AV. Theoretical vibrational spectroscopy of intermediates and the reaction mechanism of the guanosine triphosphate hydrolysis by the protein complex Ras-GAP. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 166: 68-72. PMID 27214270 DOI: 10.1016/j.saa.2016.04.056  0.76
2016 Vasilevskaya T, Khrenova MG, Nemukhin AV, Thiel W. Methodological aspects of QM/MM calculations: A case study on matrix metalloproteinase-2. Journal of Computational Chemistry. PMID 27140531 DOI: 10.1002/jcc.24395  0.6
2016 Kots ED, Khrenova MG, Lushchekina SV, Varfolomeev SD, Grigorenko BL, Nemukhin AV. Modeling the Complete Catalytic Cycle of Aspartoacylase. The Journal of Physical Chemistry. B. 120: 4221-31. PMID 27089954 DOI: 10.1021/acs.jpcb.6b02542  0.76
2016 Khrenova MG, Kots ED, Nemukhin AV. Reaction Mechanism of Guanosine Triphosphate Hydrolysis by the Vision-Related Protein Complex Arl3-RP2. The Journal of Physical Chemistry. B. 120: 3873-9. PMID 27043216 DOI: 10.1021/acs.jpcb.6b03363  0.6
2015 Khrenova MG, Grigorenko BL, Kolomeisky AB, Nemukhin AV. Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme. The Journal of Physical Chemistry. B. 119: 12838-45. PMID 26374425 DOI: 10.1021/acs.jpcb.5b07238  0.76
2015 Khrenova MG, Grigorenko BL, Mironov VA, Nemukhin AV. Why does mutation of Gln61 in Ras by the nitro analog NGln maintain activity of Ras-GAP in hydrolysis of guanosine triphosphate? Proteins. 83: 2091-9. PMID 26370130 DOI: 10.1002/prot.24927  0.76
2015 Vasilevskaya T, Khrenova MG, Nemukhin AV, Thiel W. Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling. Journal of Computational Chemistry. 36: 1621-30. PMID 26132652 DOI: 10.1002/jcc.23977  0.76
2015 Grigorenko BL, Nemukhin AV, Polyakov IV, Khrenova MG, Krylov AI. A Light-Induced Reaction with Oxygen Leads to Chromophore Decomposition and Irreversible Photobleaching in GFP-Type Proteins. The Journal of Physical Chemistry. B. 119: 5444-52. PMID 25867185 DOI: 10.1021/acs.jpcb.5b02271  0.76
2015 Khrenova MG, Nemukhin AV, Domratcheva T. Theoretical Characterization of the Flavin-Based Fluorescent Protein iLOV and its Q489K Mutant. The Journal of Physical Chemistry. B. 119: 5176-83. PMID 25830816 DOI: 10.1021/acs.jpcb.5b01299  0.6
2015 Mironov VA, Khrenova MG, Lychko LA, Nemukhin AV. Computational characterization of the chemical step in the GTP hydrolysis by Ras-GAP for the wild-type and G13V mutated Ras. Proteins. 83: 1046-53. PMID 25820867 DOI: 10.1002/prot.24802  0.6
2015 Mironov VA, Bravaya KB, Nemukhin AV. Role of zwitterions in kindling fluorescent protein photochemistry. The Journal of Physical Chemistry. B. 119: 2467-74. PMID 25365115 DOI: 10.1021/jp5075219  0.76
2014 Khrenova MG, Savitsky AP, Topol IA, Nemukhin AV. Exploration of the zinc finger motif in controlling activity of matrix metalloproteinases. The Journal of Physical Chemistry. B. 118: 13505-12. PMID 25375834 DOI: 10.1021/jp5088702  0.6
2014 Khrenova MG, Mironov VA, Grigorenko BL, Nemukhin AV. Modeling the role of G12V and G13V Ras mutations in the Ras-GAP-catalyzed hydrolysis reaction of guanosine triphosphate. Biochemistry. 53: 7093-9. PMID 25339142 DOI: 10.1021/bi5011333  0.76
2014 Khrenova MG, Nemukhin AV, Grigorenko BL, Wang P, Zhang JP. All-atom structures and calcium binding sites of the bacterial photosynthetic LH1-RC core complex from Thermochromatium tepidum. Journal of Molecular Modeling. 20: 2287. PMID 24852455 DOI: 10.1007/s00894-014-2287-4  0.76
2014 Khrenova MG, Nemukhin AV, Savitsky AP. Computational characterization of ketone-ketal transformations at the active site of matrix metalloproteinases. The Journal of Physical Chemistry. B. 118: 4345-50. PMID 24684684 DOI: 10.1021/jp501674b  0.6
2013 Grigorenko BL, Nemukhin AV, Polyakov IV, Krylov AI. Triple-Decker Motif for Red-Shifted Fluorescent Protein Mutants. The Journal of Physical Chemistry Letters. 4: 1743-7. PMID 26282988 DOI: 10.1021/jz4006288  0.76
2013 Mironov VA, Khrenova MG, Grigorenko BL, Savitsky AP, Nemukhin AV. Thermal isomerization of the chromoprotein asFP595 and its kindling mutant A143G: QM/MM molecular dynamics simulations. The Journal of Physical Chemistry. B. 117: 13507-14. PMID 24079704 DOI: 10.1021/jp407406k  0.76
2013 Grigorenko BL, Nemukhin AV, Polyakov IV, Morozov DI, Krylov AI. First-principles characterization of the energy landscape and optical spectra of green fluorescent protein along the A→I→B proton transfer route. Journal of the American Chemical Society. 135: 11541-9. PMID 23837665 DOI: 10.1021/ja402472y  0.76
2013 Grigorenko BL, Polyakov IV, Savitsky AP, Nemukhin AV. Unusual emitting states of the kindling fluorescent protein: appearance of the cationic chromophore in the GFP family. The Journal of Physical Chemistry. B. 117: 7228-34. PMID 23697758 DOI: 10.1021/jp402149q  0.76
2013 Nemukhin AV, Grigorenko BL, Morozov DI, Kochetov MS, Lushchekina SV, Varfolomeev SD. On quantum mechanical--molecular mechanical (QM/MM) approaches to model hydrolysis of acetylcholine by acetylcholinesterase. Chemico-Biological Interactions. 203: 51-6. PMID 22982775 DOI: 10.1016/j.cbi.2012.08.027  0.76
2012 Grigorenko BL, Nemukhin AV, Morozov DI, Polyakov IV, Bravaya KB, Krylov AI. Toward Molecular-Level Characterization of Photoinduced Decarboxylation of the Green Fluorescent Protein: Accessibility of the Charge-Transfer States. Journal of Chemical Theory and Computation. 8: 1912-20. PMID 26593825 DOI: 10.1021/ct300043e  0.76
2012 Laurent AD, Mironov VA, Chapagain PP, Nemukhin AV, Krylov AI. Exploring structural and optical properties of fluorescent proteins by squeezing: modeling high-pressure effects on the mStrawberry and mCherry red fluorescent proteins. The Journal of Physical Chemistry. B. 116: 12426-40. PMID 22988813 DOI: 10.1021/jp3060944  0.76
2012 Savitsky AP, Rusanov AL, Zherdeva VV, Gorodnicheva TV, Khrenova MG, Nemukhin AV. FLIM-FRET Imaging of Caspase-3 Activity in Live Cells Using Pair of Red Fluorescent Proteins. Theranostics. 2: 215-26. PMID 22375160 DOI: 10.7150/thno.3885  0.6
2012 Bravaya KB, Grigorenko BL, Nemukhin AV, Krylov AI. Quantum chemistry behind bioimaging: insights from ab initio studies of fluorescent proteins and their chromophores. Accounts of Chemical Research. 45: 265-75. PMID 21882809 DOI: 10.1021/ar2001556  0.76
2011 Grigorenko BL, Kaliman IA, Nemukhin AV. Minimum energy reaction profiles for ATP hydrolysis in myosin. Journal of Molecular Graphics & Modelling. 31: 1-4. PMID 21839658 DOI: 10.1016/j.jmgm.2011.07.005  0.76
2011 Rusanov AL, Mironov VA, Goryashenko AS, Grigorenko BL, Nemukhin AV, Savitsky AP. Conformational partitioning in pH-induced fluorescence of the kindling fluorescent protein (KFP). The Journal of Physical Chemistry. B. 115: 9195-201. PMID 21671654 DOI: 10.1021/jp1094245  0.76
2011 Bravaya KB, Khrenova MG, Grigorenko BL, Nemukhin AV, Krylov AI. Effect of protein environment on electronically excited and ionized states of the green fluorescent protein chromophore. The Journal of Physical Chemistry. B. 115: 8296-303. PMID 21591720 DOI: 10.1021/jp2020269  0.76
2011 Khrenova MG, Domratcheva T, Schlichting I, Grigorenko BL, Nemukhin AV. Computational characterization of reaction intermediates in the photocycle of the sensory domain of the AppA blue light photoreceptor. Photochemistry and Photobiology. 87: 564-73. PMID 21155828 DOI: 10.1111/j.1751-1097.2010.00861.x  0.76
2010 Konyukhov SS, Kupchenko IV, Moskovsky AA, Nemukhin AV, Akimov AV, Kolomeisky AB. Rigid-Body Molecular Dynamics of Fullerene-Based Nanocars on Metallic Surfaces. Journal of Chemical Theory and Computation. 6: 2581-90. PMID 26616062 DOI: 10.1021/ct100101y  0.64
2010 Lushchekina SV, Nemukhin AV, Morozov DI, Varfolomeev SD. Correlation between the substrate structure and the rate of acetylcholinesterase hydrolysis modeled with the combined quantum mechanical/molecular mechanical studies. Chemico-Biological Interactions. 187: 59-63. PMID 20398640 DOI: 10.1016/j.cbi.2010.04.005  0.48
2009 Rocha-Rinza T, Christiansen O, Rajput J, Gopalan A, Rahbek DB, Andersen LH, Bochenkova AV, Granovsky AA, Bravaya KB, Nemukhin AV, Christiansen KL, Nielsen MB. Gas phase absorption studies of photoactive yellow protein chromophore derivatives. The Journal of Physical Chemistry. A. 113: 9442-9. PMID 19642665 DOI: 10.1021/jp904660w  0.76
2009 Nemukhin AV, Kaliman IA, Moskovsky AA. Modeling negative ion defect migration through the gramicidin A channel. Journal of Molecular Modeling. 15: 1009-12. PMID 19198898 DOI: 10.1007/s00894-009-0463-8  0.64
2008 Akimov AV, Nemukhin AV, Moskovsky AA, Kolomeisky AB, Tour JM. Molecular Dynamics of Surface-Moving Thermally Driven Nanocars. Journal of Chemical Theory and Computation. 4: 652-6. PMID 26620940 DOI: 10.1021/ct7002594  0.64
2008 Bravaya KB, Bochenkova AV, Granovsky AA, Savitsky AP, Nemukhin AV. Modeling photoabsorption of the asFP595 chromophore. The Journal of Physical Chemistry. A. 112: 8804-10. PMID 18729441 DOI: 10.1021/jp804183w  0.76
2008 Nemukhin AV, Lushchekina SV, Bochenkova AV, Golubeva AA, Varfolomeev SD. Characterization of a complete cycle of acetylcholinesterase catalysis by ab initio QM/MM modeling. Journal of Molecular Modeling. 14: 409-16. PMID 18343962 DOI: 10.1007/s00894-008-0287-y  0.76
2008 Domratcheva T, Grigorenko BL, Schlichting I, Nemukhin AV. Molecular models predict light-induced glutamine tautomerization in BLUF photoreceptors. Biophysical Journal. 94: 3872-9. PMID 18263659 DOI: 10.1529/biophysj.107.124172  0.76
2007 Pehkonen S, Marushkevich K, Khriachtchev L, Räsänen M, Grigorenko BL, Nemukhin AV. Photochemical synthesis of H2O2 from the H2O...O(3P) van der Waals complex: experimental observations in solid krypton and theoretical modeling. The Journal of Physical Chemistry. A. 111: 11444-9. PMID 17948973 DOI: 10.1021/jp075233s  0.76
2007 Grigorenko BL, Rogov AV, Topol IA, Burt SK, Martinez HM, Nemukhin AV. Mechanism of the myosin catalyzed hydrolysis of ATP as rationalized by molecular modeling Proceedings of the National Academy of Sciences of the United States of America. 104: 7057-7061. PMID 17438284 DOI: 10.1073/pnas.0701727104  0.76
2007 Rogacheva MV, Bochenkova AV, Kuznetsova SA, Saparbaev MK, Nemukhin AV. Impact of pyrophosphate and O-ethyl-substituted pyrophosphate groups on DNA structure. The Journal of Physical Chemistry. B. 111: 432-8. PMID 17214495 DOI: 10.1021/jp065947n  0.32
2007 Grigorenko BL, Nemukhin AV, Shadrina MS, Topol IA, Burt SK. Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations. Proteins. 66: 456-66. PMID 17094109 DOI: 10.1002/prot.21228  0.76
2006 Grigorenko BL, Rogov AV, Nemukhin AV. Mechanism of triphosphate hydrolysis in aqueous solution: QM/MM simulations in water clusters. The Journal of Physical Chemistry. B. 110: 4407-12. PMID 16509742 DOI: 10.1021/jp056395w  0.76
2005 Grigorenko BL, Nemukhin AV, Cachau RE, Topol IA, Burt SK. Computational study of a transition state analog of phosphoryl transfer in the Ras-RasGAP complex: AlF(x) versus MgF3-. Journal of Molecular Modeling. 11: 503-8. PMID 16052311 DOI: 10.1007/s00894-005-0259-4  0.76
2005 Grigorenko BL, Nemukhin AV, Topol IA, Cachau RE, Burt SK. QM/MM modeling the Ras-GAP catalyzed hydrolysis of guanosine triphosphate. Proteins. 60: 495-503. PMID 15906320 DOI: 10.1002/prot.20472  0.76
2004 Topol IA, Cachau RE, Nemukhin AV, Grigorenko BL, Burt SK. Quantum chemical modeling of the GTP hydrolysis by the RAS-GAP protein complex. Biochimica Et Biophysica Acta. 1700: 125-36. PMID 15210132 DOI: 10.1016/j.bbapap.2004.04.007  0.76
2002 Nemukhin AV, Grigorenko BL, Khriachtchev L, Tanskanen H, Pettersson M, Räsänen M. Intermolecular complexes of HXeOH with water: stabilization and destabilization effects. Journal of the American Chemical Society. 124: 10706-11. PMID 12207525 DOI: 10.1021/ja0266870  0.76
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