The full list of my
peer-reviewed publications is given
below. Alternatively, it may be
found in my Web
Of Science Author Profile
along with citation metrics and
references to citing papers.
1.
Klinov, S.V., Davydov,
D.R., Lisovskaya, N.P., Tarasov, O.S., and
Kurganov, B.I. (1980) Kinetics of the interaction of
muscle glycogen phosphorylase-B with glycogen. Molecular Biology
[
2. Klinov, S.V., Chebotarieva, N.A., Lissovskaya, N.P., Davydov, D.R., and Kurganov, B.I. (1980) The interaction of muscle glycogen phosphorylase B with glycogen. Biochim. Biophys. Acta 709:91-98.
3.
Davydov,
D.R. and Kurganov, B.I. (1982) Comparative
investigation of the kinetics of the reduction of
cytochrome P-450 by nadph-cytochrome-P-450 reductase
and dithionite. Biochemistry (
4. Archakov, A.I., Borodin, E.A., Davydov, D.R., Karyakin, A.I., and Borovyagin, V.L. (1982) Random distribution of NADPH-specific flavoprotein and cytochrome P-450 in liver microsomes. Biochem. Biophys. Res. Commun. 109:832-840.
5. Davydov, D.R., Karyakin, A.V., Binas, B., Kurganov, B.I., and Archakov, A.I. (1985) Kinetic studies on reduction of cytochromes P-450 and b5 by dithionite. Eur. J. Biochem. 150:155-159.
6. Kanaeva, I.P., Skotselyas, E.D., Turkina, I.F., Petrochenko, E.V., Davydov, D.R., Kondrashin, S.K., Dzuzenova, CH. S., Bachmanova, G.I., and Archakov, A.I. (1987) Reconstitution and catalytic properties of cytochrome P-450 LM2 in soluble system containing monomeric carriers. Biochem. Biophys. Res. Commun. 147:1295-1299.
7.
Khailova, L.S.,
Kurganov, B.I.,
8.
Kariakin, A.V.,
and Davydov, D.R. (1988) Kinetics of the
electron transfer reaction of the monooxygenase
system. Vestnik
Akademii Meditsinskikh Nauk SSSR [Proc. Acad. Med.
Sci., USSR, in Russian] 1:53-62.
9. Kurganov, B.I., Shkarina, T.N., Malakhova, E.A., Davydov, D.R., and Chebotareva, N.A. (1989) Kinetics of soybean lipoxygenase reaction in hydrated reversed micelles. Biochimie 71:573-578.
10. Shkarina, T.N., Malakhova, E.A., Kurganov, B.I., Davydov, D.R., and Chebotareva, N.A. (1989) Kinetics of the action of soybean lipoxygenase in hydrated reversed micelles. Biologicheskie Membrany [Russian] 6:362-371.
11.
Chebotareva,
N.A., Kurganov, B.I, Liubarev, A.E., and Davydov,
D.R. (1990) New approach to the study of binding
of specific ligand by associating enzyme-system:
Interaction of flavin mononucleotide with muscle
glycogen phosphorylase-B. Doklady Akadenii
Nauk SSSR [Proc.
Acad. Sci
12.
Chebotareva,
N.A., Kurganov, B.I., Lyubarev, A.E., Davydov,
D.R., and
13. Kurganov, B.I., Khailova, L.S., and Davydov, D.R. (1991) Kinetics of chemical modification of oligomeric enzymes attended with conformational transitions of subunits. J. Chem. Biochem. Kinetics 1:321-330.
14.
Davydov,
D.R., Darovsky, B.V., Dedinsky, I.R., Kanaeva,
I.P., Bachmanova, G.I., Blinov, V.M., and Archakov,
A.I. (1992) Cytochrome c(Fe2+) as a
competitive inhibitor
of NA
15. Kanaeva, I.P., Nikityuk, O.V., Davydov, D.R., Dedinskii, I.R.; Koen, Y.M.; Kuznetsova, G.P., Skotselyas, E.D., Bachmanova, G.I., and Archakov, A.I. (1992) Comparative study of monomeric reconstituted and membrane microsomal monooxygenase systems of the rabbit liver. II. Kinetic parameters of reductase and monooxygenase reactions. Arch. Biochem. Biophys. 298:403-412.
16. Davydov, D.R., Knyshko, T.V., and Hui Bon Hoa, G. (1992) High pressure induced inactivation of ferrous cytochrome P-450 LM2 (IIB4) CO-complex: Evidence for the presence of two conformers in the oligomer. Biochem. Biophys. Res. Commun. 188:216-221.
17.
Davydov,
D.R., Erlikh,
18. Jung, C., Hui Bon Hoa, G., Davydov, D.R., Gill, E., and Heremans, K. (1995) Compressibility of the heme pocket of substrate analogue complexes of cytochrome P-450cam-CO - The effect of hydrostatic pressure on the Soret band. Eur. J. Biochem. 233:600-606.
19. Davydov, D.R., Deprez, E., Hui Bon Hoa, G., Knyushko, T.V., Kuznetsova, G.P., Koen, Y.M., and Archakov, A.I. (1995) High-pressure-induced transitions in microsomal cytochrome P450 2B4 in solution: Evidence for conformational inhomogeneity in the oligomers. Arch. Biochem. Biophys. 320:330-344.
20. Renaud, J.-P., Davydov, D.R., Heirwegh, K.P.M., Mansuy, D., and Hui Bon Hoa, G. (1996) Thermodynamic studies of substrate binding and spin transitions in human cytochrome P450 3A4 expressed in yeast microsomes. Biochem. J., 319:675-681.
21.
Davydov,
D.R., Knyushko, T.V., Kanaeva, I.P., Koen, Y.M.,
Samenkova, N.F., Archakov, A.I., and Hui Bon Hoa, G.
(1996) Interactions of cytochrome P450 2B4 with
NADPH-cytochrome P450 reductase studied by fluorescent
probe - Biochime,
78:734-743.
22. Davydov, D.R., Hui Bon Hoa, G. and Peterson, J.A. (1999) Dynamics of protein-bound water in the heme domain of P450BM3 studied by high-pressure spectroscopy: Comparison with P450cam and P450 2B4. Biochemistry 38:751-761.
23. Davydov, D.R., Kariakin, A.A., Petushkova, N.A., and Peterson, J.A. (2000) Association of cytochromes P450 with their reductases: opposite sign of the electrostatic interactions in P450 BM-3 as compared with the microsomal 2B4 system. Biochemistry 39:6489-6497.
24. Davydov, D.R., Petushkova, N.A., Archakov, A.I., and Hui Bon Hoa, G. (2000) Stabilization of P450 2B4 by its association with P450 1A2 revealed by high-pressure spectroscopy. Biochem. Biophys. Res. Commun. 276:1005-1012.
25. Davydov, D.R. (2001) Microsomal monooxygenase in apoptosis: another target for cytochrome c signaling? Trends Biochem. Sci., 26:155-161.
26.
Davydov,
D.R., Petushkova, N.A., Bobrovnikova, E.V.,
Knyushko, T.V., and Dansette, P. (2001) Association of
cytochromes P450 1A2 and 2B4: are the interactions
between different P450 species involved in the control
of the monooxygenase activity and coupling? Adv. Exp. Med.
Biol. 500:335-338. 
27. Davydov, D.R., Kumar, S., and Halpert, J.R. (2002) Allosteric mechanisms in P450eryF probed with 1-pyrenebutanol, a novel fluorescent substrate. Biochem Biophys Res. Commun. 294:806-812.
28. Kariakin,
A., Davydov, D., Peterson, J.A., and Jung,
C. (2002) A new approach to the study of
protein-protein interaction by FTIR: Complex
formation between cytochrome P450BM3 heme domain
and
29.
Davydov,
D.R., Halpert, J.R., Renaud J.-P., Hui Bon Hoa,
G. (2003) Conformational heterogeneity of cytochrome
P450 3A4 revealed by high-pressure spectroscopy. Biochem.Biophys.Res.Commun.,312,121-130.
30. Zangar, R. C., Davydov, D.R., Verma, S. (2004) Mechanisms that regulate production of reactive oxygen species by cytochrome P450 Toxicology & Applied Pharmacology, 119, 316-334
31. Davydov, D.R., Botchkareva AE., Kumar S., He YQ., and Halpert JR. (2004) An Electrostatically Driven Conformational Transition Is Involved in the Mechanisms of Substrate Binding and Cooperativity in Cytochrome P450eryF. Biochemistry. 43(21):6475-85.
32. Davydov, D.R., Botchkareva E.B., Davydova N.E., Halpert J.R. (2005) Resolution of Two Substrate-Binding Sites in an Engineered Cytochrome P450eryF Bearing a Fluorescent Probe. Biophys. J., 89(1):418-432
33. Kumar, S.; Davydov, D.R.; and Halpert, J.R. (2005) Role of Cytochrome b5 in modulating peroxide-supported CYP3A4 activity: evidence for a conformational transition and P450 heterogeneity. Drug Metab. Disp., 33(8):1131-1136.
34. Davydov, D.R.; Fernando, H.; Baas, B.J.; Sligar, S.G.; Halpert, J.R. (2005) Kinetics of dithionite-dependent reduction of cytochrome P450 3A4:Heterogeneity of the enzyme caused by its oligomerization. Biochemistry, 44(42):13902-13913
35. Davydov, D.R.; Fernando, H.; Halpert, J.R. (2006) Variable path length and counter-flow continuous variation methods for the study of the formation of high-affinity complexes by absorbance spectroscopy. An application to the studies of substrate binding in cytochrome P450. Biophys. Chem., 123, 95-101.
36. Fernando, H.; Halpert, J.R.; Davydov, D.R. (2006) Resolution of multiple substrate binding sites in cytochrome P450 3A4: The stoichiometry of the enzyme-substrate complexes probed by FRET and Job's titration. Biochemistry, 45 (13), 4199-4209.
37. Tsalkova, T.N., Davydova, N.E., Halpert, J.R., Davydov, D.R. (2007) Mechanism of interactions of alpha-naphthoflavone with cytochrome P450 3A4 explored with an engineered enzyme bearing a fluorescent probe. Biochemistry, 46 (1), 106-119
38. Fernando, H., Davydov, D.R., Chin, C. C., and Halpert, J. R. (2007) Role of subunit interactions in P450 oligomers in the loss of homotropic cooperativity in the cytochrome P450 3A4 mutant L211F/D214E/F304W, Arch. Biochem. Biophys. 460, 129-140.
39. Davydov, D.R., Baas, B.J., Sligar, S.G., Halpert, J.R. (2007) Allosteric mechanisms in cytochrome P450 3A4 studied by high-pressure spectroscopy: pivotal role of substrate-induced changes in the accessibility and degree of hydration of the heme pocket. Biochemistry 46, 7852-7864
40. Fernando, H., Halpert, J.H., Davydov, D.R. (2007) Kinetics of electron transfer in the complex of cytochrome P450 3A4 with the flavin domain of cytochrome P450BM-3 as evidence of functional heterogeneity of the heme protein. Arch. Biochem. Biophys. 471, 20–31
41. Davydov, D.R.; Davydova, N.Y.; Tsalkova, T.N.; Halpert, J.R. (2008) Effect of glutathione on homo- and heterotropic cooperativity in cytochrome P450 3A4 – Arch. Biochem. Biophys., 471 (2), 134-145.
42. Davydov, D.R.; Davydova, N.Y.; Halpert, J.R.; Davydova N. Y.; Halpert, J. R. (2008) Allosteric transitions in cytochrome P450eryF explored with pressure-perturbation spectroscopy, lifetime FRET, and a novel fluorescent substrate, Fluorol-7GA - Biochemistry, 47 (43), 11348-11359.
43. Davydov, D.R.; Halpert, J.R. (2008) Allosteric P450 mechanisms: multiple binding sites, multiple conformers or both? - Expert Opinion Drug Metab. Toxicol., 4 (2), 1523-1535.
44. Davydov, D.R.; Sineva, E.V.; Sistla, S.; Davydova, N.Y.; Frank, D.J.; Sligar, S.G.; Halpert, J.R. (2010) Electron transfer in the complex of membrane-bound human cytochrome P450 3A4 with the flavin domain of P450BM-3: The effect of oligomerization of the heme protein and intermittent modulation of the spin equilibrium - Biochim. Biophys. Acta Bioenergetics, 1797 (3), 378-390
45. Sineva, E.V.; Davydov, D.R. (2010) Cytochrome P450 from Photobacterium profundum SS9, a piezophilic bacterium, exhibits tightenedcontrol of water access to the active site - Biochemistry, 49 (50), 10636-10646.
46. Sineva, E.V.; Davydov, D.R. (2010) Constrained water access to the active site of cytochrome P450 from the piezophilic bacterium Photobacterium profundum – High Pressure Res., 30 (4), 466-474.
47. Talakad, J.C.; Wilderman, P.R.; Davydov, D.R.; Kumar, S.; Halpert, J.R. (2010) Rational engineering of cytochromes P450 2B6 and 2B11 for enhanced stability: Insights into structural importance of residue 334 - Arch. Biochem. Biophys., 494 (2), 151-158.
48. Davydov, D.R. (2011) Microsomal monooxygenase as a multienzyme system: the role of P450-P450 interactions - Expert Opinion Drug Metabolism and Toxicology, 7 (5), 543-558.
49. Fernando, H.; Rumfeldt, J.A.O.; Davydova, N.Y.; Halpert, J.R.; Davydov, D.R. ( 2011) Multiple substrate-binding sites are retained in cytochrome P450 3A4 mutants with decreased cooperativity - Xenobiotica, 41 (4), 281-289.
50. Davydov, D.R.; Rumfeldt, J.A.O.; Sineva, E.V.; Fernando, H.; Davydova, N.Y.; Halpert, J.R. (2012) Peripheral ligand-binding site in cytochrome P450 3A4 located with fluorescence resonance energy transfer (FRET) - J. Biol. Chem., 287 (9), 6797-6809.
51.
Davydov,
D.R. (2012) Merging thermodynamics and
evolution: how the studies of high-pressure adaptation
may help to understand enzymatic mechanisms
(editorial) - J.
Thermodynam. Cat., 3, e110 (doi:
10.4172/2157-7544.1000e110).
52. Davydov, D.R., Sligar S.G. (2013) In memoriam of Bill Peterson (editorial) - Biotechnology and Applied Biochemistry, 60 (1), 2-3
53.
Davydov,
D.R.; Sineva, E.V.; Davydova, N.Y.; Bartlett,
D.H.; Halpert, J.R. (2013) CYP261 enzymes from deep
sea bacteria: a clue to conformational heterogeneity
in cytochromes P450. Biotechnology
and Applied Biochemistry, 60 (1) 30-40.
54.
Davydov,
D.R.; Ponomarev, G.V.; Bobrovnikova-Marjon, E.;
55. Davydov, D.R., Davydova, N. Y., Sineva, E. V., Kufareva, I. and Halpert, J. R. (2013) Pivotal role of P450–P450 interactions in CYP3A4 allostery: the case of α-naphthoflavone. - Biochem. J. 453 (2), 219-230
56. Sineva, E.V., Rumfeldt, J.A.O., Halpert, J.R., and Davydov, D.R. (2013) A large-scale allosteric transition in cytochrome P450 3A4 revealed by luminescence resonance energy transfer (LRET) PLOS One, 8 (12), e83898 (DOI: 10.1371/journal.pone.0083898).
57. Jang, H.H., Davydov, D.R., Lee, G.Y., Yun CH, Halpert J.R. (2014) The role of cytochrome P450 2b6 and 2b4 substrate access channel residues predicted based on crystal structures of the amlodipine complexes. Arch. Biochem. Biophys., 545, 100–107
58. Muller, C.S., Knehans, T., Davydov, D.R., Bounds, P.L., von Mandach, U., Halpert, J.R., Caflisch, A., Koppenol, W.H. (2015) Concurrent cooperativity and substrate inhibition in the epoxidation of carbamazepine by cytochrome P450 3A4 active site mutants inspired by molecular dynamics simulations. Biochemistry 54(3) 711- 721
59.
Davydov, D.R.,
60.
Davydov, D.R.
(2015) Molecular organization of the microsomal
oxidative system: a new connotation for an old term.
Biochemistry (
61. Davydov, D.R., Yang, Z.Y., Davydova, N., Halpert, J.R., Hubbell, WL (2016) Conformational mobility in cytochrome P450 3A4 explored by pressure-perturbation EPR spectroscopy, Biophys. J., 110 (7), 1485-1498
62.
Davydov,
D.R.,
63.
Rodgers, J.T.,
Davydova, N.Y., Paragas, E.M., Jones, J.P., and Davydov,
D.R. (2018) Kinetic mechanism of time-dependent
inhibition of CYP2D6 by
3,4-methylenedioxymethamphetamine (MDMA): Functional
heterogeneity of the enzyme and the reversibility of
its inactivation. Biochem.
Pharm., 156, 86-98
64. Davydova, N. Y., Dangi, B., Maldonado, M. A., Vavilov, N. E., Zgoda, V. G., and Davydov, D. R. (2019) Toward a systems approach to cytochrome P450 ensemble: interactions of CYP2E1 with other P450 species and their impact on CYP1A2, Biochem J. 476, 3661-3685.
65. Gerringer ME, Yancey PH, Tikhonova OV, Vavilov NE, Zgoda VG, Davydov DR. (2020) Pressure tolerance of deep-sea enzymes can be evolved through increasing volume changes in protein transitions: a study with lactate dehydrogenases from abyssal and hadal fishes. FEBS J., 287, 5394-5410
66. Zhang B, Lewis KM, Abril A, Davydov DR, Vermerris W, Sattler SE, Kang C. (2020). Structure and Function of the Cytochrome P450 Monooxygenase, Cinnamate 4-hydroxylase (C4H1) from Sorghum bicolor. Plant Physiology, 183, 957-973
67. Dangi, B.,
Davydova, N.Y., Vavilov, N.E., Zgoda, V.G. and Davydov,
D.R. (2020) Nonadditivity in Human Microsomal
Drug-Metabolizing Ensemble Revealed with Coumarin-152,
a Polyspecific Cytochrome P450 Substrate, Xenobiotica,
50, 1393-1405
68. Dangi, B.,
Davydova, N. Y., Maldonado, M.A., Abbasi, A., Vavilov,
N. E., Zgoda, V. G. and Davydov, D. R. (2021)
Effects of alcohol-induced increase in CYP2E1 content
in human liver microsomes on the activity and
cooperativity of CYP3A4, Arch.
Biochem. Biophys., 698, 108677
69. Dangi, B.,
Davydova, N. Y., Maldonado, M. A., Ahire, D., Prasad,
B., and Davydov, D. R. (2021) Probing
functional interactions between cytochromes P450 with
principal component analysis of substrate saturation
profiles and targeted proteomics, Arch
Biochem Biophys 708, 108937
70. Davydov, D.R.,
Prasad B. (2021) Assembling the P450 puzzle: on the
sources of nonadditivity in drug metabolism, Trends
Pharm Sci 42, 988-997
71. Davydov, D. R.,
Dangi, B., Yue, G., Ahire, D. S., Prasad, B., and
Zgoda, V. G. (2022) Exploring the Interactome of
Cytochrome P450 2E1 in Human Liver Microsomes with
Chemical Crosslinking Mass Spectrometry, Biomolecules
12, 185
72. Zhang, B.X.; Kang, C.;
Davydov, D.R. (2022) Conformational
Rearrangements in the Redox Cycling of
NADPH-Cytochrome P450 Reductase from Sorghum bicolor
Explored with FRET and Pressure-Perturbation
Spectroscopy. Biology-Basel
2022, 11,
73. Zhang, B.X.;
Munske, G.R.; Timokhin, V.I.; Ralph, J.; Davydov,
D.R.; Vermerris, W.; Sattler, S.E.; Kang, C.
(2022) Functional and structural insight into the
flexibility of cytochrome P450 reductases from Sorghum
bicolor and its implications for lignin composition. J.
Biol. Chem. 2022, 298
74. Davydova, N.Y.;
Hutner, D.A.; Gaither, K.A.; Singh, D.K.; Prasad, B.;
Davydov, D.R. (2023) High-throughput assay of
cytochrome P450-dependent drug demethylation reactions
and Its use to re-evaluate the pathways of ketamine
metabolism. Biology-Basel
2023, 12