Molecular dynamics and experimental study of structural behavior of alcohol dehydrogenase enzyme on graphitic sorbent surfaces: orientational features of titratable amino acid residues

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Abstract

The identification of the characteristic structural conformations of enzymes and proteins, especially key titratable amino acids, may become a necessary stage of further research in the implementation of natural and computational experiments, which are carried out by varying the pH values, charges and concentrations of the water-salt environment. In this work, computer molecular dynamics (MD) and experimental studies of the enzyme alcohol dehydrogenase and its cofactor (ADH+NAD) solvated with water on a graphite carbon surface are carried out. The snapshots of the adsorption process of ADH+NAD on the surface of a graphitic carbon surface during long-term 100 nanosecond dynamical conformational and rotational changes are obtained. The MD-analysis provides mapping of the ADH+NAD enzyme orientation adsorption, thereby allowing for the detailed observation of changes in protein conformation in the region of titratable amino acid residues of ADH. Next, based on an extension of the MD-model implementation, the mechanism of conformational changes in the entire system (ADH+NAD + water / graphitic carbon surface), as well as the orientation adsorption of the entire protein system along with key titratable amino acids are considered and the MD simulation data are compared with the experimental observations.

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About the authors

I. A. Baigunov

Dubna State University

Email: kholmirzo@gmail.com

Department of Chemistry, New Technologies and Materials

Russian Federation, Dubna, Moscow Region, 141980

P. P. Gladyshev

Dubna State University

Email: kholmirzo@gmail.com

Department of Chemistry, New Technologies and Materials

Russian Federation, Dubna, Moscow Region, 141980

Kh. T. Kholmurodov

Dubna State University; Joint Institute for Nuclear Research; Lomonosov Moscow State University
S. U. Umarov Physical-Technical Institute (PhTI)

Author for correspondence.
Email: kholmirzo@gmail.com

Department of Chemistry, New Technologies and Materials, Frank Laboratory of Neutron Physics, Faculty of Physics, Department of Fundamental Nuclear Interactions

Russian Federation, Dubna, Moscow Region, 141980; Dubna, Moscow Region, 141980; Moscow, 119991; Dushanbe, 734063, Republic of Tajikistan

H. Elhaes

Ain Shams University

Email: kholmirzo@gmail.com

Physics Department, Faculty of Women for Arts, Science and Education

Egypt, Cairo, 11757

M. Ibrahim

National Research Centre

Email: kholmirzo@gmail.com

Molecular Spectroscopy and Modeling Unit, Spectroscopy Department

Egypt, Dokki, Giza, 12622

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Supplementary files

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2. Fig. 1. Methods of immobilization of enzyme-cofactor systems on conductive carriers.

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3. Fig. 2. Crystal structure of the alcohol dehydrogenase (ADH) complex. The coordinate system (blue, red and green arrows) was introduced with the subsequent purpose of studying the molecular dynamics processes of interaction of the ADH molecule with the sorbent surface, determining the most probable direction of orientation and the place of adsorption of ADH on the surface (see below). The arrows are directed from the center of ADH to the region containing titratable amino acids sensitive to changes in the pH values ​​of the solution, towards the catalytic gaps and substrate centers.

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4. Fig. 3. Dependence of the degree of protonation (F) on the pH of the solution.

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5. Fig. 4. Dependences of the energy of electrostatic interaction of ADH (alcohol dehydrogenase) with a positively charged surface on the angle of rotation of the globule around its axis passing through the center of mass along the maximum size of the globule, and the pH of the solution (Z is the total charge of the globule).

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6. Fig. 5. General molecular design of the system ADH + NAD + water + graphite carbon surface: a – atomic-molecular structure of the enzyme ADH + surface; b – sheet “ribbon” structure of ADH + surface; c – atomic-molecular structure of the system ADH + surface + water.

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7. Fig. 6. General molecular design of the system ADH + NAD + water + graphite carbon surface: a – atomic-molecular structure of the system ADH + surface + water; b – section of the structure ADH + surface + water; c – structure of the system ADH + surface + water.

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8. Fig. 7. Comparison of the orientation of ADH with titratable amino acid residues ASP54, HIS252, ASP268 in the initial (a) state of the ADH molecule (t = 0), t = 10 (b) and 20 ns (c) in relaxed states.

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9. Fig. 8. Comparison of the orientation of ADH with titratable amino acid residues ASP54 (a), HIS252 (b), ASP268 (c) at t = 0, 10 and 20 ns in the relaxed state.

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10. Fig. 9. Details of the orientation of the titratable amino acid residue HIS252 are shown at t = 0, 10 and 20 ns in relaxed states; side (a) and top (b) views are shown from left to right.

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11. Fig. 10. Adsorption of ADH + NAD on graphitic carbon (C-surface) for 100 ns, dynamic and conformational changes: a – initially relaxed state; b – intermediate and c – final equilibrium states.

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12. Fig. 11. Results of MD calculations for the dependence on the ADH + NAD/C-surface distance of the three above-mentioned titratable amino acid residues – ASP54 (a), HIS252 (b) and ASP268 (c) in the initial relaxed state.

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13. Fig. 12. The initial and resulting positions of ADH + NAD + water on the C-surface change dynamically and orientationally over 100 ns. The spatial positions of ADH + NAD on the C-surface are shown for the initially relaxed state (a) and the final adsorbing position of the molecule in the final state t = 100 ns (b).

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14. Fig. 13. Results of MD calculation for the dependence on the ADH + NAD/C-surface distance of the three above-mentioned titratable amino acid residues – ASP54 (a), HIS252 (b) and ASP268 (c) in the final state (t = 100 ns).

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15. Fig. 14. Behavior of the catalytic loops of the enzyme during the adsorption of ADH + NAD on the graphite carbon surface for the initial relaxed state (a), intermediate (b) and final equilibrium state for 100 ns (c); left – side view, right – top view.

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