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In silico profiling and structural insights of zinc metal ion on O6-methylguanine methyl transferase and its interactions using molecular dynamics approach

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Abstract

O6-methylguanine DNA methyl transferase (MGMT) is a metalloenzyme participating in the repair of alkylated DNA. In this research, we performed a comparative study for evaluating the impact of zinc metal ion on the behavior and interactions of MGMT in the both enzymatic forms of apo MGMT and holo MGMT. DNA and proliferating cell nuclear antigen (PCNA), as partners of MGMT, were utilized to evaluate molecular interactions by virtual microscopy of molecular dynamics simulation. The stability and conformational alterations of each forms (apo and holo) MGMT-PCNA, and (apo and holo) MGMT-DNA complexes were calculated by MM/PBSA method. A total of seven systems including apo MGMT, holo MGMT, free PCNA, apo MGMT-PCNA, holo MGMT-PCNA, apo MGMT–DNA, and holo MGMT-DNA complexes were simulated. In this study, we found that holo MGMT was more stable and had better folding and functional properties than that of apo MGMT. Simulation analysis of (apo and holo) MGMT-PCNA complexes displayed that the sequences of the amino acids involved in the interactions were different in the two forms of MGMT. The important amino acids of holo MGMT involved in its interaction with PCNA included E92, K101, A119, G122, N123, P124, and K125, whereas the important amino acids of apo MGMT included R128, R135, S152, N157, Y158, and L162. Virtual microscopy of molecular dynamics simulation showed that the R128 and its surrounding residues were important amino acids involved in the interaction of holo MGMT with DNA that was exactly consistent with X-ray crystallography structure. In the apo form of the protein, the N157 and its surrounding residues were important amino acids involved in the interaction with DNA. The binding free energies of − 387.976, − 396.226, − 622.227, and − 617.333 kcal/mol were obtained for holo MGMT-PCNA, apo MGMT-PCNA, holo MGMT-DNA, and apo MGMT-DNA complexes, respectively. The principle result of this research was that the area of molecular interactions differed between the two states of MGMT. Therefore, in investigations of metalloproteins, the metal ion must be preserved in their structures. Finally, it is recommended to use the holo form of metalloproteins in in vitro and in silico researches.

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Abbreviations

Apo:

Without Zn

DSSP:

Determine the secondary structure of protein

ED:

Essential dynamics

FEL:

Free energy landscape

Holo:

With Zn

HTH:

Helix Turn Helix

IDCL:

Interdomain connector loop

MD:

Molecular dynamics

MDS:

Molecular dynamics simulation

MGMT:

O6-methylguanine DNA methyl transferase

MM/PBSA:

Molecular mechanics/Poisson Boltzmann surface area

NPT:

Fixed number of particles, pressure, and temperature

NVT:

Fixed number of particles, volume, and temperature

PCA:

Principle component analysis

PCHR:

Proline, Cysteine, Histidine, Arginine

PCNA:

Proliferating cell nuclear antigen

PDB:

Protein Data Bank

PIP:

PCNA-interacting protein

PME:

Particle mesh Ewald

RESP:

Restrained electrostatic potential

Rg:

Radius of gyration

RMSD:

Root mean square deviation

RMSF:

Root mean square fluctuation

SASA:

Solvent accessible surface area

SN1:

The SN1 reactions happen in two steps: 1. The leaving group leaves, and the substrate forms a carbocation intermediate. 2. The nucleophile attacks the carbocation, forming the product

SN2:

The SN2 reaction is a type of nucleophilic substitution reaction mechanism that one bond is broken and one bond is formed synchronously, i.e., in one step

Zn:

Zinc

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Acknowledgments

We are grateful to Dr. Fatemeh Ravari for providing computational chemistry laboratory. We acknowledge the help of Dr. Mohammad Fathabadi for advice in some analysis.

Funding

This is part of a doctoral dissertation and is funded by the researchers themselves.

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Authors and Affiliations

  1. Department of Biochemistry, Neyshabur Branch, Islamic Azad University, Neyshabur, Iran

    Marzieh Gharouni & Jamshid Mehrzad

  2. Department of Chemistry, Isfahan University of Technology, Isfahan, Iran

    Hamid Mosaddeghi

  3. Department of Biology, Mashhad Branch, Islamic Azad University, Mashhad, Iran

    Ali Es-haghi

  4. Department of Chemistry, Neyshabur Branch, Islamic Azad University, Neyshabur, Iran

    Hamid Mosaddeghi & Alireza Motavalizadehkakhky

Authors
  1. Marzieh Gharouni
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  2. Hamid Mosaddeghi
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  3. Jamshid Mehrzad
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  4. Ali Es-haghi
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  5. Alireza Motavalizadehkakhky
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Contributions

The project was designed and directed by Jamshid Mehrzad. Marzieh Gharouni developed the theory and performed the computations. Hamid Mosaddeghi provided guidance in performing computer calculations and data analysis. Ali Es-haghic and Alireza Motavalizadehkakhky were consultants for the entire project. All authors contributed to the writing of the paper.

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Correspondence to Hamid Mosaddeghi or Jamshid Mehrzad.

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Gharouni, M., Mosaddeghi, H., Mehrzad, J. et al. In silico profiling and structural insights of zinc metal ion on O6-methylguanine methyl transferase and its interactions using molecular dynamics approach. J Mol Model 27, 40 (2021). https://doi.org/10.1007/s00894-020-04631-x

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