Comparative Investigation of R213G Mutation in DNA-Binding Domain of P53 Protein via Molecular Dynamics Simulation

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AKBARI ELHAM; TAGHIZADEH MOHAMMAD; Nemati Fahimeh

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Journal: Journal of Health and Biomedical Informatics Year:2021 | Volume:8 | Issue:1 Page(s): 105-116

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Information Journal Paper

Title

Comparative Investigation of R213G Mutation in DNA-Binding Domain of P53 Protein via Molecular Dynamics Simulation

Author(s)

AKBARI ELHAM | TAGHIZADEH MOHAMMAD | Nemati Fahimeh | Issue Writer Certificate

Keywords

Root Mean Square Fluctuation (RMSF)Q1

Protein FlexibilityQ1

P53 ProteinQ1

Missense MutationQ1

Molecular dynamics simulationQ1

Abstract

Introduction: P53 is a tumor suppressor protein with numerous Missense Mutations identified in its gene. These mutations are observed in a vast number of cancers. R213G is one of them which has a role in metastatic lung cancers. In this research, R213G was studied in comparison with the wild type via Molecular dynamics simulation. Method: For the three-dimensional structure of the wild-type P53 Protein, chain A was used from crystallographic structure with PDB ID: 1TSR. For R213G mutation, residue 213 of this structure was changed to glycine. Molecular dynamics simulation was repeated twice for 15 ns using Gromacs 5. 1. 2 software package, AMBER99SB force field, and TIP3P as water model. RMSD, RMSF, radius of gyration, and potential energy analyses were performed on resulted trajectories. Results: RMSF analysis showed that the R213G mutation changes the flexibility of 11 residues including R-248. These residues are not near the mutated position, but all of them are located on 220-250 fragment of this domain or are residues in the neighbor of this fragment. The radius of gyration and potential energy results confirmed a reduction in stability of this protein as a result of this mutation. Conclusion: RMSF analysis of R213G mutation beside the changes in stability and radius indicated that this mutation could greatly affect the P53 interactions with other macromolecules.

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APA: Copy

AKBARI, ELHAM, TAGHIZADEH, MOHAMMAD, & Nemati, Fahimeh. (2021). Comparative Investigation of R213G Mutation in DNA-Binding Domain of P53 Protein via Molecular Dynamics Simulation. JOURNAL OF HEALTH AND BIOMEDICAL INFORMATICS, 8(1 ), 105-116. SID. https://sid.ir/paper/410443/en

Vancouver: Copy

AKBARI ELHAM, TAGHIZADEH MOHAMMAD, Nemati Fahimeh. Comparative Investigation of R213G Mutation in DNA-Binding Domain of P53 Protein via Molecular Dynamics Simulation. JOURNAL OF HEALTH AND BIOMEDICAL INFORMATICS[Internet]. 2021;8(1 ):105-116. Available from: https://sid.ir/paper/410443/en

IEEE: Copy

ELHAM AKBARI, MOHAMMAD TAGHIZADEH, and Fahimeh Nemati, “Comparative Investigation of R213G Mutation in DNA-Binding Domain of P53 Protein via Molecular Dynamics Simulation,” JOURNAL OF HEALTH AND BIOMEDICAL INFORMATICS, vol. 8, no. 1 , pp. 105–116, 2021, [Online]. Available: https://sid.ir/paper/410443/en

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