CMSP Seminar IN PERSON (Atomistic Simulation Seminar Series) 29 June at 11:00, Prof. Narayan Prasad Adhikari

[CMSP Seminars Secretariat]

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Atomistic Simulation Seminar Series
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IN PERSON: Luigi Stasi Seminar Room (Leonardo Building, 2nd floor)

Also via Zoom. Link to advance registration: 
https://zoom.us/meeting/register/tJ0kd-2orDgpE9RZuPjTzuUYdrlCqVSP6MYl

** * * **Wednesday, 29 June 2022 at 11:00**CET* * **

Speaker: *Narayan Prasad Adhikari *(Central Department of Physics 
Tribhuvan, University Kathmandu)

Title:** *Repair Mechanism of AGT for Methyl-induced DNA Damage* *
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Abstract:
O6-alkylguanine-DNA alkyltransferase (AGT) is considered a demethylation 
agent of the methylated DNA. We model two catalytic states of AGT-DNA 
interactions and an AGT-DNA covalent complex and explore structural 
features using molecular dynamics (MD) simulations. The umbrella 
sampling method is used to investigate the changes in the free energy of 
the interactions in two different AGT-DNA catalytic states, one with 
methylated GUA in DNA and the other with methylated CYS145 in AGT. These 
non-covalent complexes represent the pre- and post-repair complexes. 
Therefore, our study encompasses the process of recognition, complex 
formation, and separation of the AGT and the damaged (methylated) DNA 
base. The use of parameters for the amino acid and nucleotide 
modifications and for the protein-DNA covalent bond will allow 
investigations of the DNA repair mechanism. Further, we discuss the 
binding mechanism of SARS/SARS-CoV 2 spike protein with human protein.

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CMSP, Condensed Matter & Statistical Physics Section
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The Abdus Salam International Centre for Theoretical Physics
https://www.ictp.it/

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