Bulletin of the American Physical Society
APS March Meeting 2023
Volume 68, Number 3
Las Vegas, Nevada (March 5-10)
Virtual (March 20-22); Time Zone: Pacific Time
Session AA09: V: Molecular Biophysics
5:00 AM–7:00 AM,
Monday, March 20, 2023
Room: Virtual Room 9
Sponsoring
Unit:
DBIO
Chair: Aniket Bhattacharya, University of Central Florida
Abstract: AA09.00003 : Investigating recognition and sequence preference of Kaiso interactions with methylated DNA*
5:24 AM–5:36 AM
Presenter:
Bidhya Thapa
(Tribhuvan University, Kirtipur, Nepal.)
Authors:
Bidhya Thapa
(Tribhuvan University, Kirtipur, Nepal.)
Narayan P Adhikari
(Central Department of Physics Tribhuvan University)
Purushottam TIwari
(Georgetown University, Washington D.C., USA)
Prem P Chapagain
(Florida International University, Miami, Florida, USA)
Zinc finger (ZF) protein Kaiso is a methyl CpG binding protein that recognize the methylated CpG (mCpG) sites in DNA and mediates the transcription regulation. The C-terminal C2H2 ZF domains of Kaiso are involved in recognition of two mCpG sites in DNA. Study of the molecular mechanism of the Kaiso interactions with methylated DNA (meDNA) is crucial to understand the role of Kaiso in recognition of the mCpG sites and translation of methylation signal into downstream transcription outcomes. Structural investigation on sequence-specific interactions of Kaiso with meDNA sequences are still lacking. In this work, we performed molecular dynamics simulations to investigate recognition mechanism and binding of Kaiso to two distinct meDNA sequences, MeCG2 and MeECad. Our results reveal that Kaiso has sequence preference in its interactions to meDNA and interactions of the crucial residue E535 in Kaiso is different for the two distinct meDNA sequences. Kaiso showed an enhanced binding to MeECad sequence with 5’- flanking C/G base pair as compared to MeCG2 sequence with 5’- flanking T/A pair. Our results also show that, in addition to the core mCGmCG site, the flanking nucleotides are also important for the recognition of meDNA by Kaiso and formation of the stable Kaiso-MeDNA complex.
*BT and NPA acknowledge the TWAS research grant RG 20-316. PBT acknowledges the computational resources acquired with a research restart discretionary fund from the office of the Dean for Research at Georgetown University Medical Center.
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700