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Journal of Cellular Signaling

ISSN: 2692-0638

Original Research Open Access
Volume 4 | Issue 1 | DOI: https://doi.org/10.33696/Signaling.4.089

A Computational Investigation on Rho-related GTP-binding Protein RhoB through Molecular Modeling and Molecular Dynamics Simulation Study

Shamrat Kumar Paul1,#, Chowdhury Lutfun Nahar Metu1,#, Sunita Kumari Sutihar1, Md. Saddam1, Bristi Paul3, Md. Lutful Kabir1,2,*, Md. Mostofa Uddin Helal4,*
  • #Authors contributed equally
  • 1Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
  • 2Department of Chemistry and Biochemistry, Kent State University, 800 E Summit St, Kent, OH 44240, USA
  • 3Department of Fisheries and Marine Bioscience, Faculty of Biological Science, Jashore University of Science and Technology, Jashore 7408, Bangladesh
  • 4State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, People’s Republic of China
+ Affiliations - Affiliations

Corresponding Author

Md. Lutful Kabir, kabir.bmb@bsmrstu.edu.bd;

Md. Mostofa Uddin Helal, mostofa.agr12@gmail.com

Received Date: February 14, 2023

Accepted Date: March 19, 2023

Citation:

Paul SK, Metu CLN, Sutihar SK, Saddam M, Paul B, Kabir ML, et al. A Computational Investigation on Rho-related GTP-binding Protein RhoB through Molecular Modeling and Molecular Dynamics Simulation Study. J Cell Signal.
2023;4(1):30-48.


Copyright: © 2023 Paul SK, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Abstract

Background: An indispensable member of the Rho family, RhoB is an isoprenylated small GTPases that modulate the cellular cytoskeletal organization. While DNA gets damaged, it takes part in the neoplastic apoptotic mechanism. In this study, we evaluated the structure of Rho-related GTP-binding protein RhoB due to the unavailability of 3D structure in the protein data bank database.

Results: The expected pI value of RhoB was 5.10 (acidic). The target–template alignment was computed using the GMQE value meanwhile 6hxu.1.A from Homo sapiens was selected as the template structure. The Swiss model was exploited to complete the model construction task. The structural compatibility and stability were revealed after a 100ns molecular dynamics simulation using GROMACA employing the OPLS-AA force field. Based on their fluctuating activity and their location between 100 and 110 and 140 and 150, PCA analysis discovered relevant residues.

Conclusion: By providing an insight into the biophysical phenomenon of Rho-related GTP-binding protein RhoB inhibitors, this study will assist future investigations addressing the relationship between gene mutation and abnormalities produced by protein Rho-related GTPbinding protein RhoB in apoptotic events.

Keywords

Homology modeling, Molecular dynamics simulation, PCA, RhoB

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A Computational Investigation on Rho-related GTP-binding Protein RhoB through Molecular Modeling and Molecular Dynamics Simulation Study

An indispensable member of the Rho family, RhoB is an isoprenylated small GTPases that modulate the cellular cytoskeletal organization. While DNA gets damaged, it takes part in the neoplastic apoptotic mechanism. In this study, we evaluated the structure of Rho-related GTP-binding protein RhoB due to the unavailability of 3D structure in the protein data bank database.

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