A computational investigation on Rho-related GTP-binding protein RhoB through molecular modeling and molecular dynamics simulation study

Abstract

RhoB is a key member of the Rho family of isoprenylated small GTPases which modulate the cellular cytoskeletal organization. It has a crucial role in the neoplastic apoptotic mechanism after DNA damage. Due to the unavailability of 3D structure in the protein data bank database, in this study, we evaluated the structure of a protein, Rho related GTP binding protein RhoB. RhoB has a predicted pI of 5.10, indicating that it is acidic. The GMQE value was used to compute the target template alignment, and 6hxu.1.A from Homo sapiens was chosen as the template structure, with the model construction task completed using swiss model. The structural compactibility and stability were revealed after a 100ns molecular dynamics simulation using GROMACA employing the OPLSAA force field. PCA analysis found residues that are relevant based on their fluctuation acitivity while their location is between 100 to 110 and 140 to 150. This study will benefit future investigations addressing the association between gene mutation and abnormalities generated by protein Rho-related GTP binding protein RhoB in apoptotic events by offering insight into the biophysical phenomenon of Rho related GTP binding protein RhoB inhibitors.