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.
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 GTP-binding protein RhoB in apoptotic events.
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