Dynamics of TUBB protein with five majorly occurring natural variants: a risk of cortical dysplasia

• Published in: Journal of molecular modeling 2023-04, Vol.29 (4), p.100-100, Article 100
• Main Authors: Janakiraman, V., Sudhan, M., Alzahrani, Khalid J., Alshammeri, Saleh, Ahmed, Shiek S. S. J., Patil, Shankargouda
• Format: Article
• Language: English
• Subjects: Amino acids; Axon Guidance - genetics; Central nervous system; Characterization and Evaluation of Materials; Chemistry; Chemistry and Materials Science; Computer Appl. in Life Sciences; Computer Applications in Chemistry; Dynamic structural analysis; Humans; Malformations of Cortical Development - genetics; Molecular dynamics; Molecular Dynamics Simulation; Molecular Medicine; Original Paper; Proteins; Theoretical and Computational Chemistry; Tubulin - genetics; Tubulin - metabolism
• ISSN: 1610-2940; 0948-5023
• DOI: 10.1007/s00894-023-05506-7

Beta-tubulin (TUBB) protein is one of the components of the microtubule cytoskeleton that plays a critical role in the central nervous system. Genetic variants of TUBB cause cortical dysplasia, a developmental brain defect implicated in axonal guidance and the neuron migration. In this study, we assess pathogenic variants (Q15K, Y222F, M299V, V353I, and E401K) of TUBB protein and compared with non-pathogenic variant G235S to determine their impact on protein dynamic to cause cortical dysplasia. Among the analyzed variants, Q15K, Y222F, M299V, and E401K were noticed to have deleterious effect. Then, variant structures were modeled and their affinity with their known cofactor Guanosine-5'-triphosphate (GTP) was assessed which showed diverse binding energies ranged between (-7.436 to -6.950 kcal/mol) for the variants compared to wild-type (-7.428 kcal/mol). Finally, the molecular dynamics simulation of each variant was investigated which showed difference in trajectory between the pathogenic and non-pathogenic variant. Our analysis suggests change in amino acid residue of TUBB structure has notably affects the protein flexibility and their interactions with known cofactor. Overall, our findings provide insight on the relationship between TUBB variants and their structural dynamics that may cause diverse effects leading to cortical dysplasia.