Structural insights and influence of V599 mutations on the overall dynamics of BRAF protein against its kinase domains

Mutations in the BRAF gene are well known for their oncogenic effects. Point mutations in V599 are particularly oncogenic and are considered important for therapeutic purposes. Along with wild type, other V599 mutated BRAF variants viz. V599E, V599D and V599R are reported and crystals of the former two with inhibitor (BAY43-9006) are further detailed. Both wild-type and mutated BRAF forms show similar interaction patterns with BAY43-9006, but the 599th residue did not show any involvement in the interactions. Upon BAY43-9006 binding, kinase domains of both forms were found adopting essentially identical conformations. However, BAY43-9006 shows a varied activity profile in the case of the wild and V599E variant of the BRAF protein. Furthermore, MMGBSA binding energy results for all four BRAF variants, further revealed the importance of the 599th residue. In-depth analysis viz. molecular dynamics, residue correlation studies and residue interaction network (RIN) analyses were conducted, providing a deep insight into the 599th residue and its impact on the overall dynamics of BRAF protein. Our findings reveal that the mutated residue at the 599th position not only changed the BAY43-9006-BRAF binding behaviour but also produced a massive impact on the overall dynamic behaviour of the protein. The insights obtained herein could be of great relevance for designing new BRAF inhibitors aimed at getting ideal activity against all BRAF forms.