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Background  B-RAF kinase plays an important role both in tumour induction and maintenance in several cancers and it is an attractive new drug target. However, the structural basis of the B-RAF activation is still not well understood.    Results  In this study we suggest a novel molecular basis of B-RAF activation based on molecular dynamics (MD) simulations of B-RAF WT  and the B-RAF V600E , B-RAF K601E  and B-RAF D594V  mutants. A strong hydrogen bond network was identified in B-RAF WT  in which the interactions between Lys601 and the well known catalytic residues Lys483, Glu501 and Asp594 play an important role. It was found that several mutations, which directly or indirectly destabilized the interactions between these residues within this network, contributed to the changes in B-RAF activity.    Conclusion  Our results showed that the above mechanisms lead to the disruption of the electrostatic interactions between the A-loop and the αC-helix in the activating mutants, which presumably contribute to the flipping of the activation segment to an active form. Conversely, in the B-RAF D594V  mutant that has impaired kinase activity, and in B-RAF WT  these interactions were strong and stabilized the kinase inactive form.

An in silico study of the molecular basis of B-RAF activation and conformational stability