Aim: Oncogenic mutations involving KRAS are human cancer's most common driving force. We aimed to determine specific conformational features of the active KRAS regarding downstream signaling activation, especially in mutant forms of KRAS.
Main methods: We applied Molecular Dynamics (MD) simulations in triplicate and post-MD analytical methods on the KRAS and its G12 mutant structures. In addition, clustering, umbrella sampling, and principal component analysis were conducted to improve the significant conformations related to the activity of the KRAS variants. The results were generally represented as the probability of the conformations regarding different structural aspects, including β2-strand length, main residual distances, and critical residue interactions.
Key findings: Our results showed that the KRAS β2-strand length was a convenient structural criterion to show the KRAS activity. Accordingly, the active conformations of KRAS were the most probable to have 9-10 residue numbers of β2-strand. Based on this observation, it was also shown that the GDP forms of KRAS G12 mutants could be in the active mode because of increased β2-strand length. Moreover, the distance between the E37 and A59 residues differed in relation to β2-β3 sheet length and can be considered another KRAS activity indicator. Interestingly, β2-strand length could also predict the KRAS activity in the presence of a direct mutant KRAS inhibitor.
Significance: As a result, our observations provide a new mechanism regarding the high efficacy of direct inhibition of KRAS-GDP in cancer therapy. In addition, designing and screening the mutant KRAS inhibitors can be more achievable using the β2-strand length probability.
Keywords: Beta-sheet; Downstream signaling; KRAS; MD simulation; Protein structure.
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