E studies by Guerrero et al. [25], who demonstrated that KRAS codon

E studies by Guerrero et al. [25], who demonstrated that KRAS codon 12 mutations confer a more aggressive tumor phenotype than codon 13 mutations by altering the threshold for the induction of apoptosis. Theoretically, codon 12-mutated KRAS remains in an active GTP-bound state longer than codon 13-mutated or WT KRAS. Herein, we have demonstrated that mutations in codon 13 can confer similar protein structure dynamics to WT KRAS. To gain better insight into why patients with metastatic Tubastatin-A cost colorectal cancer (mCRC) and the KRAS c.38G.A (p.G13D) mutation appear to benefit from anti-EGFR therapy, the role of the KRAS c.38G.A (p.G13D) mutation in mCRC needs to be further investigated.Computational Analysis of KRAS MutationsConclusionsIn this study, we have applied computational methods to understand the structural implications of c.35G.A (p.G12D) and c.38G.A (p.G13D) in the KRAS protein. Our findings underscore that the KRAS c.38G.A (p.G13D) mutation may exhibit similar behavior as KRAS WT. In summary, our data make sense in light of five recent studies [26?0], which demonstrated that KRAS codon 13 mutations, but not codon 12 mutations, conferred benefit from cetuximab therapy in advanced colorectal cancer.the course of the simulation; (B) the pocket distances between the mass center of residues 12?3 and the mass center of residues 32?34 for WT, G12D, and G13D, respectively. (PDF)Figure S6 Analysis of atomic fluctuations in the third repeated MD simulations. The structures of (A) WT, (B) G12D and, (C) G13D KRAS proteins are drawn in cartoon putty representations at the P-loop, switch I and II regions; blue represents the lowest and red the highest B-factor value. In addition, the size of the tube reflects the value of the B-factor, in that the larger the B-factor, the thicker the tube. The structures in the other regions are colored in white and displayed in cartoon tube representation, where the size of the tube is independent of the B-factors. (PDF) Figure S7 Prevalence of the KRAS gene mutation in CRC and distribution of KRAS mutational status in a Spanish population. A total of 252 patients with mCRC confirmed at the Pathology Department of General Yague ?Hospital (Burgos, Spain) were included in the present study. Mutant KRAS in exon 2 was detected using a validated KRAS mutation kit (DxS Ltd, Manchester, United Kingdom) that identifies seven somatic mutations located in codons 12 and 13 using allele-specific real-time polymerase chain reaction. Central laboratory personnel validated the assays for their analytic and diagnostic performance, established acceptance criteria, included appropriate quality controls for each assay, and performed the KRAS analysis in a blinded fashion. The analysis was performed in an ABI Prism 7500 buy LED 209 instrument (Applied Biosystems). (TIF)Supporting InformationFigure S1 Protein dynamics simulation analysis. RMSD plots of the WT (blue), G12D (red) and G13D (green) KRAS proteins with respect to the initial conformation during the course of MD simulations. (TIF) Figure S2 The calculation of covariance matrices forWT, c.35G.A (p.G12D), and c.35G.A (p.G13D). Covariance matrices calculated from MD trajectories for (A) WT, (B) G12D and (C) G13D. (TIF)Figure S3 The second repeated molecular dynamics trajectories for: (A) Comparison of the RMSD plots of the sensitive sites (P-loop, switch I and II regions) of WT, G12D and G13D structures with respect to the initial conformation during the course of the simulation; (B) the po.E studies by Guerrero et al. [25], who demonstrated that KRAS codon 12 mutations confer a more aggressive tumor phenotype than codon 13 mutations by altering the threshold for the induction of apoptosis. Theoretically, codon 12-mutated KRAS remains in an active GTP-bound state longer than codon 13-mutated or WT KRAS. Herein, we have demonstrated that mutations in codon 13 can confer similar protein structure dynamics to WT KRAS. To gain better insight into why patients with metastatic colorectal cancer (mCRC) and the KRAS c.38G.A (p.G13D) mutation appear to benefit from anti-EGFR therapy, the role of the KRAS c.38G.A (p.G13D) mutation in mCRC needs to be further investigated.Computational Analysis of KRAS MutationsConclusionsIn this study, we have applied computational methods to understand the structural implications of c.35G.A (p.G12D) and c.38G.A (p.G13D) in the KRAS protein. Our findings underscore that the KRAS c.38G.A (p.G13D) mutation may exhibit similar behavior as KRAS WT. In summary, our data make sense in light of five recent studies [26?0], which demonstrated that KRAS codon 13 mutations, but not codon 12 mutations, conferred benefit from cetuximab therapy in advanced colorectal cancer.the course of the simulation; (B) the pocket distances between the mass center of residues 12?3 and the mass center of residues 32?34 for WT, G12D, and G13D, respectively. (PDF)Figure S6 Analysis of atomic fluctuations in the third repeated MD simulations. The structures of (A) WT, (B) G12D and, (C) G13D KRAS proteins are drawn in cartoon putty representations at the P-loop, switch I and II regions; blue represents the lowest and red the highest B-factor value. In addition, the size of the tube reflects the value of the B-factor, in that the larger the B-factor, the thicker the tube. The structures in the other regions are colored in white and displayed in cartoon tube representation, where the size of the tube is independent of the B-factors. (PDF) Figure S7 Prevalence of the KRAS gene mutation in CRC and distribution of KRAS mutational status in a Spanish population. A total of 252 patients with mCRC confirmed at the Pathology Department of General Yague ?Hospital (Burgos, Spain) were included in the present study. Mutant KRAS in exon 2 was detected using a validated KRAS mutation kit (DxS Ltd, Manchester, United Kingdom) that identifies seven somatic mutations located in codons 12 and 13 using allele-specific real-time polymerase chain reaction. Central laboratory personnel validated the assays for their analytic and diagnostic performance, established acceptance criteria, included appropriate quality controls for each assay, and performed the KRAS analysis in a blinded fashion. The analysis was performed in an ABI Prism 7500 instrument (Applied Biosystems). (TIF)Supporting InformationFigure S1 Protein dynamics simulation analysis. RMSD plots of the WT (blue), G12D (red) and G13D (green) KRAS proteins with respect to the initial conformation during the course of MD simulations. (TIF) Figure S2 The calculation of covariance matrices forWT, c.35G.A (p.G12D), and c.35G.A (p.G13D). Covariance matrices calculated from MD trajectories for (A) WT, (B) G12D and (C) G13D. (TIF)Figure S3 The second repeated molecular dynamics trajectories for: (A) Comparison of the RMSD plots of the sensitive sites (P-loop, switch I and II regions) of WT, G12D and G13D structures with respect to the initial conformation during the course of the simulation; (B) the po.