In silico analysis of wild-type and mutant KRAS

Frengki Frengki, Dedi Prima Putra, Fatma Sriwahyuni, Daan Khambri, Henni Vanda

Abstract


The mutations of the KRAS gene at codons 12, 13, and 61 have been widely reported with different prognosis. In silico is one approach to explain the characteristics of the mutant genes. This study aimed to reveal the potential energy and fluctuations of the binding site and active site of wild-type KRAS (KRAS Wt) and mutant KRAS (KRAS Mt) at codons 12, 13, and 61. The samples used in this study were the sequences of KRAS Wt and KRAS Mt genes, which were subjected to in-silico analysis that included molecular homology, docking, and dynamics using MOE, PyMOL, and online CABS servers. The results showed that fluctuations in the binding site of all KRAS Mt were lower than that of KRAS Wt. On the contrary, the active site (switch I and switch II) of KRAS Mt fluctuated more widely than KRAS Wt. The potential energy of KRAS Mt before forming a complex with GTP was higher (p<0.01) than KRAS Wt. After this formation, it remained higher at codons 12 and 61 but lower at codons 11 and 13 (p <0.001). Mt G12A did not show any changes. The higher fluctuations in the switch I and switch II regions and the post energy of KRAS-GTP complexes may explain why types of cancers with mutations at codons 11 and 13 have a better prognosis than those with mutations at codons 12 and 61.

Keywords


Fluctuations; in silico; KRas; polymorphism; potential energy

Full Text:

PDF

References


Chen, C.C., Er, T.K., Liu, Y.Y., Hwang, J.K., Barrio, M.J., Rodrigo, M., Garcia-Toro, E., Herreros, M., 2013, Computational Analysis of KRAS Mutations: Implications for Different Effects on the KRAS p.G12D and p.G13D Mutations, PLoS ONE 8(2): e55793

De Roock W, Claes B, Bernasconi D, De Schutter J, Biesmans B, Fountzilas G, Kalogeras KT, Kotoula V, Papamichael D, Laurent-Puig P, Penault-Llorca F, Rougier P, Vincenzi B, Santini D, Tonini G, Cappuzzo F, Frattini M, Molinari F, Saletti P, De Dosso S, Martini M, Bardelli A, Siena S, Sartore-Bianchi A, Tabernero J, Macarulla T, Di Fiore F, Gangloff AO, Ciardiello F, Pfeiffer P, Qvortrup C, Hansen TP, Van Cutsem E, Piessevaux H, Lambrechts D, Delorenzi M, Tejpar S, 2010, Effects of KRAS, BRAF, NRAS, and PIK3CA mutations on the efficacy of cetuximab plus chemotherapy in chemotherapy-refractory metastatic colorectal cancer: a retrospective consortium analysis, Lancet Oncol, 11(8):753-762

Forbes, S., Clements, J., Dawson, E., Bamford, S., Webb. T., Dogan, A., Flanagan, A., Teague, J., Wooster, R., Futreal, P.A, 2006, COSMIC 2005, Br J Cancer, 94:318–322

Forbes, S.A., Bindal, N., Bamford, S., Cole, C., Kok, C.Y., 2011, COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer Nucleic acids research, 39: 945-950

Forbes, S.A., Tang, G., Bindal, N., Bamford, S., Dawson, E., Cole, C., Kok, C.Y., Jia, M., Ewing, R., Menzies, A., Teague. J.W., Stratton, M.R., Futreal, P.A., 2009, COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer, Nucleic Acids Res, 38: D652–D657

Futatsugi, N., and Tsuda, M., 2001, Molecular dynamics simulations of Gly-12->Val mutant of p21(ras): dynamic inhibition mechanism, Biophys J, 81:3483-3488

Gao, C., Leif, A., 2013, Impact of Mutations on KRAS-p120GAP Interaction. Computational Molecular, Bioscience, 3: 9-17

Garcea, G., Neal, C.P., Pattenden, C.J., 2005, Molecular prognostic markers in pancreatic cancer: A systematic review, Eur J Cancer, 41:2213–2236.

Hardono, B.Y., Santoso, B., and Da’i, M., 2013, Analisis Molecular Docking Energi Ikatan Turunan Diketoperazin (DKP) Sebagai Inhibitor Histon Deasetilasi (HDACi), Master Thesis, Universitas Muhammadiyah Surakarta

Hongyo, T., Buzard, G.S., Palli, D., Weghorst, C.M., Amorosi, A., Galli, M., 1995. Mutations of the KRAS and p53 genes in gastric adenocarcinomas from a high-incidence region around Florence, Italy. Cancer Res. 55:2665–2672.

Hunter, J.C., Manandhar, A., Carrasco, M.A., Gurbani, D., Gondi, S., and Westover, K.D., 2015, Biochemical and Structural Analysis of Common Cancer-Associated KRAS Mutations, Mol Cancer Res. 13(9): 1325-1335

Ihle, N.T., Byers, L.A., Kim, E.S., Saintigny, P., Lee, J.J., Blumenschein, G.R., Tsao, A., Liu, S., Larsen, J.E., Wang, J., Diao, L., Coombes, .R., Chen, L., Zhang, S., Abdelmelek, M.F., Tang,X, Papadimitrakopoulou, V., Minna, J.D., Lippman, S.M., Hong, W.K., Herbst, R.S., Wistuba, I.I., Heymach, J.V., Powis, G., 2012, Effect of KRAS Oncogene Substitutions on Protein Behavior: Implications for Signaling and Clinical Outcome, J Natl Cancer Inst; 104(3): 228–239

Karnoub, A.E., & Weinberg, R.A., 2008, RAS oncogenes: split personalities. Nature Reviews Molecular Cell Biology. 9: 517-53

Knickelbein, K., Zhang, L., 2014, Mutant KRAS as a critical determinant of the therapeutic response of colorectal cancer, Genes and Diseases, 2(1): 4–12

Krengel, U., Schlichting, I., Scherer, A., Schumann, R., Frech, M., John, J., Kabsch, U., Pai, E.F., Wittinghofer, A., 1990, Three-dimensional structures of HRAS p21 mutants: molecular basis for their inability to function as signal switch molecules, Cell 62(3): 539–548.

Miyakura, Y., Sugano, K., Fukayama, N., Konishi, F., Nagai, H., 2002, Concurrent mutations of KRAS oncogene at codons 12 and 22 in colon cancer. Jpn J Clin Oncol. 32(6):219-21

Petsko, G.A., Ringe, D., 2004, Protein structure and function. London: New Science Press.

Scheffzek, K., Ahmadian, M.R., Kabsch, W., Wiesmüller, L., Lautwein, A., Schmitz, F., Wittinghofer, A., 1997, The RAS-RASGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants, Science 277(5324):333-338