Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling

PLoS Comput Biol. 2018 Sep 10;14(9):e1006458. doi: 10.1371/journal.pcbi.1006458. eCollection 2018 Sep.

Abstract

A mutated KRAS protein is frequently observed in human cancers. Traditionally, the oncogenic properties of KRAS missense mutants at position 12 (G12X) have been considered as equal. Here, by assessing the probabilities of occurrence of all KRAS G12X mutations and KRAS dynamics we show that this assumption does not hold true. Instead, our findings revealed an outstanding mutational bias. We conducted a thorough mutational analysis of KRAS G12X mutations and assessed to what extent the observed mutation frequencies follow a random distribution. Unique tissue-specific frequencies are displayed with specific mutations, especially with G12R, which cannot be explained by random probabilities. To clarify the underlying causes for the nonrandom probabilities, we conducted extensive atomistic molecular dynamics simulations (170 μs) to study the differences of G12X mutations on a molecular level. The simulations revealed an allosteric hydrophobic signaling network in KRAS, and that protein dynamics is altered among the G12X mutants and as such differs from the wild-type and is mutation-specific. The shift in long-timescale conformational dynamics was confirmed with Markov state modeling. A G12X mutation was found to modify KRAS dynamics in an allosteric way, which is especially manifested in the switch regions that are responsible for the effector protein binding. The findings provide a basis to understand better the oncogenic properties of KRAS G12X mutants and the consequences of the observed nonrandom frequencies of specific G12X mutations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Mutational Analysis
  • Genes, ras*
  • Guanosine Diphosphate / chemistry
  • Guanosine Triphosphate / chemistry
  • Humans
  • Hydrophobic and Hydrophilic Interactions
  • Ligands
  • Markov Chains
  • Molecular Conformation
  • Molecular Dynamics Simulation
  • Mutation
  • Mutation, Missense*
  • Neoplasms / genetics*
  • Principal Component Analysis
  • Probability
  • Proto-Oncogene Proteins p21(ras) / genetics*

Substances

  • KRAS protein, human
  • Ligands
  • Guanosine Diphosphate
  • Guanosine Triphosphate
  • Proto-Oncogene Proteins p21(ras)

Grants and funding

The study was supported by the Academy of Finland (http://www.aka.fi/en) (grant 276509 to AP) and Biocenter Finland/DDCB (http://ddcb.fi/en/ddcb/biocenter_finland/) (TL). IV and SR acknowledge the Academy of Finland (http://www.aka.fi/en) (Center of Excellence program (grant no. 307415)) and the European Research Council (https://erc.europa.eu) (Advanced Grant CROWDED-PRO-LIPIDS (grant no. 290974)) for financial support. SR thanks the Graduate School program of Tampere University of Technology and Alfred Kordelin Foundation (https://kordelin.fi) for financial support. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.