| Abstract | The most stabilizing point mutation was D27F, which is located in the active site of the protein, rendering it inactive. |
| Comparison with other methods | PopMusic shows also strong performance with highly statistically significant 1’ = 0.55 between theory and experiment, however the limitation of this method is that it can consider only single point mutations . |
| Computational identification of stabilizing single point mutations | Computational identification of stabilizing single point mutations |
| Computational identification of stabilizing single point mutations | All possible single point mutations of DHFR (159 * 19 = 3,021) were simulated with the Monte Carlo protein unfolding simulation protocol. |
| Computational identification of stabilizing single point mutations | The distribution of predicted melting temperatures (averaged over the 3 metrics) for all 3021 point mutants is shown in Fig. |
| Discussion | However using MCPU we were able to efficiently explore stabilities of all possible point mutants for an essential enzyme of a typical size (159 amino acids) in a manageable amount of computational time (approx. |
| Experimental characterization of predicted mutants | We cloned, expressed, and purified the 23 single point mutants of DHFR listed in 81 Table, as well as the multiple mutants listed in Table 1 (see Materials and Methods). |
| Experimental characterization of predicted mutants | Of the selected 22 single point mutations , 10 mutations were stabilizing, according to their Tm or Cm values (82 Table). |
| Introduction | Here, we use a Monte Carlo protein unfolding approach (MCPU) with an all-atom simulation method and knowledge-based potential developed earlier in our lab [16,30,31] to simulate unfolding and predict melting temperatures for all possible single point mutants of E. coli Dihydrofolate Reductase (DHFR). |
| Site-directed protein mutagenesis of DHFR | Single point mutations of DHFR were constructed based on a two-step PCR-mutagenesis strategy [70], in which the template for the PCR is the plasmid of WT DHFR. |
| Cell Treatments and Fractionation | Four cell lines [SH-SY5Y, LAN-6, SMS-KCN, and SK-N-BE(2)] were selected for further studies because of different point mutations in ALK, p53 status, RTK expression, morphology, and growth characteristics. |
| Phosphoproteomics | Four cell lines [SH-SY5Y, LAN-6, SMS-KCN, and SK-N-BE(2)] were selected for further studies because of their different point mutations in ALK, p53 status, RTK expression, morphology, and growth patterns. |
| RTK Pathways in Neuroblastoma and Neural Crest | Point mutations in the RTK, ALK, are the primary cause of familial neuroblastoma and account for 8—12% of sporadic neuroblastomas [15]. |