To quantify the stepwise patterns observed in single molecule FRET-time traces for G4 unwinding, average EFRET values and the dwell time of each unwinding step were determined using the automated step-finding method used in previous single molecule FRET studies (Kerssemakers et al., 2006; Myong et al., 2007; Lee et al., 2012).
The identities of partial transcripts obtained in the HMM profiling step were determined using pplacer (Matsen et al. 2010), by calculating the maximum-likelihood branching point for each fragment on the corresponding phylogenetic tree, conditioned on the alignment used to construct the tree and previous maximum-likelihood estimates of the branch lengths and other model parameters.
Then, the cumulative gas produced directly and indirectly from the start of time and until the end of the time step is determined using Eqs.
The length of the burn-in period of each MCMC step, which is used to estimate the E-step, was determined using Geweke's convergence diagnostics (Geweke, 1992).
18 In all these methods, model sequencing is determined by the original algorithm, while the coefficients of the parameters at each step are determined using ordinary least squares.
Second, step-counts were determined using the Yamax Digi-Walker CW701 and the GT1M accelerometer.
In all purification and processing steps, protein concentrations were determined using a BCA assay (ThermoScientific, Waltham, MA) and by absorbance at 280 nm using Beer's Law, and a CRP extinction coefficient of 1.95 mg/mL or 44,740 (mol/L)−1 cm−1.
The molecular mass and the purification steps of PCPEL2 were determined using SDS-PAGE (12% polyacrylamide).
In the third step the damage parameters were determined using a set of solid propellant test data.
Step-rate cut-points were determined using receiver operating characteristic (ROC) curves.
