Secondary Structure Analysis Toolkit for Evaluating Iron-Sulfur Cluster Nest Formation

An analysis toolkit was developed for evaluating molecular dynamics trajectories generated by Tinker v8.1.2 (dasher.wustl.edu/tinker/) for aqueous models of free amino acids and short peptides containing at least two Cysteine residues. Current functionalities include:

1. S(Cys)…S(Cys) distance plot as a function of simulation time;
2. histogram of S(Cys)…S(Cys) distances;
3. 3D cross correlated diagram of the three pairs of S(Cys)…S(Cys) distances;
4. upper-limit for [4Fe-4S] nesting defined by non-threading orientation of the peptide backbone with respect of the S,S,S-triangle;
5. [2Fe-2S] and [4Fe-4S] cluster nests on the basis of shape complementarity;
6. lifetime of cluster nesting sites;
7. cumulative rate of nest formation, as a measure of reaching an equilibrium state with respect to nest formation and disappearance;
8. Ramachandran plot of phi(C-N–alphaC-C) and psi(N-alphaC–C-C) as a graphical representation for the sampling of peptide conformational space;
9. cross-correlation of peptide backbone conformations between two trajectories.

A tutorial style description, Python source code, a worked out example for peptide CIACGAC, description of each algorithm, and the sensitivity of each input parameter with respect to the definition of cluster shapes, min/max distances are provided.

The plots generated by the programs can be directly visualized in PSI-Plot (Poly Software International, Pearl River, NY).