October 2, 2018 Software Open Access

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

Rebecca Hanscam; Robert K Szilagyi

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 CIACGAC and CGGCGGC peptides, 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).

Version 2.0 contains much improvements in torsional angle analysis for wrapped and mirrored Ramachandran plots, and in the efficiency of the crossover analysis. The S...S distance toolking can now recognize deprotonated Cys, homoCys, and thioGly residues. Please see the versions.log file in the "analysis code.zip" file for the modification of each utility.