Hekate: Software Suite for the Mass Spectrometric Analysis and Three-Dimensional Visualization of Cross-Linked Protein Samples

Chemical cross-linking
of proteins combined with mass spectrometry
provides an attractive and novel method for the analysis of native
protein structures and protein complexes. Analysis of the data however
is complex. Only a small number of cross-linked peptides are produced
during sample preparation and must be identified against a background
of more abundant native peptides. To facilitate the search and identification
of cross-linked peptides, we have developed a novel software suite,
named Hekate. Hekate is a suite of tools that address the challenges
involved in analyzing protein cross-linking experiments when combined
with mass spectrometry. The software is an integrated pipeline for
the automation of the data analysis workflow and provides a novel
scoring system based on principles of linear peptide analysis. In
addition, it provides a tool for the visualization of identified cross-links
using three-dimensional models, which is particularly useful when
combining chemical cross-linking with other structural techniques.
Hekate was validated by the comparative analysis of cytochrome c (bovine heart) against previously reported data. Further validation was carried out on known structural
elements of DNA polymerase III, the catalytic α-subunit of the Escherichia coli DNA replisome along with new insight
into the previously uncharacterized C-terminal domain of the protein.