As software and methodology develop, key aspects of molecular interactions such as detailed energetics and flexibility are continuously better represented in docking simulations. In the latest iteration of the XPairIt API and Docking Protocol, we perform a blind dock of a peptide into the cleavage site of the Anthrax lethal factor (LF) metalloprotein. Molecular structures are prepared from RCSB:1JKY and we demonstrate a reasonably accurate docked peptide through analysis of protein motion and, using NCI Plot, visualize and characterize the forces leading to binding. We compare our docked structure to the 1JKY crystal structure and the more recent 1PWV structure, and discuss both captured and overlooked interactions. Our results offer a more detailed look at secondary contact and show that both van der Waals and electrostatic interactions from peptide residues further from the enzyme's catalytic site are significant.
The development of smart peptide binders requires an understanding of the fundamental mechanisms of recognition
which has remained an elusive grail of the research community for decades. Recent advances in automated discovery and
synthetic library science provide a wealth of information to probe fundamental details of binding and facilitate the
development of improved models for a priori prediction of affinity and specificity. Here we present the modeling portion
of an iterative experimental/computational study to produce high affinity peptide binders to the Protective Antigen (PA)
of Bacillus anthracis. The result is a general usage, HPC-oriented, python-based toolkit based upon powerful third-party
freeware, which is designed to provide a better understanding of peptide-protein interactions and ultimately predict and
measure new smart peptide binder candidates. We present an improved simulation protocol with flexible peptide docking
to the Anthrax Protective Antigen, reported within the context of experimental data presented in a companion work.
Recent advances in synthetic library engineering continue to show promise for the rapid production of reagent
technology in response to biological threats. A synthetic library of peptide mutants built off a bacterial host offers a
convenient means to link the peptide sequence, (i.e., identity of individual library members) with the desired molecular
recognition traits, but also allows for a relatively simple protocol, amenable to automation. An improved understanding
of the mechanisms of recognition and control of synthetic reagent isolation and evolution remain critical to success. In
this paper, we describe our approach to development of peptide affinity reagents based on peptide bacterial display
technology with improved control of binding interactions for stringent evolution of reagent candidates, and tailored
performance capabilities. There are four key elements to the peptide affinity reagent program including: (1) the diverse
bacterial library technology, (2) advanced reagent screening amenable to laboratory automation and control, (3) iterative
characterization and feedback on both affinity and specificity of the molecular interactions, and (3) integrated multiscale
computational prescreening of candidate peptide ligands including in silico prediction of improved binding
performance. Specific results on peptides binders to Protective Antigen (PA) protein of Bacillus anthracis and
Staphylococcal Enterotoxin B (SEB) will be presented. Recent highlights of on cell vs. off-cell affinity behavior and
correlation of the results with advanced docking simulations on the protein-peptide system(s) are included. The potential
of this technology and approach to enable rapid development of a new affinity reagent with unprecedented speed (less
than one week) would allow for rapid response to new and constantly emerging threats.
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