Discerning the catalytic mechanism of Staphylococcus aureus sortase A with QM/MM free energy calculations

• Published in: Journal of molecular graphics & modelling 2016-06, Vol.67, p.33-43
• Main Authors: Shrestha, Pooja, Wereszczynski, Jeff
• Format: Article
• Language: English
• Subjects: Aminoacyltransferases - chemistry; Aminoacyltransferases - metabolism; Bacteria; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Biocatalysis; Catalysis; Cysteine Endopeptidases - chemistry; Cysteine Endopeptidases - metabolism; Enzymes; Free energy; Mathematical models; Models, Molecular; Molecular Dynamics Simulation; QM/MM; Quantum Theory; Sortases; Sorting; Staphylococcus aureus; Staphylococcus aureus - enzymology; Temperature; Thermodynamics; Walls
• ISSN: 1093-3263; 1873-4243
• DOI: 10.1016/j.jmgm.2016.04.006

[Display omitted] •The binding and catalysis of two substrate conformations by sortase A is explored.•Conventional MD simulations show a slight preference for the “Threonine In” state.•Also, QM/MM metadynamics calculations show lower free energy barriers in this state. Sortases are key virulence factors in Gram-positive bacteria. These enzymes embed surface proteins in the cell wall through a transpeptidation reaction that involves recognizing a penta-peptide “sorting signal” in a target protein, cleaving it, and covalently attaching it to a second substrate that is later inserted into the cell wall. Although well studied, several aspects of the mechanism by which sortases perform these functions remains unclear. In particular, experiments have revealed two potential sorting signal binding motifs: a “Threonine-Out” (Thr-Out) structure in which the catalytically critical threonine residues protrudes into solution, and a “Threonine-In” (Thr-In) configuration in which this residue inserts into the binding site. To determine which of these is the biologically relevant state, we have performed a series of conventional and hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations of the Staphylococcus aureus sortase A (SrtA) enzyme bound to a sorting signal substrate. Through the use of multi-dimensional metadynamics, our simulations were able to both map the acylation mechanism of SrtA in the Thr-In and Thr-Out states, as well as determine the free energy minima and barriers along these reactions. Results indicate that in both states the catalytic mechanisms are similar, however the free energy barriers are lower in the Thr-In configuration, suggesting that Thr-In is the catalytically relevant state. This has important implications for advancing our understanding of the mechanisms of sortase enzymes, as well we for future structure based drug design efforts aimed at inhibiting sortase function in vivo.