Rapid Heme Transfer Reactions between NEAr Transporter Domains of Staphylococcus aureus: A Theoretical Study Using QM/MM and MD Simulations

Abstract

In vertebrates, most iron is present as heme or is chelated by proteins. Thus, Gram-positive pathogens such as Staphylococcus aureus have evolved an iron-regulated surface determinant (Isd) system that transports heme across thick cell walls into the cytoplasm. Recent studies have demonstrated that heme is rapidly transferred between the NEAr Transporter (NEAT) domains of the Isd system, despite its high affinity toward each domain, suggesting the presence of an intermediate NEAT•heme•NEAT complex. In the present study, we performed short restrained molecular dynamics (MD) simulations to dock the acceptor NEAT domain to the donor NEAT•heme complex and obtained models where the two NEAT domains were arranged with two-fold pseudo symmetry around the heme molecule. After turning off the restraints, complex structures were stably maintained during subsequent unrestrained MD simulations, except for the hydrogen bond between the propionate group of the heme molecule and the donor NEAT domain, potentially facilitating the transition of heme from the donor to the acceptor. Subsequent structural optimization using the quantum mechanics/molecular mechanics (QM/MM) method showed that two tyrosine residues, one from each NEAT domain, were simultaneously coordinated to the ferric heme iron in the intermediate complex only if they were deprotonated. Based on these results, we propose a reaction scheme for heme transfer between NEAT domains.

Identification of a novel mechanism of action of bovine IgG antibodies specific for Staphylococcus aureus

“…The molecular mechanisms of S. aureus infection is under investigation; however, several molecules expressed by S. aureus are involved in pathogenesis [ 34 ]. For example, exotoxin (staphylococcal enterotoxins and toxic shock syndrome toxin-1) [ 35 , 36 ], binding molecules (clumping factors and fibronectin binding proteins) [ 37 ], and receptors (iron acquisition factors and manganese uptake receptors) [ 38 , 39 ] are virulence factors involved in the pathogenesis. Therefore, numerous studies of virulence molecules were performed to develop an effective vaccine to protect humans as well as dairy cattle from infectious diseases caused by S. aureus .…”

“…Sortase-A-dependent cell-wall-associated proteins play important roles in infection by S. aureus and mediate adhesion to host cells and evasion of the pathogen of the host’s immune system [ 37 ]. In addition, such proteins are also involved in absorbing nutrients, such as iron [ 38 ]. However, our results acquired using S. aureus JE2ΔSrtA show that the inhibition of bacterial growth by anti- S. aureus was sortase-A-independent (Figure 5 ).…”

NEAr Transporter (NEAT) Domains: Unique Surface Displayed Heme Chaperones That Enable Gram-Positive Bacteria to Capture Heme-Iron From Hemoglobin

“…Independently, using molecular docking and atomic structures of isolated NEAT domains, Grigg et al (2011) also proposed that rapid transfer occurs via a “handclasp” complex. Molecular simulations have provided insight into the IsdA to IsdC heme transfer mechanism, which was modeled to occur via an intermediate in which the tyrosine ligands from each NEAT domain simultaneously form axial linkages to heme’s iron atom such that it is hexacoordinate ( Moriwaki et al, 2015 ). In the intermediate, the metal is coordinated by the primary and secondary tyrosines in the donor and acceptor, respectively, further explaining the functions of these residues in the S/YXXXY motif.…”