Molecular dynamics simulation of metal free structure of Lmb, a laminin-binding adhesin of Streptococcus agalactiae: metal removal and its structural implications

Abstract

Metal-binding receptors are one of the extracellular components of ATP-binding cassette transporters that are essential for regulation of metal homeostasis in bacteria. Laminin-binding adhesin (Lmb) of Streptococcus agalactiae falls under this class of solute binding proteins. It binds to zinc with a high affinity. Crystal structure of Lmb solved previously by our group reveals that the zinc is tetrahedrally coordinated by three histidines and a glutamate at the interdomain cleft. Lmb contains a long disordered loop close to the metal-binding site whose precise function is unknown. Several experimental attempts to produce apo-Lmb failed and this prompted us to carry out in silico studies to analyse the structural importance of the metal in Lmb. Here, we present the results of the molecular dynamics (MD) simulation studies of native, apo-(metal removed) and the long loop truncated Lmb models along with a homologous protein, TroA from Treponema pallidum that was taken up for validating the MD results of Lmb. Absence of a metal results in significant structural changes in Lmb, particularly at the metal-binding pocket and with the long loop, although the overall fold is retained. This study thus revealed that the Lmb can exist in different conformational states with subtle differences in the overall fold based on the presence or absence of the metal. This could be functionally important for a putative metal uptake and release and also for the adhesive function of Lmb in recognizing laminin, which contains a high number of zinc finger motifs.

Molecular typing and prevalence of antibiotic resistance and virulence genes in Streptococcus agalactiae isolated from Chinese dairy cows with clinical mastitis

“…In this study, PCR showed that the cfb, cylE, fbsA, fbsB, hylB, and enolase virulence genes were present in all isolates, whereas the bac and lmb genes were not; the detection rates were the same with those reported for isolates in Argentina [67]. These virulence factors provide essential assistance for allowing pathogenic bacteria to invade the host and to be directly involved in the invasion process [68]. Notably, cylE is a pore-forming toxin involved in tissue damage and systemic dissemination of bacteria [69].…”

Structural Features Mediating Zinc Binding and Transfer in the AztABCD Zinc Transporter System

“…Unlike AztC, the apo form of TroA does not show any significant displacement of the Z-Loop relative to the holo form [ 40 ]. Although no apo structure exists for Lmb or Lbp, a recent molecular dynamics simulation of both Lmb and TroA indicated significant flexibility of the Z-Loop in the apo form and displacement away from the zinc binding site upon zinc loss [ 41 ].…”

How Zinc-Binding Systems, Expressed by Human Pathogens, Acquire Zinc from the Colonized Host Environment: A Critical Review on Zincophores

“…The flexible loop, typical of zinc-specific binding proteins, is present but does not contain the His-rich motif [ 75 ]. Their mechanism of metal binding and release has been only hypothesised by means of molecular dynamics simulation [ 76 ]. Despite the structural similarities and the genetic homology with Spn AdcAII, the laminin-binding ability has not been confirmed in the case of Spn AdcAII and the analysis of the surface charge distribution between Sag Lmb and Spn AdcAII revealed significant differences, attributable to the “extra” adhesion functionality [ 52 , 77 ].…”