Structural Basis of How Ferric Binding Proteins Utilize pH Differences for Controlled Release of Iron

Abstract

Human transferrin (hTF) binds and delivers Fe+3 to cells; lowered pH within the endosome (5.6) is implicated in the controlled release of bound ions [1]. Although the kinetics of the process is well studied, detailed molecular mechanisms at work are unknown. Bacterial transferrin, also known as ferric binding protein(FBP), is involved in scavenging iron from hTf [2]. These host/pathogen iron uptake proteins are thought to be distantly related through divergent evolution from an anion binding function; FBP displays similarity to one of the iron binding lobes of hTf in structural fold and highly conserved set of iron-coordinating residues.Perturbation response scanning (PRS) takes advantage of the differences between ligand-bound/unbound conformations to decipher residues having a direct effect on binding mechanisms [3]. PRS on apo and holo forms of FBP implicates D52, a charged residue located ca. 30 A from the bound ion, as playing a crucial role in ion release. Using pKa calculations [4] we find D52 is the most sensitive to subtle pH variations in the physiological range. The effect of protonation and D52A mutation in both the apo and holo forms was investigated via a series of molecular dynamics simulations. Only in the protonated and D52A holo FBP is an hinge motion triggering opening of the iron binding site observed. Our results lend clues as to how a single residue may be utilized for pH regulation of protein binding modes in iron transport proteins such as FBP and hTf.1.Steere et al., Biochim. Biophys. Acta, 1820, 326 (2012)2.Noinaj et al., Nature, 483, 53 (2012)3.Atilgan and Atilgan, PLoS Comput Biol 5, e1000544 (2009)4.Kantardjiev and Atanasov, Nucl. Acids Res., 37, W422 (2009)5.Parker-Siburt et al., Biochim. Biophys. Acta, 1820, 326 (2012)