A Model Peptide Reveals Insights into the Interaction of Human Hemopexin with Heme

Abstract

Under hemolytic conditions, toxic heme is scavenged by hemopexin. Recently, the heme-binding properties of hemopexin have been reassessed, which revealed a KD of ~ 0.32 nM as well as a stoichiometry of one to two heme molecules binding to hemopexin. A 66mer hemopexin-derived peptide that spans over three heme-binding motifs was used to verify the earlier suggested heme-recruiting mechanism. Herein, we employed spectroscopic and computational methods to substantiate the hypothesis of more than one heme molecule binding to hemopexin and to analyze the heme-binding mode. Both, hemopexin and the 66mer peptide, were found to bind heme in mixed penta- and hexacoordinated states, which strongly indicates that heme binding follows distinct criteria and increases rigidity of the peptide-heme complex. Additional in silico molecular dynamics simulations support these experimental findings and, thus, contribute to our understanding of the molecular basis of the heme-hemopexin interaction. This analysis provides further details for consideration of hemopexin in biomedical applications.

Host and viral proteins involved in SARS‐CoV‐2 infection differentially bind heme

“…Snapshots were selected from the production phase from the final 100 ns of the MD simulation and analyzed for the surface accessibility of the earlier described HBMs (i.e., in protein 7a: VK H 58 V Y 60 QLRA; in spike glycoprotein: FLGV Y 144 Y 145 H 146 KN and I Y 204 SK H 207 TPIN; in ACE2: PL Y 237 E H 239 L H 241 A Y 243 , SFIR Y 515 Y 516 TRT, and AMRQ Y 654 FLKV) 20 . These poses were then subjected to molecular focused docking studies of heme to the respective HBMs by using YASARA, as described in detail for other protein/peptide–heme complexes before 39,40,53,56,60,62 . The ligand heme was downloaded from the ChemSpider database (ID: 16739951) 63 .…”

“…Snapshots were selected from the production phase from the final 100 ns of the MD simulation and analyzed for the surface accessibility of the earlier described HBMs (i.e., in protein 7a: VKH 58 20 These poses were then subjected to molecular focused docking studies of heme to the respective HBMs by using YASARA, as described in detail for other protein/peptide-heme complexes before. 39,40,53,56,60,62 The ligand heme was downloaded from the ChemSpider database (ID: 16739951). 63 For each pose, a cubic simulation cell (10 Â 10 Â 10 Å) was built around the expected coordinating residue of the respective HBMs.…”