De Novo-Designed β-Sheet Heme Proteins

Abstract

The field of de novo protein design has met with considerable success over the past few decades. Heme, a cofactor, has often been introduced to impart a diverse array of functions to a protein, ranging from electron transport to respiration. In nature, heme is found to occur predominantly in α-helical structures over β-sheets, which has resulted in significant designs of heme proteins utilizing coiled-coil helices. By contrast, there are only a few known β-sheet proteins that bind heme and designs of β-sheets frequently result in amyloid-like aggregates. This review reflects on our success in designing a series of multistranded β-sheet heme binding peptides that are well folded in both aqueous and membrane-like environments. Initially, we designed a β-hairpin peptide that self-assembles to bind heme and performs peroxidase activity in membrane. The β-hairpin was optimized further to accommodate a heme binding pocket within multistranded β-sheets for catalysis and electron transfer in membranes. Furthermore, we de novo designed and characterized β-sheet peptides and miniproteins that are soluble in an aqueous environment capable of binding single and multiple hemes with high affinity and stability. Collectively, these studies highlight the substantial progress made toward the design of functional β-sheets.

Corrole–protein interactions in H-NOX and HasA

“…However, there are few examples where de novo protein design has been exploited to bind small-molecule cofactors, namely haem or non-biological iron porphyrins. [44][45][46][47][48] This methodology has been refined and extended to design proteins that are selective for specific zinc porphyrins, enabling discrimination of both the metal centre and peripheral substituents. [49][50][51] Examples of proteins specifically designed to bind non-porphyrin cofactors are exceedingly rare.…”

Designing 1D multiheme peptide amphiphile assemblies reminiscent of natural systems

“…Instead, a “textbook” example of a bis-histidine coordinated heme molecule with Soret, 412 nm and q-band, 532, 560 nm is observed and is consistent with a similar class of β-sheet rich/heme binding peptides from the group of S. Bhattacharjya. 25 All of the binding affinities measured for PA-KF2 to PA-KF4 were within experimental error ( K D = 1.3 to 2.9 μM) whereas PA-KF1 did not bind heme but similarly to PA-KL1 encapsulated the heme molecule, Fig. S3 †…”

Interplay between membrane active host defense peptides and heme modulates their assemblies and in vitro activity

“…In common helical heme-binding proteins, heme is preferentially located in a hydrophobic pocket, where the ring is stacked to aromatic peptide residues, the central iron is coordinated axially to cysteine, histidine or tyrosine, rarely to Lys residues, however, the propionate moieties reside near to Arg or Lys peptide side chains 70 . Engineered peptides binding heme selectively, mimic this optimal binding site so that one or even more porphyrin rings are coordinated preferentially by His side chains arranged in ideal spatial distance provided by either helical 71 – 73 , β-sheet 74 , 75 , or β-hairpin 76 constrained scaffolds. Considering the cationic-hydrophobic nature of the AMPs used here, although decorated with some aromatic groups but lacking Cys and mainly lacking His and Tyr as well, their sequential setup could provide some beneficial contacts for heme, however, they lack a well-defined heme binding site.…”