Biocatalysts Based on Peptide and Peptide Conjugate Nanostructures

Abstract

Peptides and their conjugates (to lipids, bulky N-terminals, or other groups) can self-assemble into nanostructures such as fibrils, nanotubes, coiled coil bundles, and micelles, and these can be used as platforms to present functional residues in order to catalyze a diversity of reactions. Peptide structures can be used to template catalytic sites inspired by those present in natural enzymes as well as simpler constructs using individual catalytic amino acids, especially proline and histidine. The literature on the use of peptide (and peptide conjugate) α-helical and β-sheet structures as well as turn or disordered peptides in the biocatalysis of a range of organic reactions including hydrolysis and a variety of coupling reactions (e.g., aldol reactions) is reviewed. The simpler design rules for peptide structures compared to those of folded proteins permit ready ab initio design (minimalist approach) of effective catalytic structures that mimic the binding pockets of natural enzymes or which simply present catalytic motifs at high density on nanostructure scaffolds. Research on these topics is summarized, along with a discussion of metal nanoparticle catalysts templated by peptide nanostructures, especially fibrils. Research showing the high activities of different classes of peptides in catalyzing many reactions is highlighted. Advances in peptide design and synthesis methods mean they hold great potential for future developments of effective bioinspired and biocompatible catalysts.

Scheme 1. Representative Reactions among Those Discussed Extensively in the Following Text

Based on ref (57).

Figure 1

Complexation of proline–naphthyridine with a pyridinone via multiple hydrogen bonds. Reprinted with permission from ref (65). Copyright 2007 Wiley-VCH GmbH.

Scheme 2. Examples of Peptide-Based Amphiphiles Studied by the Groups of Escuder and Miravet

Based on ref (57).

Figure 2

Fibrils formed by catalytically active lipopeptide PAEPKI-C₁₆ shown in the center. TEM images at three pH values (bottom) along with images of the lipopeptide in aqueous solution at the three pH values indicated, showing formation of gel at high pH (top left) and an image of a solution at higher concentration imaged between crossed polarizers showing birefringence due to nematic ordering of the fibrils at pH 8 (top right). Reprinted with permission from ref (83). Copyright 2020 American Chemical Society.

Figure 3

Secondary structure representation (showing catalytic histidine residues) and sequence of catalytically active helix–loop–helix peptide KO-42 with the loop region GPVD shown in the middle of the sequence at the bottom. Reprinted with permission from ref (120). Copyright 1998 American Chemical Society.

Figure 4

Structure of a designed metalloprotease three-helix bundle [pdb 3PBJ]. (a) One trimer with bound metal ions. (b) Enlargement of site showing C residues around a Hg²⁺ ion (with electron density grid overlaid). (c) H residues around a Zn²⁺ ion. Reprinted by permission from Springer-Nature: Nature Chemistry ref (115). Copyright 1998.

Figure 5

Homodimeric coiled coil based on a de novo design, showing cleft (red mesh) and Zn²⁺ (sphere) binding site with highlighted histidines in the catalytic site. Reprinted with permission from ref (114). Copyright 2012 American Chemical Society.

Figure 6

Heptameric coiled coil designed by Woolfson’s group which acts to hydrolyze pNPA. The parent peptide sequence (green) was substituted with the E, H, C triad in the catalytically active heptameric structure (blue). From ref (144) based on ref (103). Reprinted by permission from Springer-Nature: Nature Chemistry ref (144). Copyright 2016.

Figure 7

Design of a Zn²⁺-dependent esterase. (a) Structure of human carbonic acid, showing expansion of the Zn²⁺ binding motif. (b) Peptide Ac-LHLHLQL-NH₂ with residues labeled. (c–e) Computational model of β-strand packing of this peptide showing (c) the overall structure of the array which constitutes a fold mimic, (d) hydrophobic core packing, and (e) the zinc coordination sphere. Reprinted from Springer-Nature: Nature Chemistry, ref (106), Copyright 2004.

Figure 8

(a) Molecular structures of Fmoc-amino acids 1 and 2 coassembled with hemin chloride 3 (with or without histidine 4) form hemin-loaded fibrils in a hydrogel. (b) The hydrogel can be used to catalyze the peroxidation of pyrogallol to purporogallin as shown. Reprinted with permission from ref (164). Copyright 2007 Wiley-VCH GmbH.

Scheme 3. Lipopeptides and Controls Studied by Guler and Stupp^,

Molecule 1 forms β-sheet nanofibrils in contrast to non-lipidated control 3 whereas 2 and 4 are analogues with proline residues to disrupt β-sheet formation. Reprinted with permission from ref (108). Copyright 2007 American Chemical Society.

Figure 9

Fluorescent labeling of cells using copper-functionalized fibrils of a peptide amphiphile (PA) to catalyze a click reaction between alkyne-functionalized cell membranes (using an alkyne-functionalized mannose amine) and azide-biotin followed by streptavidin-FITC fluorophore noncovalent binding to the biotin groups. Reprinted with permission from ref (168). Copyright 2015 American Chemical Society.

Figure 10

Retro-aldol catalysis using KLVFF-based peptide nanotubes. (a) Retro-aldol reaction of methodol to give 6-methoxy-2-naphthaldehyde, with indicated fluorescence peaks. (b) Fluorescence emission spectra (λ_ex = 330 nm) of 50 μM (±)-methodol (black line), 50 μM (±)-methodol with 1 mM Ac-KLVFFAL-NH₂ nanotubes (red line), and 50 μM methodol with 1 mM Ac-RLVFFAL-NH₂ nanotubes (green line). (c) Initial rate of production of 6-methoxy-2-naphthaldehyde by the indicated peptide assembly where the peptide concentration was 500 μM and the starting (±)-methodol concentration was 80 μM. (d), Molecular dynamics simulation of (S)-methodol docked onto the surface of Ac-KLVFFAL-NH₂ antiparallel out-of-register amyloid assembly. In the space filling models the hydrophobic LVFFAL residues are colored gray, the lysines are blue, and methodol is drawn in a stick representation with carbons colored green, oxygen red, and hydrogen white. (e and f) Detail of arrangement of methodol (space filling) on tube surface with peptides drawn as sticks. Reprinted by permission from Springer-Nature: Nature Chemistry, ref (175), Copyright 2017.

Figure 11

Lipopeptide nanotubes catalyze aldol reactions. (a) Lipopeptides based on the VFF sequence from the Aβ peptide with cationic residues X shown. (b and c) Aldol reactions in catalysis studies. (d and e) Substrates and products. Reprinted with permission from ref (176). Copyright 2020 Wiley-VCH GmbH.

Figure 12

Three-step cascade reaction leading to the development of a three-input AND logic gate. (a) Schematic of reactions. (b) Kinetics of product formation for the indicated species. (c) Bar diagram of activity of the Im-KL nanotubes (molecular structure shown in the inset along with β-strand indication) along with controls lacking the imidazole N-terminus, i.e. Ac-KL and Ac-KL with histidine. (d) Three-input Boolean logic gate, with output only in the case of all three inputs. Reprinted with permission from ref (178). Copyright 2021 Wiley-VCH GmbH.

Figure 13

Molecular structure of peptide bola-amphiphile studied by Maity et al. along with images of solution and hydrogels in vials including a hydrogel containing Pd nanoparticles and a TEM image of Pd-decorated peptide fibrils. Reprinted with permission from ref (194). Copyright 2014 Wiley-VCH GmbH.