Introduction of a specific binding domain on myoglobin surface by new chemical modification

Artificial Small Molecules as Cofactors and Biomacromolecular Building Blocks in Synthetic Biology: Design, Synthesis, Applications, and Challenges

Enzymes are essential catalysts for various chemical reactions in biological systems and often rely on metal ions or cofactors to stabilize their structure or perform functions. Improving enzyme performance has always been an important direction of protein engineering. In recent years, various artificial small molecules have been successfully used in enzyme engineering. The types of enzymatic reactions and metabolic pathways in cells can be expanded by the incorporation of these artificial small molecules either as cofactors or as building blocks of proteins and nucleic acids, which greatly promotes the development and application of biotechnology. In this review, we summarized research on artificial small molecules including biological metal cluster mimics, coenzyme analogs (mNADs), designer cofactors, non-natural nucleotides (XNAs), and non-natural amino acids (nnAAs), focusing on their design, synthesis, and applications as well as the current challenges in synthetic biology.

The Red Color of Life Transformed - Synthetic Advances and Emerging Applications of Protoporphyrin IX in Chemical Biology

Protoporphyrin IX (PPIX) is the porphyrin scaffold of heme b, a ubiquitous prosthetic group of proteins responsible for oxygen binding (hemoglobin, myoglobin), electron transfer (cytochrome c) and catalysis (cytochrome P450, catalases, peroxidases). PPIX and its metallated derivatives frequently find application as therapeutic agents, imaging tools, catalysts, sensors and in light harvesting. The vast toolkit of accessible porphyrin functionalization reactions enables easy synthetic modification of PPIX to meet the requirements for its multiple uses. In the past few years, particular interest has arisen in exploiting the interaction of PPIX and its synthetic derivatives with biomolecules such as DNA and heme-binding proteins to evolve molecular devices with new functions as well as to uncover potential therapeutic toeholds. This review strives to shine a light on the most recent developments in the synthetic chemistry of PPIX and its uses in selected fields of chemical biology.

Thermoresponsive Micellar Assembly Constructed from a Hexameric Hemoprotein Modified with Poly(N-isopropylacrylamide) toward an Artificial Light-Harvesting System

Artificial protein assemblies inspired by nature have significant potential in development of emergent functional materials. In order to construct an artificial protein assembly, we employed a mutant of a thermostable hemoprotein, hexameric tyrosine-coordinated heme protein (HTHP), as a building block. The HTHP mutant which has cysteine residues introduced on the bottom surface of its columnar structure was reacted with maleimide-tethering thermoresponsive poly(N-isopropylacrylamide), PNIPAAm, to generate the protein assembly upon heating. The site-specific modification of the cysteine residues with PNIPAAm on the protein surface was confirmed by SDS-PAGE and analytical size exclusion chromatography (SEC). The PNIPAAm-modified HTHP (PNIPAAm-HTHP) is found to provide a 43 nm spherical structure at 60 °C, and the structural changes observed between the assembled and the disassembled forms were duplicated at least five times. High-speed atomic force microscopic measurements of the micellar assembly supported by cross-linkage with glutaraldehyde indicate that the protein matrices are located on the surface of the sphere and cover the inner PNIPAAm core. Furthermore, substitution of heme with a photosensitizer, Zn protoporphyrin IX (ZnPP), in the micellar assembly provides an artificial light-harvesting system. Photochemical measurements of the ZnPP-substituted micellar assembly demonstrate that energy migration among the arrayed ZnPP molecules occurs within the range of several tens of picoseconds. Our present work represents the first example of an artificial light-harvesting system based on an assembled hemoprotein oligomer structure to replicate natural light-harvesting systems.

Successive energy transfer within multiple photosensitizers assembled in a hexameric hemoprotein scaffold

An assembly of multiple photosensitizers is demonstrated by development of a hexameric hemoprotein (HTHP) scaffold as a light harvesting model to replicate the successive energy transfer occuring within photosensitizer assemblies of natural systems. In our model, six zinc protoporphyrin IX (ZnPP) molecules are arrayed at the heme binding site of HTHP by supramolecular interactions and five fluorescein (Flu) molecules and one Texas Red (Tex) molecule as donor and acceptor photosensitizers, respectively, are attached to the HTHP protein surface with covalent linkages. The flow of excited energy from photoexcited Flu to Tex occurs via two pathways: direct energy transfer from Flu to Tex (path 1) and energy transfer via ZnPP (path 2). Steady state and time-resolved fluorescence measurements reveal that the energy transfer ratio of these pathways (path 1 : path 2) is 39 : 61. These findings indicate that the excited energy originating at five Flu and six ZnPP molecules is collected at one Tex molecule as a funnel-like bottom for light harvesting. The present system using the hexameric hemoprotein scaffold is a promising candidate for construction of an artificial light harvesting system having multiple photosensitizers to promote efficient use of solar energy.

Electron transfer and oxidase activities in reconstituted hemoproteins with chemically modified cofactors

Protoheme IX is a typical iron porphyrin cofactor, showing a variety of reactivities in many hemoproteins under the reaction environments provided by protein matrices. Chemical modification of the protoheme cofactor is expected to be a versatile strategy to design hemoproteins possessing unique functions. This review focuses on the conversion of a hemoprotein, mainly myoglobin (an oxygen-storage hemoprotein), into a protein having different functions from the original ones by replacement of the protoheme cofactor with synthetic cofactors. The myoglobin having anionic patches pended to the heme propionates effectively binds electron-accepting proteins or small cationic organic molecules on the protein surface, resulting in enhanced efficiency of the photoinduced electron transfers from the myoglobin to these electron acceptors. Furthermore, the peroxidase and peroxygenase activities are also enhanced due to the facile substrate accesses. The attachment of the chemically active moiety such as flavin at the heme terminal is also important to give P450-like function to the native myoglobin. The employment of a structural isomer of porphyrin as an artificial cofactor gives rise to remarkably high dioxygen affinity and peroxidase activity in myoglobin, and allows us to easily detect high-valent species of the porphyrin isomer in HRP. These examples provide a clear insight into hemoprotein modifications based on synthetic chemistry as well as genetic amino acid mutations.

Metal ion-dependent fluorescent dynamics of photoexcited zinc-porphyrin and zinc-myoglobin modified with ethylenediaminetetraacetic acid

The reconstituted zinc-myoglobin (ZnMb) dyads, ZnMb-[M(II)(edta)], have been prepared by incorporating a zinc-porphyrin (ZnP) cofactor modified with ethylenediaminetetraacetic acid (H(4)edta) into apo-Mb. In case of the monomeric ZnP(edta) cofactor coordinated by one pyridine molecule, ZnP(py)(edta), a spontaneous 1:1 complex with a transient metal ion was formed in an aqueous solvent, and the photoexcited singlet state of ZnP, (1)(ZnP)*, was quenched by the [Cu(II)(edta)] moiety through intramolecular photoinduced electron-transfer (ET) reaction. The rate constant for the intramolecular quenching ET (k(q)) at 25 degrees C was successfully obtained as k(q) = 5.1 x 10(9) s(-1). In the case of Co(2+), Ni(2+), and Mn(2+), intersystem crossing by paramagnetic effect was mainly considered between (1)(ZnP)* and the [M(II)(edta)] complex. For the ZnMb-[M(II)(edta)] systems, the intramolecular ET reaction between the excited singlet state of (1)(ZnMb)* and the [Cu(II)(edta)] moieties provided the slower quenching rate constant, k(q) = 2.1 x 10(8) s(-1), compared with that of the ZnP(py)(edta) one. Kinetic studies also presented the efficient fluorescence quenching of the (1)(ZnMb)*-[Co(II)(edta)] dyad. Our study clearly demonstrates that wrapping of the ZnP cofactor by the apoprotein matrix and synthetic manipulation at the Mb surface ensure metal ion-sensitive fluorescent dynamics of ZnMb and provides valuable information to elucidate the complicated mechanism of the biological photoinduced ET reactions of hemoproteins.

Self-Assembled Architectures from Biohybrid Triblock Copolymers

The synthesis and self-assembly behavior of biohybrid ABC triblock copolymers consisting of a synthetic diblock, polystyrene-b-polyethylene glycol (PSm-b-PEG113), where m is varied, and a hemeprotein, myoglobin (Mb) or horse radish peroxidase (HRP), is described. The synthetic diblock copolymer is first functionalized with the heme cofactor and subsequently reconstituted with the apoprotein or the apoenzyme to yield the protein-containing ABC triblock copolymer. The obtained amphiphilic block copolymers self-assemble in aqueous solution into a large variety of aggregate structures. Depending on the protein and the polystyrene block length, micellar rods, vesicles, toroids, figure eight structures, octopus structures, and spheres with a lamellar surface are formed.

Photoinduced Intramolecular Electron-Transfer Reactions of Reconstituted Met- and Zinc-Myoglobins Appending Acridine and Methylacridinium Ion as DNA-Binders

Three types of reconstituted met- and zinc-myoglobin (metMb and ZnMb) dyads, ZnMbAc(4)Me+, ZnMbAc(6)Me+, and metMbAc(6) have been prepared by incorporating chemically modified metalloporphyrin cofactor appending an acridine (Ac) or a methylacridinium ion ([AcMe]+) into apo-Mb. In the bimolecular system between ZnMb and [AcMe]+, the photoexcited triplet state of ZnMb, 3(ZnMb)*, was successfully quenched by [AcMe]+ to form the radical pair of ZnMb cation (ZnMb*+) and reduced methylacridine ([AcMe]*), followed by a thermal back ET reaction. The rate constants for the intermolecular quenching ET (kq) and the back ET reaction (kb) at 25 degrees C were successfully obtained as kq = (8.8 +/- 0.4) x 10(7) M(-1) s(-1) and kb = (1.2 +/- 0.1) x 10(8) M(-1) s(-1), respectively. On the other hand, in case of the intramolecular photoinduced ET reactions of ZnMbAc(4)Me+ and ZnMbAc(6)Me+ dyads, the first-order quenching rate constants (kET) of 3(ZnMb)* by [AcMe]+ moiety were determined to be kET = 2.6 x 10(3) and 2.5 x 10(3) s(-1), respectively. When such ET occurs along the alkyl spacer via through-bond mechanism at the surface of Mb, the obtained kET is reasonable to provide decay constant of beta (1.0-1.3 A(-1)). Upon photoirradiation of [AcMe]+ moiety, kinetic studies also presented the intramolecular quenching reactions from the excited singlet state, 1([AcMe]+)*, whose likely process is the photoinduced energy-transfer reaction. For metMbAc(6) dyad, steady-state fluorescence was almost quenched, while the signal around 440 nm gradually appeared in the presence of various concentrations of DNA. Our study implies that synthetic manipulation at the Mb surface, by using an artificial DNA-binder coupled with photoinduced reaction, may provide valuable information to construct new Mb-DNA complex and sensitive fluorescent for DNA.

New functionalization of myoglobin by chemical modification of heme-propionates

The reconstitution of myoglobin with an artificially created prosthetic group is a unique method for introducing a new chemical function into the protein. Particularly, the modification of two heme-propionates gives us an effective binding domain or binding site on the protein surface. This Account traces the design and construction of the highly ordered binding domain around the entrance of the heme pocket. The discussion includes the protein-small molecule or protein-protein recognition, electron transfer reaction within the complex, and enhancement of the chemical reactivity of the myoglobin with a substrate binding site. The synthetic approach to modifying a protein will be a new trend in engineering a novel function in naturally occurring hemoprotein.