Rational Fine-Tuning of the Redox Potentials in Chemically Synthesized Rubredoxins

Unusual Reduction Mechanism of Copper in Cysteine-Rich Environment

Copper-cysteine interactions play an important role in Biology and herein we used the copper-substituted rubredoxin (Cu-Rd) from Desulfovibrio gigas to gain further insights into the copper-cysteine redox chemistry. EPR spectroscopy results are consistent with Cu-Rd harboring a Cu^II center in a sulfur-rich coordination, in a distorted tetrahedral structure ( g_∥,⊥ = 2.183 and 2.032 and A_∥,⊥ = 76.4 × 10^-4 and 12 × 10^-4 cm^-1). In Cu-Rd, two oxidation states at Cu-center (Cu^II and Cu^I) are associated with Cys oxidation-reduction, alternating in the redox cycle, as pointed by electrochemical studies that suggest internal geometry rearrangements associated with the electron transfer processes. The midpoint potential of [Cu^I(S-Cys)₂(Cys-S-S-Cys)]/[Cu^II(S-Cys)₄] redox couple was found to be -0.15 V vs NHE showing a large separation of cathodic and anodic peaks potential (Δ E_p = 0.575 V). Interestingly, sulfur-rich Cu^II-Rd is highly stable under argon in dark conditions, which is thermodynamically unfavorable to Cu-thiol autoreduction. The reduction of copper and concomitant oxidation of Cys can both undergo two possible pathways: oxidative as well as photochemical. Under O₂, Cu^II plays the role of the electron carrier from one Cys to O₂ followed by internal geometry rearrangement at the Cu site, which facilitates reduction at Cu-center to yield Cu^I(S-Cys)₂(Cys-S-S-Cys). Photoinduced (irradiated at λ_ex = 280 nm) reduction of the Cu^II center is observed by UV-visible photolysis (above 300 nm all bands disappeared) and tryptophan fluorescence (∼335 nm peak enhanced) experiments. In both pathways, geometry reorganization plays an important role in copper reduction yielding an energetically compatible donor-acceptor system. This model system provides unusual stability and redox chemistry rather than the universal Cu-thiol auto redox chemistry in cysteine-rich copper complexes.

A few key residues determine the high redox potential shift in azurin mutants

The wide range of variability of the reduction potential (E(0)) of blue-copper proteins has been the subject of a large number of studies in the past several years. In particular, a series of azurin mutants have been recently rationally designed tuning E(0) over a very broad range (700 mV) without significantly altering the redox-active site [Marshall et al., Nature, 2009, 462, 113]. This clearly suggests that interactions outside the primary coordination sphere are relevant to determine E(0) in cupredoxins. However, the molecular determinants of the redox potential variability are still undisclosed. Here, by means of atomistic molecular dynamics simulations and hybrid quantum/classical calculations, the mechanisms that determine the E(0) shift of two azurin mutants with high potential shifts are unravelled. The reduction potentials of native azurin and of the mutants are calculated obtaining results in good agreement with the experiments. The analysis of the simulations reveals that only a small number of residues (including non-mutated ones) are relevant in determining the experimentally observed E(0) variation via site-specific, but diverse, mechanisms. These findings open the path to the rational design of new azurin mutants with different E(0).

Sulfonamido tripods: tuning redox potentials via ligand modifications

A series of Fe^II-OH₂ complexes were synthesized with ligands based on the tetradentate sulfonamido tripod N,N',N"-[2,2',2"-nitrilotris(ethane-2,1-diyl)]-tris-({R-Ph}-sulfonamido). These complexes differ by the substituent on the aryl rings and were fully characterized, including their molecular structures via X-ray diffraction methods. All the complexes were five-coordinate with trigonal bipyramidal geometry. A linear correlation was observed between the electronic effects of each ligand, given by the Hammett constants of the para-substituents, and the potential of the Fe^II/Fe^III redox couple, which were determined using cyclic voltammetry. It was found that the range of redox potentials for the complexes spanned approximately 160 mV.

Engineered proteins: redox properties and their applications

Oxidoreductases and metalloproteins, representing more than one third of all known proteins, serve as significant catalysts for numerous biological processes that involve electron transfers such as photosynthesis, respiration, metabolism, and molecular signaling. The functional properties of the oxidoreductases/metalloproteins are determined by the nature of their redox centers. Protein engineering is a powerful approach that is used to incorporate biological and abiological redox cofactors as well as novel enzymes and redox proteins with predictable structures and desirable functions for important biological and chemical applications. The methods of protein engineering, mainly rational design, directed evolution, protein surface modifications, and domain shuffling, have allowed the creation and study of a number of redox proteins. This review presents a selection of engineered redox proteins achieved through these methods, resulting in a manipulation in redox potentials, an increase in electron-transfer efficiency, and an expansion of native proteins by de novo design. Such engineered/modified redox proteins with desired properties have led to a broad spectrum of practical applications, ranging from biosensors, biofuel cells, to pharmaceuticals and hybrid catalysis. Glucose biosensors are one of the most successful products in enzyme electrochemistry, with reconstituted glucose oxidase achieving effective electrical communication with the sensor electrode; direct electron-transfer-type biofuel cells are developed to avoid thermodynamic loss and mediator leakage; and fusion proteins of P450s and redox partners make the biocatalytic generation of drug metabolites possible. In summary, this review includes the properties and applications of the engineered redox proteins as well as their significance and great potential in the exploration of bioelectrochemical sensing devices.

Bioorthogonal chemistry: recent progress and future directions

The ability to use covalent chemistry to label biomolecules selectively in their native habitats has greatly enhanced our understanding of biomolecular dynamics and function beyond what is possible with genetic tools alone. To attain the exquisite selectivity that is essential in this covalent approach a "bottom-up" two-step strategy has achieved many successes recently. In this approach, a bioorthogonal chemical functionality is built into life's basic building blocks-amino acids, nucleosides, lipids, and sugars-as well as coenzymes; after the incorporation, an array of biophysical probes are selectively appended to the tagged biomolecules via a suitable bioorthogonal reaction. While much has been accomplished in the expansion of non-natural building blocks carrying unique chemical moieties, the dearth of robust bioorthogonal reactions has limited both the scope and utility of this promising approach. Here, we summarize the recent progress in the development of bioorthogonal reactions and their applications in various biological systems. A major emphasis has been placed on the mechanistic and kinetic studies of these reactions with the hope that continuous improvements can be made with each reaction in the future. In view of the gap between the capabilities of the current repertoire of bioorthogonal reactions and the unmet needs of outstanding biological problems, we also strive to project the future directions of this rapidly developing field.

Design of functional metalloproteins

Metalloproteins catalyse some of the most complex and important processes in nature, such as photosynthesis and water oxidation. An ultimate test of our knowledge of how metalloproteins work is to design new metalloproteins. Doing so not only can reveal hidden structural features that may be missing from studies of native metalloproteins and their variants, but also can result in new metalloenzymes for biotechnological and pharmaceutical applications. Although it is much more challenging to design metalloproteins than non-metalloproteins, much progress has been made in this area, particularly in functional design, owing to recent advances in areas such as computational and structural biology.

Biosynthetic Inorganic Chemistry

Inorganic chemistry and biology can benefit greatly from each other. Although synthetic and physical inorganic chemistry have been greatly successful in clarifying the role of metal ions in biological systems, the time may now be right to utilize biological systems to advance coordination chemistry. One such example is the use of small, stable, easy-to-make, and well-characterized proteins as ligands to synthesize novel inorganic compounds. This biosynthetic inorganic chemistry is possible thanks to a number of developments in biology. This review summarizes the progress in the synthesis of close models of complex metalloproteins, followed by a description of recent advances in using the approach for making novel compounds that are unprecedented in either inorganic chemistry or biology. The focus is mainly on synthetic "tricks" learned from biology, as well as novel structures and insights obtained. The advantages and disadvantages of this biosynthetic approach are discussed.

Design and engineering of metalloproteins containing unnatural amino acids or non-native metal-containing cofactors

An emerging branch of metalloprotein design and engineering is on the horizon, where unnatural amino acids or non-native metal-containing cofactors are employed in the design and engineering process. These endeavors have been shown to be quite effective in elucidating the precise roles of key residues in protein structures and functions, in providing guiding principles on protein design, in fine-tuning the protein properties to an unprecedented level, and in expanding the repertoire of protein functionalities, and thus its range of applications.

Expanding the Genetic Code

Although chemists can synthesize virtually any small organic molecule, our ability to rationally manipulate the structures of proteins is quite limited, despite their involvement in virtually every life process. For most proteins, modifications are largely restricted to substitutions among the common 20 amino acids. Herein we describe recent advances that make it possible to add new building blocks to the genetic codes of both prokaryotic and eukaryotic organisms. Over 30 novel amino acids have been genetically encoded in response to unique triplet and quadruplet codons including fluorescent, photoreactive, and redox-active amino acids, glycosylated amino acids, and amino acids with keto, azido, acetylenic, and heavy-atom-containing side chains. By removing the limitations imposed by the existing 20 amino acid code, it should be possible to generate proteins and perhaps entire organisms with new or enhanced properties.

Discontinuum between a thiolate and a thiol ligand

The effect of H-bond donation to the thiolate ligand of (eta(5)-C(5)H(5))Fe(CO)(2)SR (1) to give H-bond adducts (1 small middle dotHX) and eventually protonation to give [(eta(5)-C(5)H(5))Fe(CO)(2)(HSR)](+) (1H(+)()) has been investigated experimentally and computationally. The electronic structures of 1(R = Me), several derivatives of 1(R = Me) small middle dotHX, and 1(R = Me)H(+)() have been investigated using DFT (density functional theory) computational methods. As previously suggested, these calculations indicate the HOMO of 1 is Fedpi-Sppi antibonding and largely sulfur in character. The calculations indicate the electronic structure of 1 is not altered markedly by H-bond donation to the S center, but protonation results in a reorganization of the electronic structure of 1H(+)() and a HOMO that is largely metal in character. The reduction of Fe-S distances upon protonation of 1(R = Ph) to give 1(R = Ph)H(+)() small middle dotBF(4)()(-)() (2.282(2) and 2.258(2) A, respectively), as determined by single-crystal X-ray crystallography, also indicates diminished Fedpi-Sppi antibonding. Using the carbonyl stretching frequencies as a gauge of the donor ability of the thiolate ligand, we conclude that H-bonding has a continuous effect on the donor properties of the thiolate ligand of 1 (i.e., is a function of the pK(a) of the H-bond donor). A discontinuous effect results when the pK(b) of 1 is reached and the complex is protonated. For our study of 1, the maximal effect of H-bonding is about 30% of protonation. Because the position of acid-base equilibrium depends on the relative basicities of the thiolate ligand and the conjugate base of the H-bond donor (and the relative heats of solvation of the acids and their conjugate bases), a true continuum of effects can be anticipated only for systems that are pK-matched in their given environments. Thus, when the conjugate base of the H-bond donor is a stronger base than the thiolate ligand (as in the present case), H-bond donation has a relatively small effect, but protonation triggers a large, discontinuous effect on the electronic structure of 1.

Total synthesis of cytochrome b562 by native chemical ligation using a removable auxiliary

We have completed the total chemical synthesis of cytochrome b562 and an axial ligand analogue, [SeMet(7)]cyt b562, by thioester-mediated chemical ligation of unprotected peptide segments. A novel auxiliary-mediated native chemical ligation that enables peptide ligation to be applied to protein sequences lacking cysteine was used. A cleavable thiol-containing auxiliary group, 1-phenyl-2-mercaptoethyl, was added to the alpha-amino group of one peptide segment to facilitate amide bond-forming ligation. The amine-linked 1-phenyl-2-mercaptoethyl auxiliary was stable to anhydrous hydrogen fluoride used to cleave and deprotect peptides after solid-phase peptide synthesis. Following native chemical ligation with a thioester-containing segment, the auxiliary group was cleanly removed from the newly formed amide bond by treatment with anhydrous hydrogen fluoride, yielding a full-length unmodified polypeptide product. The resulting polypeptide was reconstituted with heme and folded to form the functional protein molecule. Synthetic wild-type cyt b562 exhibited spectroscopic and electrochemical properties identical to the recombinant protein, whereas the engineered [SeMet(7)]cyt b562 analogue protein was spectroscopically and functionally distinct, with a reduction potential shifted by approximately 45 mV. The use of the 1-phenyl-2-mercaptoethyl removable auxiliary reported here will greatly expand the applicability of total protein synthesis by native chemical ligation of unprotected peptide segments.

Synthesis of native proteins by chemical ligation

In just a few short years, the chemical ligation of unprotected peptide segments in aqueous solution has established itself as the most practical method for the total synthesis of native proteins. A wide range of proteins has been prepared. These synthetic molecules have led to the elucidation of gene function, to the discovery of novel biology, and to the determination of new three-dimensional protein structures by both NMR and X-ray crystallography. The facile access to novel analogs provided by chemical protein synthesis has led to original insights into the molecular basis of protein function in a number of systems. Chemical protein synthesis has also enabled the systematic development of proteins with enhanced potency and specificity as candidate therapeutic agents.

Synthesis of a three zinc finger protein, Zif268, by native chemical ligation

Protein synthesis by native chemical ligation has been an effective approach for the synthesis of proteins of moderate size. The utility of this approach for protein synthesis is demonstrated by the synthesis of a transcription factor, Zif 268 that contains three zinc finger domains. This synthesis highlights the modular nature of the chemical ligation approach and the ability to synthesize, handle and fold multiple domain proteins.

Chemical protein synthesis

Since the mid-1990s, chemical synthesis has emerged as a powerful technique for the study of structure/function relationships in proteins. During the review period, the applicability of chemical protein synthesis techniques has been significantly broadened by increases in the size of synthetically accessible proteins through two new techniques: solid-phase protein synthesis and expressed protein ligation. Also in the period under review, synthetic access to novel classes of proteins has been established, including metalloproteins with tuned properties and integral membrane proteins.