Chemical activation of cytochrome c proteins via crown ether complexation: cold-active synzymes for enantiomer-selective sulfoxide oxidation in methanol

Early postmortem muscle proteome and metabolome of beef longissimus thoracis muscle classified by pH at 6 hours postmortem

The objective was to identify metabolome and proteome differences at 1 h and 1 d postmortem between longissimus thoracis (LT) muscle classified based on 6 h pH values. Twenty beef LT rib sections were sorted based on 6 h postmortem pH values into low (LpH; pH < 5.55; n = 9) and high (HpH; pH > 5.84; n = 8) pH classifications. Warner-Bratzler shear force (WBSF), desmin degradation, and calpain-1 autolysis were measured. Two-dimensional difference in gel electrophoresis (3-10, 4-7, and 6-9 pH range) and Tandem mass tagging (TMT) protein analyses were employed to determine how the sarcoplasmic protein profile varied across pH classification. Non-targeted metabolomic analyses were conducted on extracts prepared at 1 h and 1 d postmortem. The LpH classification had a lower WBSF value at 1 d postmortem, which was explained by greater calpain-1 autolysis and desmin degradation at 1 d postmortem. Proteome and metabolome analysis revealed a phenotype that promotes more rapid energy metabolism in the LpH group. Proteome and metabolome analyses identified energy production, apoptotic, calcium homeostasis, and proteasome systems influencing pH classifications that could explain the observed pH, proteolysis, and beef tenderness differences. SIGNIFICANCE: This study is the first to identify proteomic and metabolomic variations early (1 h and 1 day) postmortem that are linked to differences in early (6 h) postmortem pH values and to tenderness differences at 1 day postmortem. This study integrates postmortem biochemical features (protein degradation, proteome, and metabolome variations) to postmortem pH decline and eating quality of beef steaks. Potential biomarkers of more rapid postmortem metabolism linked to earlier tenderization in beef are suggested. Identification of these biochemical features will assist in predicting the eating quality of beef products.

What do we learn from enzyme behaviors in organic solvents? - Structural functionalization of ionic liquids for enzyme activation and stabilization

Enzyme activity in nonaqueous media (e.g. conventional organic solvents) is typically lower than in water by several orders of magnitude. There is a rising interest of developing new nonaqueous solvent systems that are more "water-like" and more biocompatible. Therefore, we need to learn from the current state of nonaqueous biocatalysis to overcome its bottleneck and provide guidance for new solvent design. This review firstly focuses on the discussion of how organic solvent properties (such as polarity and hydrophobicity) influence the enzyme activity and stability, and how these properties impact the enzyme's conformation and dynamics. While hydrophobic organic solvents usually lead to the maintenance of enzyme activity, solvents carrying functional groups like hydroxys and ethers (including crown ethers and cyclodextrins) can lead to enzyme activation. Ionic liquids (ILs) are designable solvents that can conveniently incorporate these functional groups. Therefore, we systematically survey these ether- and/or hydroxy-functionalized ILs, and find most of them are highly compatible with enzymes leading to high activity and stability. In particular, ILs carrying both ether and tert-alcohol groups are among the most enzyme-activating solvents. Future direction is to learn from enzyme behaviors in both water and nonaqueous media to design biocompatible "water-like" solvents.

Complexes of Crown Ether Macrocycles with Methyl Guanidinium: Insights into the Capture of Charge in Peptides

Crown ethers are well known as modulating agents of protein function and interactions. The action of crown ethers is driven by an alteration of the charged moieties of proteins through the capping of cationic amino acid side chains. This study evaluates the conformational features involved in the binding of crown ethers to the side chain of arginine. For this purpose, isolated complexes of methyl guanidinium with 12-crown-4 and 18-crown-6 are characterized with infrared action vibrational spectroscopy and quantum chemical computations. The conformational landscapes of the two complexes comprise an extensive ensemble of conformations close in energy. In the 12-crown-4 complex, the crown ether has the plane of its backbone approximately perpendicular to that of the guanidinium moiety and coordinates to two or three of its NH^δ+ bonds. In the 18-crown-6 complex, the crown ether backbone is partially folded and tilted with respect to guanidinium and fixes its position in order to facilitate up to a four-fold coordination in the complex. The access of the complexes to multiple conformations leads to broad band structures in the N-H stretching region of their vibrational spectra.

The cytochrome c–cyclo[6]aramide complex as a supramolecular catalyst in methanol

A hydrogen-bonded aromatic amide macrocycle forms a host–guest complex with cytochrome c, which acts as a supramolecular catalyst for the oxidation of benzhydrol even at low temperatures.

12-Crown-4 Ether Disrupts the Patient Brain-Derived Amyloid-β-Fibril Trimer: Insight from All-Atom Molecular Dynamics Simulations

Recent experimental data elucidated that 12-crown-4 ether molecule can disrupt Aβ40 fibrils but the mechanism of disruption remains elusive. We have performed a series of all-atom molecular dynamics simulations to study the molecular mechanism of Aβ40 fibril disruption by 12-crown-4. In the present study we have used the Aβ40 fibril trimer as it is the smallest unit that maintains a stable U-shaped structure, and serves as the nucleus to form larger fibrils. Our study reveals that 12-crown-4 ether can enter into the hydrophobic core region and form competitive, hydrophobic interactions with key hydrophobic residues; these interactions break the intersheet hydrophobic interactions and lead to the opening of the U-shaped topology and a loss of β-sheet structure. Furthermore, we observed periods of time when 12-crown-4 was in the hydrophobic core and periods of time when it interacted with Lys28 (chain C), a "tug of war"; the 12-crown-4 binding with Lys28 destabilizes the salt-bridge between Asp23 and Lys28. In addition to the two aforementioned binding modes, the 12-crown-4 binds with Lys16, which is known to form a salt-bridge with Glu22 in antiparallel arranged Aβ fibrils. Our results are in good agreement with experimental results and suggest that molecules that have the ability to interact with both the hydrophobic core region and positively charged residues could serve as potential inhibitors of Aβ fibrils.

Protein Camouflage: Supramolecular Anion Recognition by Ubiquitin

Progress in the field of bio-supramolecular chemistry, the bottom-up assembly of protein-ligand systems, relies on a detailed knowledge of molecular recognition. To address this issue, we have characterised complex formation between human ubiquitin (HUb) and four supramolecular anions. The ligands were: pyrenetetrasulfonic acid (4PSA), p-sulfonato-calix[4]arene (SCLX4), bisphosphate tweezers (CLR01) and meso-tetrakis (4-sulfonatophenyl)porphyrin (TPPS), which vary in net charge, size, shape and hydrophobicity. All four ligands induced significant changes in the HSQC spectrum of HUb. Chemical shift perturbations and line-broadening effects were used to identify binding sites and to quantify affinities. Supporting data were obtained from docking simulations. It was found that these weakly interacting ligands bind to extensive surface patches on HUb. A comparison of the data suggests some general indicators for the protein-binding specificity of supramolecular anions. Differences in binding were observed between the cavity-containing and planar ligands. The former had a preference for the arginine-rich, flexible C terminus of HUb.

Crowning proteins: modulating the protein surface properties using crown ethers

Crown ethers are small, cyclic polyethers that have found wide-spread use in phase-transfer catalysis and, to a certain degree, in protein chemistry. Crown ethers readily bind metallic and organic cations, including positively charged amino acid side chains. We elucidated the crystal structures of several protein-crown ether co-crystals grown in the presence of 18-crown-6. We then employed biophysical methods and molecular dynamics simulations to compare these complexes with the corresponding apoproteins and with similar complexes with ring-shaped low-molecular-weight polyethylene glycols. Our studies show that crown ethers can modify protein surface behavior dramatically by stabilizing either intra- or intermolecular interactions. Consequently, we propose that crown ethers can be used to modulate a wide variety of protein surface behaviors, such as oligomerization, domain–domain interactions, stabilization in organic solvents, and crystallization.

A new, facile method to prepare hybrid calcium poly(styrene-phenylvinylphosphonate)–phosphate materials for a superior performance catalyst support

Various pores or channels produced by modification of the PS-PVPA chain could contribute to significant impact on the excellent catalytic activity.

Molecular recognition: from solution science to nano/materials technology

In the 25 years since its Nobel Prize in chemistry, supramolecular chemistry based on molecular recognition has been paid much attention in scientific and technological fields. Nanotechnology and the related areas seek breakthrough methods of nanofabrication based on rational organization through assembly of constituent molecules. Advanced biochemistry, medical applications, and environmental and energy technologies also depend on the importance of specific interactions between molecules. In those current fields, molecular recognition is now being re-evaluated. In this review, we re-examine current trends in molecular recognition from the viewpoint of the surrounding media, that is (i) the solution phase for development of basic science and molecular design advances; (ii) at nano/materials interfaces for emerging technologies and applications. The first section of this review includes molecular recognition frontiers, receptor design based on combinatorial approaches, organic capsule receptors, metallo-capsule receptors, helical receptors, dendrimer receptors, and the future design of receptor architectures. The following section summarizes topics related to molecular recognition at interfaces including fundamentals of molecular recognition, sensing and detection, structure formation, molecular machines, molecular recognition involving polymers and related materials, and molecular recognition processes in nanostructured materials.

Dominant structural factors for complexation and denaturation of proteins using carboxylic acid receptors

Complexation accompanied by denaturation of protein with synthetic carboxylic acid receptors was investigated, to evaluate the key factors for recognition of proteins. The synthetic receptors used were tetraphenylporphyrin (TPP) derivatives and receptors bearing multiple (2-8) carboxylic acid groups. The complexation behavior was quantified from the absorption in the far UV CD spectrum attributed to the secondary structure of the protein. TPP derivatives bearing multiple carboxylic acid groups in the side chains exhibited higher affinity than other receptors that were smaller and had fewer carboxylic acid groups. As the degree of complexation was influenced by the pH and ionic strength in aqueous solution, electrostatic interaction was one of the most important factors for the recognition of proteins. Complexation was also estimated by observation of fluorescence quenching of the TPP derivatives. The stoichiometry of the complexes between lysozyme and the porphyrins was investigated by quantitative analysis of the denaturation using CD spectra. From the results of Job plots and slope analysis for the amount of denatured protein, formation of 1:1 complexes was confirmed. The equilibrium association constants (K(ass)) for lysozyme and the TPP receptors ranged from 0.6×10(6) to 1.1×10(6)M(-1). The lytic activity of lysozyme was partially lost in the presence of anionic TPP derivatives, due to complexation and denaturation.

Thermodynamic studies of partitioning behavior of cytochrome c in ionic liquid-based aqueous two-phase system

The ionic liquid/aqueous two-phase extraction systems (ATPSs) based on imidazolium ionic liquids were used to extract cytochrome c. Effects of the alkyl chain length of the ionic liquid cations, concentration of potassium citrate, temperature and pH on the extraction efficiency have been investigated. The thermodynamic parameters (ΔG(T)°, ΔH(T)° and ΔS(T)°) associated with Cyt-c partitioning in aqueous two phase systems were determined. Thermodynamic studies indicated that the partitioning of Cyt-c was driven by both hydrophobic and electrostatic interactions in the extraction process. Under the optimum conditions, experiment results showed that 94% of the cytochrome c could be extracted into the ionic liquid-rich phase in a one-step extraction. The structural characterization of Cyt-c in the IL ATPS was investigated by UV-vis and circular dichroism (CD) spectra. The results demonstrated that no direct bonding interaction observed between ionic liquid and cytochrome c, while the native properties of the cytochrome c were not altered. Compared with traditional liquid-liquid extractions based on toxic organic solvents, ionic liquid/aqueous two phase extraction offers clear advantages due to no use of volatile organic solvent and low consumption of imidazolium ionic liquids.

Characterization of peroxide-bound heme species generated in the reaction of thermally tolerant cytochrome c552 with hydrogen peroxide

Peroxide-bound heme species have been considered difficult to detect under physiological conditions because of their intrinsically transient properties. Cytochrome c552 (cyt c552), from Thermus thermophirus HB8, bearing a mutation to an alanine at Met69 (M69A) reacts with hydrogen peroxide (H(2)O(2)) to generate a detectable hydroperoxo-ferric heme ([Fe(3+)--OOH]) species at ambient temperature. EPR measurements during appropriate reaction periods reveal that the [Fe(3+)--OOH] species is in a preequilibrium state between the resting form of the cyt c552 variant and a subsequent intermediate, compound II with a protein radical. Addition of ascorbic acid to the reaction mixture of the cyt c552 variant and H(2)O(2) does not affect the formation of the [Fe(3+)--OOH] species,a result suggesting that the species is incompetent for the oxidation of even an oxidatively fragile substrate such as ascorbic acid. Another variant bearing an additional mutation to aspartic acid at Val49 (V49D/M69A) reveals that a highly hydrophobic heme cavity in cyt c552 accounts for the generation of the durable [Fe(3+)--OOH] species. The less polar environment inside the cavity is expected to prevent H(2)O from approaching the cavity. This would suppress protonation of the distal oxygen atom of the [Fe(3+)--OOH] species and retard subsequent dissociation of H(2)O from the OOH moiety.

Extractive solubilization, structural change, and functional conversion of cytochrome c in ionic liquids via crown ether complexation

This article reports on the extraction behavior of heme proteins from an aqueous phase into ionic liquids (ILs) with dicyclohexano-18-crown-6 (DCH18C6), and the structure-function relationship of cytochrome c (Cyt-c) dissolved in ILs. We have found that DCH18C6 enables transfer of Lys-rich proteins into ILs via supramolecular complexation. The hydrophobicity and functional groups of ILs have a great influence on protein partitioning, and a hydroxyl group-containing IL with DCH18C6 is capable of the quantitative partitioning of Cyt-c. On the other hand, protein transfer using conventional organic solvents is negligibly small. UV-visible, CD, and resonance Raman spectroscopic characterizations indicate that the sixth ligand Met 80 in the heme group of the Cyt-c-DCH18C6 complex in IL is replaced by other amino acid residues of the peptide chain and that a non-natural, six-coordinate, low-spin ferric heme structure is induced in IL. Solubilization of Cyt-c in IL causes the environmental change of the heme vicinity of Cyt-c, which triggers the functional conversion of Cyt-c from an electron-transfer protein to peroxidase. The Cyt-c-DCH18C6 complex in IL provides remarkably high peroxidase activity compared with native Cyt-c, because of enhancement of the affinity for H2O2.

Proteo-Dendrimers Designed for Complementary Recognition of Cytochromec: Dendrimer Architecture toward Nanoscale Protein Complexation

"Proteo-dendrimers" in which polyanionic hepta(glutamic acids), fluorescent zinc porphyrinate cores, hydrophilic polyether surfaces, and nonpeptide hydrophobic dendrons are combined, were developed as a new series of synthetic receptors for protein recognition. They have polyanionic "patch" structures on their surfaces and undergo complementary electrostatic interactions with a positively charged cytochrome c patch, as observed in biological protein-protein recognition systems. Stability constants of the resulting supramolecular complexes were determined in phosphate buffer (pH 7) by monitoring the fluorescence quenching of the zinc porphyrinates. These proteo-dendrimer receptors exhibited higher affinities with cytochrome c proteins in aqueous solutions than with biological cytochrome b5. Furthermore, they effectively blocked complexation of biological cytochrome b5 with cytochrome c, indicating that the proteo-dendrimers and cytochrome b5 similarly occupy the polycationic patch of cytochrome c.

Crown Ether-Mediated Extraction and Functional Conversion of Cytochrome c in Ionic Liquids

We report that a macrocyclic ligand enables transfer of a protein from an aqueous phase to ionic liquids. The extraction behavior of heme protein cytochrome c (Cyt-c) from an aqueous phase into ionic liquids was investigated with crown ethers. A hydroxyl-group-containing ionic liquid with dicyclohexano-18-crown-6 was found to be capable of quantitative partitioning of Cyt-c, whereas the protein transfer using conventional organic solvents was negligibly small. Furthermore, we clarified that Cyt-c solubilized in ionic liquids caused a structural transformation of Cyt-c, which triggers its functional conversion from an electron-transfer protein to peroxidase.

Selective extraction and recovery of cytochrome c by liquid-liquid extraction using a calix[6]arene carboxylic acid derivative

Recently, we reported that a calix[6]arene carboxylic acid derivative can selectively extract the lysine-rich protein cytochrome c by interacting with amino groups on the protein surface. In the present article, quantitative extraction and recovery of cytochrome c using this calix[6]arene carboxylic acid derivative are described. Both adjustment of the pH under acidic conditions and addition of an alcohol are necessary to strip the extracted protein from an organic solution to an aqueous solution. Separation of cytochrome c and lysozyme using the calix[6]arene was achieved under the optimal conditions. In the forward extraction stage, 93% of the cytochrome c was extracted, while lysozyme remained in the solution. In the subsequent stripping stage, the extracted cytochrome c was quantitatively recovered in an aqueous solution. Finally, separation of these proteins, which have similar molecular weights and isoelectric points, was accomplished.