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Selective methane oxidation is difficult chemistry. Here we describe a strategy for the electrocatalysis of selective methane oxidation by immobilizing tricopper catalysts on the cathodic surface. In the presence of dioxygen and methane, the activation of these catalysts above a threshold cathodic potential can initiate the dioxygen chemistry for O atom transfer to methane. The catalytic turnover is completed by facile electron injections into the tricopper catalysts from the electrode. This technology leads to dramatic enhancements in performance of the catalysts toward methane oxidation. Unprecedented turnover frequencies (40 min

The active site of methanol dehydrogenase (MDH) contains a rare disulfide bridge between adjacent cysteine residues. As a vicinal disulfide, the structure is highly strained, suggesting it might work together with the pyrroloquinoline quinone (PQQ) prosthetic group and the Ca2+ ion in the catalytic turnover during methanol (CH3OH) oxidation. We purify MDH from Methylococcus capsulatus (Bath) with the disulfide bridge broken into two thiols. Spectroscopic and high-resolution X-ray crystallographic studies of this form of MDH indicate that the disulfide bridge is redox active. We observe an internal redox process within the holo-MDH that produces a disulfide radical anion concomitant with a companion PQQ radical, as evidenced by an optical absorption at 408 nm and a magnetically dipolar-coupled biradical in the EPR spectrum. These observations are corroborated by electron-density changes between the two cysteine sulfurs of the disulfide bridge as well as between the bound Ca2+ ion and the O5-C5 bond of the PQQ in the high-resolution X-ray structure. On the basis of these findings, we propose a mechanism for the controlled redistribution of the two electrons during hydride transfer from the CH3OH in the alcohol oxidation without formation of the reduced PQQ ethenediol, a biradical mechanism that allows for possible recovery of the hydride for transfer to an external NAD+ oxidant in the regeneration of the PQQ cofactor for multiple catalytic turnovers. In support of this mechanism, a steady-state level of the disulfide radical anion is observed during turnover of the MDH in the presence of CH3OH and NAD+.

Prion diseases are transmissible fatal neurodegenerative disorders spreading between humans and other mammals. The pathogenic agent, prion, is a protease‐resistant, β‐sheet‐rich protein aggregate, converted from a membrane protein called PrP(C). PrP(Sc) is the misfolded form of PrP(C) and undergoes self‐propagation to form the infectious amyloids. Since the key hallmark of prion disease is amyloid formation, identifying and studying which segments are involved in the amyloid core can provide molecular details about prion diseases. It has been known that the prion protein could also form non‐infectious fibrils in the presence of denaturants. In this study, we employed a combination of site‐directed nitroxide spin‐labeling, fibril seeding, and electron spin resonance (ESR) spectroscopy to identify the structure of the in vitro‐prepared full‐length mouse prion fibrils. It is shown that in the in vitro amyloidogenesis, the formation of the amyloid core is linked to an α‐to‐β structural transformation involving the segment 160‐224, which contains strand 2, helix 2, and helix 3. This method is particularly suitable for examining the hetero‐seeded amyloid fibril structure, as the unlabeled seeds are invisible by ESR spectroscopy. It can be applied to study the structures of different strains of infectious prions or other amyloid fibrils in the future.

Methanotrophs mediate the conversion of methane (CH4) into methanol selectively and efficiently near ambient conditions so we can learn from microbes to develop biomimetic catalysts capable of performing this difficult chemistry. This review highlights the development of a tricopper cluster catalyst that functions similar to the particulate methane monooxygenase enzyme in methanotrophic bacteria. The performance of this catalytic system formulated for quasi-heterogeneous catalysis is compared with other heterogeneous catalysts derived from Cu- and Fe-based zeolites and Cu mordenites known to activate CH4 stoichiometrically near 200 °C. We also highlight a unique catalytic system, in which the oxidizing power of both O atoms of the O2 molecule can be harnessed for oxidation of toluene to yield benzaldehyde at room temperature.

The particulate methane monooxygenase (pMMO) is the first enzyme in the C1 metabolic pathway in methanotrophic bacteria. As this enzyme converts methane into methanol efficiently near room temperature, it has become the paradigm for developing an understanding of this difficult C1 chemistry. pMMO is a membrane-bound protein with three subunits (PmoB, PmoA, and PmoC) and 12-14 coppers distributed among different sites. X-ray crystal structures that have revealed only three mononuclear coppers at three sites have neither disclosed the location of the active site nor the catalytic mechanism of the enzyme. Here we report a cyro-EM structure of holo-pMMO from Methylococcus capsulatus (Bath) at 2.5 A, and develop quantitative electrostatic-potential profiling to scrutinize the nonprotein densities for signatures of the copper cofactors. Our results confirm a mononuclear CuI at the A site, resolve two CuIs at the B site, and uncover additional CuI clusters at the PmoA/PmoC interface within the membrane (D site) and in the water-exposed C-terminal subdomain of the PmoB (E clusters). These findings complete the minimal set of copper factors required for catalytic turnover of pMMO, offering a glimpse of the catalytic machinery for methane oxidation according to the chemical principles underlying the mechanism proposed earlier.

In this focused review, we portray the recently reported 2.5 A cyro-EM structure of the particulate methane monooxygenase (pMMO) from M. capsulatus (Bath). The structure of the functional holo-pMMO near atomic resolution has uncovered the sites of the copper cofactors including the location of the active site in the enzyme. The three coppers seen in the original X-ray crystal structures of the enzyme are now augmented by additional coppers in the transmembrane domain as well as in the water-exposed C-terminal subdomain of the PmoB subunit. The cryo-EM structure offers the first glimpse of the catalytic machinery capable of methane oxidation with high selectivity and efficiency. The findings are entirely consistent with the biochemical and biophysical findings previously reported in the literature, including the chemistry of hydrocarbon hydroxylation, regeneration of the catalyst for multiple turnovers, and the mechanism of aborting non-productive cycles to ensure kinetic competence.

Recently, we have reported on a dicopper system (CuIII(μ-O)2CuIII complex immobilized in mesoporous silica nanoparticles) that can mediate the catalytic conversion of toluene into benzaldehyde by O2, in which the oxidizing power of both O atoms is harnessed for catalytic turnover. This is the first example of a CuIII(μ-O)2CuIII complex capable of functioning like a “dioxygenase” in hydrocarbon oxidation. We have undertaken a mechanistic study to clarify how this catalytic conversion is accomplished without the input of sacrificial reductants. While the first O atom in the CuIII(μ-O)2CuIII complex can actively insert into a C–H bond, the second O atom left in the CuII(μ-O)CuII complex is inert. We show that a second molecule of O2 is involved in activating the dicopper catalyst, forming an O2 complex with the CuII(μ-O)CuII intermediate to give a species with the [Cu2O3]2+ core, which then mediates the transfer of the remaining O atom of the original O2 molecule to the organic substrate to complete the cata...

The active site of methanol dehydrogenase (MDH) contains a rare disulfide bridge between adjacent cysteine residues. As a vicinal disulfide, the structure is highly strained, suggesting it might work together with the pyrroloquinoline quinone (PQQ) prosthetic group and the Ca

The controlled oxidation of light alkanes is challenging chemistry. Here, we describe the further development of a catalytic system consisting of a tricopper cluster complex immobilized in mesoporous silica nanoparticles, which we have recently shown to be capable of efficient conversion of methane into methanol without overoxidation under ambient conditions, to follow the oxidation of (i) ethane to ethanol, (ii) propane to isopropanol and acetone, and (iii) a 1:1:1 mixture of methane, ethane and propane. The efficacy of the system to mediate the catalytic conversion of these light alkanes in natural gas into liquid oxidized products is also assessed.

Shrimp nodaviruses, including Penaeus vannamei (PvNV) and Macrobrachium rosenbergii nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of T = 3 and T = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the ∆N-ARM-PvNV shell-domain (S-domain) in T = 1 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic N-terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls T = 3 and T = 1 assemblies. Increasing the N/C-termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement., Nai-Chi Chen et al. solved the structures of two shrimp nodaviruses, focusing on the major domains to improve understanding of capsid organization. By combining cryo-EM and x-ray crystallography, the authors were able to observe the structures at a high resolution.

Selective methane (CH4) oxidation is extremely difficult chemistry. Methane monooxygenases (MMOs ) facilitate the biological conversion of CH4 into methanol in methanotrophs under ambient temperatures and pressures. Methanotrophs typically express the membrane-bound particulate form of MMO (pMMO ), but the soluble form of MMO (sMMO ) is often expressed under copper-limiting conditions. Numerous biochemical and biophysical approaches have been explored to elucidate the mechanisms of pMMO and sMMO over the past four decades, especially to examine the structures and the functional roles of the active sites. In this chapter, the biochemistry, including structural and functional features of MMOs, will be described. We first summarize the biochemical/biophysical studies that have led to the discovery of a unique tricopper cluster as the catalytic site in pMMO and culminated in the successful development of a biomimetic catalyst capable of mediating efficient CH4 oxidation at room temperature. We then review the spectroscopic, kinetic, and structural studies that have contributed to clarification of the catalytic mechanisms near the non-heme diiron active sites in the hydroxylase of sMMO, as well as the roles played by the regulatory protein and the reductase in this chemistry.

The development of a heterogeneous catalyst capable for efficient selective conversion of methane into methanol with multiple turnovers under ambient conditions is reported here. The catalyst is assembled by immobilizing into mesoporous silica nanoparticles the tricopper complex [CuICuICuI(7-N-Etppz)]1+, where 7-N-Etppz stands for the organic ligand 3,3′-(1,4-diazepane-1,4-diyl)bis[1-(4-ethylpiperazine-1-yl)propan-2-ol]. This tricopper cluster complex has been previously shown to mediate efficient methane oxidation without over-oxidation in homogeneous solution when the catalytic turnover is driven by hydrogen peroxide in acetonitrile. The turnover mechanism of the catalyst is similar between the two formulations. However, the heterogeneous formulation exhibits dramatically higher catalytic efficiencies and turnover numbers, with commensurate improvements in chemical yields, offering the most proficient catalyst for the selective conversion of methane into methanol at room temperature developed to date. To explain the efficient methane oxidation, the over-solubility of nonpolar gases, such as methane, in liquids confined in nanoporous solids is evoked. The much higher solubility of methane within the pores of the mesoporous silica nanoparticles, as compared to the bulk solubility, led to very efficient turnover of the concentrated confined methane. This success underscores the advantages of using nanoparticles to support chemical catalysts for this difficult chemical transformation under these conditions.

Selective catalytic oxidation of hydrocarbons is challenging. Here, we show how this chemistry could be accomplished for cyclohexane (C6H12) at room temperature with good turnover numbers, excellent catalytic efficiencies, high conversion yields and product selectivity, when the catalysis is mediated by a tricopper cluster complex immobilized in the nanochannels of mesoporous silica nanoparticles. The CuICuICuI tricopper cluster is activated by dioxygen (O2) to mediate the hydrocarbon oxidation to cyclohexanol (C6H12O) and cyclohexanone (C6H10O) by a direct O-atom transfer mechanism and the turnover of the catalyst is driven by hydrogen peroxide (H2O2). The desired product is obtained by simply varying the experimental conditions. In the case of limiting H2O2, the catalytic efficiency can reach 96%. When H2O2 is in large excess, the conversion of C6H12 and selectivity to C6H10O can reach close to 100%. The nano-confined catalytic system leads to higher solubility of O2 and thus to higher activity. The heterogeneous catalyst is robust and reusable after many cycles.

The oversolubility of the non-polar methane (CH4) gas in nano-confined liquid in nanoporous silica materials is investigated. A series of mesoporous silica materials with different pore sizes, pore volumes, and different amounts of nano-confined water (H2O) are prepared using a pore-expanding reagent and surfactants of different chain-lengths, and the CH4 absorption by the silica nano-materials is studied at 298 K under low CH4 gas pressures. Analysis of the CH4 absorption data reveals unequivocal evidence for oversolubility of CH4 in the nano-confined H2O of all the hydrated nano-materials. The solubility enhancements are several hundred fold relative to the CH4 solubility in bulk H2O. Interestingly, the enhancements are 25–30% higher when a tricopper cluster complex capable of efficient selective CH4 oxidation under ambient conditions is immobilized into the nano-channels of the silica materials. This dramatic enhancement of the CH4 solubility is attributed to specific CH4 binding to the tricopper cluster complexes embedded within the mesopores of the nanoporous materials.

Guan, H., Hsieh, Y., Lin, P. et al. Structural insights into the electron/proton transfer pathways in the quinol : fumarate reductase from Desulfovibrio gigas. Sci Rep 8, 14935 (2018) doi:10.1038/s41598-018-33193-5, The membrane-embedded quinol: fumarate reductase (QFR) in anaerobic bacteria catalyzes the reduction of fumarate to succinate by quinol in the anaerobic respiratory chain. The electron/protontransfer pathways in QFRs remain controversial. Here we report the crystal structure of QFR from the anaerobic sulphate-reducing bacterium Desulfovibrio gigas (D. gigas) at 3.6 Å resolution. The structure of the D. gigas QFR is a homo-dimer, each protomer comprising two hydrophilic subunits, A and B, and one transmembrane subunit C, together with six redox cofactors including two b-hemes. One menaquinone molecule is bound near heme bL in the hydrophobic subunit C. This location of the menaquinone-binding site differs from the menaquinol-binding cavity proposed previously for QFR from Wolinella succinogenes. The observed bound menaquinone might serve as an additional redox cofactor to mediate the proton-coupled electron transport across the membrane. Armed with these structuralinsights, we propose electron/proton-transfer pathways in the quinol reduction of fumarate to succinate in the D. gigas QFR.

In this study, we describe efforts to clarify the role of the copper cofactors associated with subunit B (PmoB) of the particulate methane monooxygenase (pMMO) from Methylococcus capsulatus (Bath) (M. capsulatus). This subunit exhibits strong affinity toward Cu

High-yield production of a functionally active mimic of particulate methane monooxygenase in Escherichia coli has been presented. Investigation of its catalytic mode clarifies the role of duroquinol in biomimetic methanol production.

A tripodal tridentate copper(II) complex, CuImph (Imph = bis(4-imidazolyl methyl)benzylamine), is synthesized to mimic the active site of copper enzymes that mediate the oxidation of aliphatic C–H bonds under mild condition. By immobilizing the model complex in the nanochannels of functionalized mesoporous silica nanoparticles (MSNs), we observe the formation of a stable bis-μ-oxo species ([{CuIIIImph}2(μ-O2−)2]2+) in the presence of dioxygen or air at ambient temperature. The dioxygen-activated CuImph@MSN samples show high reactivity and selectivity toward toluene aliphatic C–H bond oxidation, converting the toluene initially to benzyl alcohol and subsequently to benzaldehyde as the major product in a kinetic consecutive reaction. No evidence for benzoic acid is obtained, unlike the over-oxidation typically associated with present-day industrial processes operating at high temperatures. In addition, the process is self-sustaining without the requirement for a sacrificial reductant to drive the catalytic turnover. The catalyst can be fully recovered and re-used for several cycles without decay of activity.

A study of the oxygen reduction reaction (ORR) on a screen printed carbon electrode surface mediated by the tricopper cluster complex Cu3(7-N-Etppz(CH2OH)) dispersed on electrochemically reduced carbon black, where 7-N-Etppz(CH2OH) is the ligand 3,3′-(6-(hydroxymethyl)-1,4-diazepane-1,4-diyl)bis(1-(4-ethyl piperazin-1-yl)propan-2-ol), is described. Onset oxygen reduction potentials of about 0.92 V and about 0.77 V are observed at pH 13 and pH 7 vs. the reversible hydrogen electrode, which are comparable to the best values reported for any synthetic copper complex. Based on half-wave potentials (E1/2), the corresponding overpotentials are about 0.42 V and about 0.68 V, respectively. Kinetic studies indicate that the trinuclear copper catalyst can accomplish the 4 e− reduction of O2 efficiently and the ORR is accompanied by the production of only small amounts of H2O2. The involvement of the copper triad in the O2 activation process is also verified.

The electronic communications between chromophores are closely related to distances and orientation of these π-conjugated systems. Reported herein is a collection of well-defined two-dimensional comb-like polymers containing porphyrin pendants obtained by ring-opening metathesis polymerizations of norbornene and cyclobutene derivatives using ruthenium or molybdenum catalysts. The spacing separating the adjacent pendants are defined by ring sizes of cycloalkenes and the orientations are determined by the stiffness of the polymeric backbone, which is, in turn, discerned by the percentage of Z-double bonds. Both peak widths of the porphyrin radical cation of the EPR spectra and the absorption profiles in the Soret band region reflect the degree of the spin delocalization and exciton coupling between porphyrin pendants in these polymers and, hence, the stiffness of the polymeric backbone. Our approach offers a useful protocol to align an array of chromophores appended onto a rigid polymeric backbone so that t...

The tricopper complex [CuICuICuI(7-N-Etppz)]1+, where 7-N-Etppz denotes the ligand 3,3′-(1,4-diazepane-1,4-diyl)bis[1-(4-ethyl piperazine-1-yl)propan-2-ol], is capable of mediating facile conversion of methane into methanol upon activation of the tricopper cluster by dioxygen and/or H2O2 at room temperature. This is the first molecular catalyst that can catalyze selective oxidation of methane to methanol without over-oxidation under ambient conditions. When this CuICuICuI tricopper complex is activated by dioxygen or H2O2, the tricopper cluster harnesses a “singlet oxene”, the strongest oxidant that could be used to accomplish facile O-atom insertion across a C–H bond. To elucidate the properties of this novel catalytic system, we examine here methane oxidation over a wider range of conditions and extend the study to other small alkanes, including components of natural gas. We illustrate how substrate solubility, substrate recognition and the amount of H2O2 used to drive the catalytic oxidation can affect the outcome of the turnover, including regiospecificity, product distributions and yields of substrate oxidation. These results will help in designing another generation of the catalyst to alleviate the limitations of the present system.

More than one third of all proteins are metalloproteins. They catalyze important reactions such as photosynthesis, nitrogen fixation and CO2 reduction. Metalloproteins such as the olfactory receptors also serve as highly elaborate sensors. Here we review recent developments in functional metalloprotein design using the genetic code expansion approach. We show that, through the site-specific incorporation of metal-chelating unnatural amino acids (UAAs), proton and electron transfer mediators, and UAAs bearing bioorthogonal reaction groups, small soluble proteins can recapitulate and expand the important functions of complex metalloproteins. Further developments along this route may result in cell factories and live-cell sensors with unprecedented efficiency and selectivity.

In this study, we describe efforts to clarify the role of the copper cofactors associated with subunit B (PmoB) of the particulate methane monooxygenase (pMMO) from Methylococcus capsulatus (Bath) (M. capsulatus). This subunit exhibits strong affinity toward Cu^I ions. To elucidate the high copper affinity of the subunit, the full-length PmoB, and the N-terminal truncated mutants PmoB_(33–414) and PmoB_(55–414), each fused to the maltose-binding protein (MBP), are cloned and over-expressed into Escherichia coli (E. coli) K12 TB1 cells. The Y374F, Y374S and M300L mutants of these protein constructs are also studied. When this E. coli is grown with the pmoB gene in 1.0 mM Cu^(II), it behaves like M. capsulatus (Bath) cultured under high copper stresswith abundant membrane accumulation and high CuI content. The recombinantPmoB proteins are verified by Western blotting of antibodies directed against the MBP sub-domain in each of the copper-enriched PmoB proteins. Cu K-edge X-rayabsorption near edge spectroscopy (XANES) of the copper ions confirms that all the PmoB recombinants are Cu^I proteins. All the PmoB proteins show evidence of a “dicopper site” according to analysis of the Cu extended X-ray absorption edge fine structure (EXAFS) of the membranes. No specific activities toward methane and propene oxidation are observed with the recombinant membrane-bound PmoB proteins. However, significant production of hydrogen peroxide is observed in the case of the PmoB_(33–414) mutant. Reaction of the dicopper site with dioxygenproduces hydrogen peroxide and leads to oxidation of the CuI ions residing in the C-terminal sub-domain of the PmoB subunit.

Following recent progress towards understanding the structure of the particulate methane monooxygenase in methanotrophic bacteria, it is now possible to attempt the development of laboratory catalysts for the conversion of methane into MeOH under ambient conditions. To this end, a class of tricopper complexes that are capable of efficiently oxidizing small hydrocarbon substrates at room temperature has recently been developed. In this Minireview, we describe the development of a tricopper cluster to accomplish the catalytic conversion of methane into MeOH, as well as a number of small n-alkanes into their corresponding alcohols and ketones, with high efficiencies. The properties of this robust catalytic system are discussed.

Six tricopper cluster complexes of the type [CuICuICuI(L)]1+ supported by a series of multidentate ligands (L) have been developed as oxidation catalysts. These complexes are capable of mediating the facile oxygen-atom transfer to hydrocarbon substrates like cyclohexane, benzene, and styrene (C6H12, C6H6 and C8H8) upon activation by hydrogen peroxide at room temperature. The processes are catalytic with high turnover frequencies (TOF), efficiently oxidizing the substrates to their corresponding alcohols, aldehydes, and ketones in moderate to high yields. The catalysts are robust with turnover numbers (TON) limited only by the availability of hydrogen peroxide used to drive the catalytic turnover. The TON is independent of the substrate concentration and the TOF depends linearly on the hydrogen peroxide concentration when the oxidation of the substrate mediated by the activated tricopper complex is rapid. At low substrate concentrations, the catalytic system exhibits abortive cycling resulting from competing reduction of the activated catalyst by hydrogen peroxide. This behaviour of the system is consistent with activation of the tricopper complex by hydrogen peroxide to generate a strong oxidizing intermediate capable of a facile direct “oxygen-atom” transfer to the substrate upon formation of a transient complex between the activated catalyst and the substrate. Some substrate specificity has also been noted by varying the ligand design. These properties of the tricopper catalyst are characteristic of many enzyme systems, such as cytochrome P450, which participate in biological oxidations.

Two tricopper complexes are developed for efficient oxidation of hydrocarbons. These catalysts are based on the tricopper cluster that has been shown to be capable of mediating facile O-atom transfer to a number of organic substrates upon activation by dioxygen. It is demonstrated that the two tricopper complexes [CuICuICuI(L)]+, with L = 3,3′-(1,4-diazepane-1,4-diyl)bis(1-(bis(pyridin-2-yl)methyl)amino)propan-2-ol (7-Dipy) and 3,3′-(1,4-diazepane-1,4-diyl)bis(1-thiomorpholinopropan-2-ol) (7-Thio), can sustain catalytic oxidation of cyclohexane to cyclohexanol and cyclohexanone with high turnover frequencies in the presence of H2O2 in acetonitrile under ambient conditions. These catalysts appear to be extremely robust, with turnover limited by the H2O2 available to drive the process. The turnover frequencies of the catalysts are found to depend linearly on the H2O2 concentration with a second-order rate constant of ∼1 × 10−2 mol−1 s−1.

Three trinuclear Cu(II) complexes [Cu3(tacp)(μ3-Cl)2](Cl)4 (1), [Cu3(tacp)(μ3-Br)2](Br)4 (2) and [Cu3(tacp)(μ3-OH)2](Cl)4 (3) (tacp, 1,10,19-trioxa-4,7,13,16,22,25-hexaazacycloheptaeicosane) are synthesized to model the oxidized tricopper cluster implicated in the particulate methane monooxygenase from Methylococcus capsulatus (Bath). In the enzyme, the three Cu(II) ions are coupled by weak ferromagnetic interactions. The Cu(II) ions in 1 and 2 are shown to be ferromagnetically coupled from magnetic susceptibility and electron paramagnetic resonance (EPR) measurements. EPR suggests anti-ferromagnetic interactions among the Cu(II) ions in 3. Density functional theory calculations reproduce well the geometric, electronic and magnetic properties observed in these complexes and provide insights into the spin-coupling interactions mediated by the bridging ligands.

X-ray absorption, circular dichroism, and EPR spectroscopy were employed to investigate the metal-core structures in the Escherichia coli transcriptional factor SoxR under reduced, oxidized, and nitrosylated conditions. The spectroscopic data revealed that the coordination environments of the metal active centers varied only very slightly between the reduced and oxidized states, similar to most other proteins containing iron-sulfur clusters. Upon nitrosylation of oxidized SoxR, however, we observed a low-temperature EPR spectrum characteristic of a protein dinitrosyl iron complex (DNIC), with an intensity corresponding to about two DNICs per iron sulfur cluster in the protein, according to spin quantification relative to a low-molecular-weight DNIC standard. In addition, there was no evidence for dichroic spectral features in the responsive region of the nitrosyl iron complexes, as well as for Fe-Fe back-scattering in the fitting of the Fe extended X-ray absorption fine structure (EXAFS) spectrum. Instead the Fe EXAFS spectrum of the nitrosylated SoxR core exhibited the same first- and second-shell coordination environments characteristic of modeled small molecular DNICs, indicating that each of the [2 Fe-2 S] cores in the homodimeric SoxR was dissociated into two individual DNICs. Similar nitrosylation of the reduced mixed-valence SoxR for 1 min led to degradation of the iron-sulfur clusters to give several iron species, including one with EPR signals characteristic of a reduced Roussin's red ester (rRRE), a diamagnetic species, presumably Roussin's red ester (RRE), and a small amount of DNIC. We also undertook in vivo time-course studies of E. coli cells containing recombinant SoxR after rapid purging of the cells with exogenous NO gas. Rapid freeze-quenched EPR experiments demonstrated rapid formation of the SoxR rRRE species, followed by fast breakup of this precursor intermediate to form the stable protein-bound DNIC species. Accordingly, under nitrosative stress, we believe that the response of SoxR to NO could depend on the intracellular redox state of E. coli, the central modulator of which could be exploited to deduce the appropriate mechanism to sense the presence of NO for physiological regulation.

While both turn formation and hydrophobic interactions play dominant roles in the initiation of protein folding, their individual contributions to the folding kinetics and to the structural stability of the protein still remain poorly understood. Here, we applied a photolabile linker to "cage" some important structural motifs, including both α-helices and β-sheets, into their non-native states. These "caged" structural motifs are then relaxed by laser-flash photolysis and their refolding events followed by photoacoustic calorimetry (PAC) and photothermal beam deflection (PBD). These experiments, combined with our previous results, revealed that spontaneous α-helix formation can occur extremely rapidly (10(8)-10(9) s(-1)) if the process is driven solely by turn formation followed by helix propagation. However, if sequestering of the side chains of hydrophobic amino acid residues participates in the refolding process, which may provide additional driving force beyond that afforded by turn formation alone, the refolding rate will be retarded, often by many orders of magnitude. This is usually the case in the formation of three-stranded β-sheets (10(7)-10(8) s(-1)) and β-hairpins (10(5)-10(6) s(-1)). Thus, we propose that proteins take advantage of the hierarchy of timescales associated with either turn formation, hydrophobic interactions, or global collapse of tertiary structure to accomplish the folding process in an orderly fashion, as these events are sufficiently separated in time and do not interfere with one another.

Adenylylsulfate reductase (adenosine 5′-phosphosulfate reductase, APS reductase or APSR, E.C.1.8.99.2) catalyzes the conversion of APS to sulfite in dissimilatory sulfate reduction. APSR was isolated and purified directly from massive anaerobically grown Desulfovibrio gigas, a strict anaerobe, for structure and function investigation. Oligomerization of APSR to form dimers–α_2β_2, tetramers–α_4β_4, hexamers–α_6β_6, and larger oligomers was observed during purification of the protein. Dynamic light scattering and ultracentrifugation revealed that the addition of adenosine monophosphate (AMP) or adenosine 5′-phosphosulfate (APS) disrupts the oligomerization, indicating that AMP or APS binding to the APSR dissociates the inactive hexamers into functional dimers. Treatment of APSR with β-mercaptoethanol decreased the enzyme size from a hexamer to a dimer, probably by disrupting the disulfide Cys156—Cys162 toward the C-terminus of the β-subunit. Alignment of the APSR sequences from D. gigas and A. fulgidus revealed the largest differences in this region of the β-subunit, with the D. gigas APSR containing 16 additional amino acids with the Cys156—Cys162 disulfide. Studies in a pH gradient showed that the diameter of the APSR decreased progressively with acidic pH. To crystallize the APSR for structure determination, we optimized conditions to generate a homogeneous and stable form of APSR by combining dynamic light scattering, ultracentrifugation, and electron paramagnetic resonance methods to analyze the various oligomeric states of the enzyme in varied environments.

The crystal structures of two active forms of dissimilatory sulphite reductase (Dsr) from Desulfovibrio gigas, Dsr-I and Dsr-II, are compared at 1.76 and 2.05 A resolution respectively. The dimeric α_2β_2γ_2 structure of Dsr-I contains eight [4Fe–4S] clusters, two saddle-shaped sirohaems and two flat sirohydrochlorins. In Dsr-II, the [4Fe–4S] cluster associated with the sirohaem in Dsr-I is replaced by a [3Fe–4S] cluster. Electron paramagnetic resonance (EPR) of the active Dsr-I and Dsr-II confirm the co-factor structures, whereas EPR of a third but inactive form, Dsr-III, suggests that the sirohaem has been demetallated in addition to its associated [4Fe–4S] cluster replaced by a [3Fe–4S] centre. In Dsr-I and Dsr-II, the sirohydrochlorin is located in a putative substrate channel connected to the sirohaem. The γ-subunit C-terminus is inserted into a positively charged channel formed between the α- and β-subunits, with its conserved terminal Cysγ104 side-chain covalently linked to the CHA atom of the sirohaem in Dsr-I. In Dsr-II, the thioether bond is broken, and the Cysγ104 side-chain moves closer to the bound sulphite at the sirohaem pocket. These different forms of Dsr offer structural insights into a mechanism of sulphite reduction that can lead to S_3O_6^(2−), S_2O_3^(2−) and S^(2−).

Adenylylsulfate reductase (adenosine 5′-phosphosulfate [APS] reductase [APSR]) plays a key role in catalyzing APS to sulfite in dissimilatory sulfate reduction. Here, we report the crystal structure of APSR from Desulfovibrio gigas at 3.1-Å resolution. Different from the α 2 β 2 -heterotetramer of the Archaeoglobus fulgidus , the overall structure of APSR from D. gigas comprises six αβ-heterodimers that form a hexameric structure. The flavin adenine dinucleotide is noncovalently attached to the α-subunit, and two [4Fe-4S] clusters are enveloped by cluster-binding motifs. The substrate-binding channel in D. gigas is wider than that in A. fulgidus because of shifts in the loop (amino acid 326 to 332) and the α-helix (amino acid 289 to 299) in the α-subunit. The positively charged residue Arg160 in the structure of D. gigas likely replaces the role of Arg83 in that of A. fulgidus for the recognition of substrates. The C-terminal segment of the β-subunit wraps around the α-subunit to form a functional unit, with the C-terminal loop inserted into the active-site channel of the α-subunit from another αβ-heterodimer. Electrostatic interactions between the substrate-binding residue Arg282 in the α-subunit and Asp159 in the C terminus of the β-subunit affect the binding of the substrate. Alignment of APSR sequences from D. gigas and A. fulgidus shows the largest differences toward the C termini of the β-subunits, and structural comparison reveals notable differences at the C termini, activity sites, and other regions. The disulfide comprising Cys156 to Cys162 stabilizes the C-terminal loop of the β-subunit and is crucial for oligomerization. Dynamic light scattering and ultracentrifugation measurements reveal multiple forms of APSR upon the addition of AMP, indicating that AMP binding dissociates the inactive hexamer into functional dimers, presumably by switching the C terminus of the β-subunit away from the active site. The crystal structure of APSR, together with its oligomerization properties, suggests that APSR from sulfate-reducing bacteria might self-regulate its activity through the C terminus of the β-subunit.

Despite growing up amid humble surroundings, I ended up receiving an excellent education at the University of California at Berkeley and postdoctoral training at Harvard. My academic career at Caltech was shaped by serendipity, inspirational colleagues, and a stimulating research environment, as well as smart, motivated students and postdocs who were willing to join my search for molecular understanding of complex biological systems. From chemical physics I allowed my research to evolve, beginning with the application of NMR to investigate the base stacking of nucleic acid bases in solution, the dynamic structure of membranes, and culminating with the use of various forms of spectroscopy to elucidate the structure and function of membrane proteins and the early kinetic events in protein folding. The journey was a biased random walk driven by my own intellectual curiosity and instincts and by the pace at which I learned biochemistry from my students and postdocs, my colleagues, and the literature and through osmosis during seminars and scientific meetings.

By means of time-resolved photoluminescence and photothermal techniques, after-effects from excited-state dynamics, energy migration, and conformational rearrangement of poly(9,9-di-n-octyl-2,7-fluorene) (PFO) and its homologues has been examined and interpreted with rotational potential maps from quantum mechanical calculations. Steady-state photoluminescence spectral changes and time-resolved photoluminescence measurements of oligofluorenes and PFO diluted in toluene suggest excited state ring torsion occurring within 30 ps of photoexitation. With all effects from internal conversion/intersystem crossing processes properly accounted for, we show that the conformational changes associated with this twisting motion can be quantitatively probed by means of photothermal methods. Results suggest mean torsion between neighboring fluorene units by ca. 40 degrees upon excitation, in agreement with the shift of rotational potential minimum from +/-40 degrees (and +/-140 degrees) in the ground state to +/-20 degrees (and +/-160 degrees) in the first excited singlet state according to results of quantum mechanical calculations.

M32 carboxypeptidases are a distinct family of HEXXH metalloproteases whose structures exhibit a narrow substrate groove that is blocked at one end. Structural alignments with other HEXXH metalloprotease-peptide complexes suggested an orientation in which the substrate is directed towards the back of the groove. This led us to hypothesize, and subsequently confirm that the maximum substrate length for M32 carboxypeptidases is restricted. Structural and sequence analyses implicate a highly conserved Arg at the back of the groove as being critical for this length restriction. However, the Thermus thermophilus and Bacillus subtilis M32 members lack this conserved Arg. Herein, we present the biochemical and structural characterization of these two proteins. Our findings support the important role of the conserved Arg in maintaining the length restriction, and reveal a proline-rich loop as an alternate blocking strategy. Based on our results, we propose that M32 carboxypeptidases from Bacilli belong to a separate subfamily. Proteins 2009. © 2009 Wiley-Liss, Inc.

The secondary structure within histone IV and its fragments obtained by cyanogen bromide (CNBr) and cleavage at Met 84 has been examined by circular dichroism and spectophotometric pH titration measurements. These studies have confirmed the existence of stable secondary structure within the C-terminal fragment of histone IV (C-peptide which can be perturbed only by 6M urea at pH greater than 8 or 8 M guanidine-HCL. In contrast, the N-terminal fragment (N-peptide) appears to lack significant secondary structure at low ionic strengths but acquires approximately 15% betasheet conformation and 5% alpha-helix upon aggregation at ionic strengths larger than or equal to 0.4. The rates of nitration of the N- and C-peptides by tetranitromethane (TNM) have also been measured as a function of ionic strengths. Under comparable conditions, the rate constant for nitration of the N-peptide was found to be about six times greater than that for the C-peptide, further evidence in support of the presence of stable secondary structure within the C-terminal region of histone IV. After binding these histone IV fragments to DNA, however, the nitration reaction rate constants for the N- and C-peptide in the bound form are found to be 2% and 27% of the corresponding free peptides. Reconstituted nucleohistone IV is about 10% as reactive to TNM as histone IV at comparable ionic strength.

Earlier work from our laboratory has indicated that a hemerythrin-like protein was over-produced together with the particulate methane monooxygenase (pMMO) when Methylococcus capsulatus (Bath) was grown under high copper concentrations. A homologue of hemerythrin had not previously been found in any prokaryote. To confirm its identity as a hemerythrin, we have isolated and purified this protein by ion-exchange, gel-filtration and hydrophobic interaction chromatography, and characterized it by mass spectrometry, UV-visible, CD, EPR and resonance Raman spectroscopy. On the basis of biophysical and multiple sequence alignment analysis, the protein isolated from M. capsulatus (Bath) is in accord with hemerythrins previously reported from higher organisms. Determination of the Fe content in conjunction with molecular-weight estimation and mass analysis indicates that the native hemerythrin in M. capsulatus (Bath) is a monomer with molecular mass 14.8 kDa, in contrast to hemerythrins from other eukaryotic organisms, where they typically exist as a tetramer or higher oligomers.

The role of the small exterior hydrophobic cluster (SEHC) in the strand region of the N-terminal β-hairpin of ubiquitin on the structural stability and the folding/unfolding kinetics of the protein have been examined. We introduce a Phe→Ala substitution at residue 4 in the strand region of the N-terminal β-hairpin of the ubiquitin. A peptide with the same amino acid sequence as the first 21 residues of the mutated ubiquitin has also been synthesized. The F4A mutation unfolds the hairpin structure of the peptide segment without disruption of the turn. The same mutation does not seem to affect the overall structure, but the stability of the mutated full-length protein decreases by approx. 2 kcal/mol. Kinetically, the entire hairpin structure is implicated in the transition state during folding of the wild type protein. The rate of refolding is retarded by the F4A mutation in ∼80% of the protein molecules. The F4A substitution also increases the unfolding rate of the protein by 10 fold. Thus the hydrophobic side-chain of Phe-4 not only contributes to the stability of the hairpin, but also to the stability of the entire protein by forming a cluster together with the hydrophobic residues on the C-terminal strand.

The crystal structure of the particulate methane monooxygenase (pMMO) from Methylococcus capsulatus (Bath) has been reported recently [Lieberman, R. L., and Rosenzweig, A. C. (2005) Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane, Nature 434, 177-182]. Subsequent work has shown that the preparation on which the X-ray analysis is based might be missing many of the important metal cofactors, including the putative trinuclear copper cluster at the active site as well as ca. 10 copper ions (E-clusters) that have been proposed to serve as a buffer of reducing equivalents to re-reduce the copper atoms at the active site following the catalytic chemistry [Chan, S. I., Wang, V. C.-C., Lai, J. C.-H., Yu, S. S.-F., Chen, P. P.-Y., Chen, K. H.-C., Chen, C.-L., and Chan, M. K. (2007) Redox potentiometry studies of particulate methane monooxygenase: Support for a trinuclear copper cluster active site, Angew. Chem., Int. Ed. 46, 1992-1994]. Since the aqueous-exposed domains of the 45 kDa subunit (PmoB) have been suggested to be the putative binding domains for the E-cluster copper ions, we have cloned and overexpressed in Escherichia coli the two aqueous-exposed subdomains toward the N- and C-termini of the subunit: the N-terminal subdomain (residues 54-178) and the C-terminal subdomain (residues 257-394 and 282-414). The recombinant C-terminal water-exposed subdomain is shown to behave like a Cu(I) sponge, taking up to ca. 10 Cu(I) ions cooperatively when cupric ions are added to the protein fragment in the presence of dithiothreitol or ascorbate. In addition, circular dichroism measurements reveal that the C-terminal subdomain folds into a beta-sheet structure in the presence of Cu(I). The propensity for the C-terminal subdomain to bind Cu(I) is consistent with the high redox potential(s) determined for the E-cluster copper ions in the pMMO. These properties of the E-clusters are in accordance with the function proposed for these copper ions in the turnover cycle of the enzyme.

Acetylene (HCCH) has a long history as a mechanism-based enzyme inhibitor and is considered an active-site probe of the particulate methane monooxygenase (pMMO). Here, we report how HCCH inactivates pMMO in Methylococcus capsulatus (Bath) by using high-resolution mass spectrometry and computational simulation. High-resolution MALDI-TOF MS of intact pMMO complexes has allowed us to confirm that the enzyme oxidizes HCCH to the ketene (C_2H_2O) intermediate, which then forms an acetylation adduct with the transmembrane PmoC subunit. LC-MS/MS analysis of the peptides derived from in-gel proteolytic digestion of the protein subunit identifies K196 of PmoC as the site of acetylation. No evidence is obtained for chemical modification of the PmoA or PmoB subunit. The inactivation of pMMO by a single adduct in the transmembrane PmoC domain is intriguing given the complexity of the structural fold of this large membrane-protein complex as well as the complicated roles played by the various metal cofactors in the enzyme catalysis. Computational studies suggest that the entry of hydrophobic substrates to, and migration of products from, the catalytic site of pMMO is controlled tightly within the transmembrane domain. Support of these conclusions is provided by parallel experiments with two related alkynes: propyne (CH3CCH) and trifluoropropyne (CF_3CCH). Finally, we discuss the implication of these findings to the location of the catalytic site in pMMO.

The bacteriohemerythrin (McHr) from Methylococcus capsulatus (Bath) is an oxygen carrier that serves as a transporter to deliver O2 from the cytosol of the bacterial cell body to the particulate methane monooxygenase residing in the intracytoplasmic membranes for methane oxidation. Here we report X-ray protein crystal structures of the recombinant wild type (WT) McHr and its L114A, L114Y and L114F mutants. The structure of the WT reveals a possible water tunnel in the McHr that might be linked to its faster autoxidation relative to hemerythrin in marine invertebrates. With Leu114 positioned at the end of this putative water tunnel, the hydrophobic side chain of this residue seems to play a prominent role in controlling the access of the water molecule required for autoxidation. This hypothesis is examined by comparing the autoxidation rates of the WT McHr with those of the L114A, L114Y and L114F mutants. The biochemical data are correlated with structural insights derived from the analysis of the putative water tunnels in the various McHr proteins provided by the X-ray structures.

We have deployed the alpha-helical hairpin peptide (alpha-helix/turn/alpha-helix) and used it as a model system to explore how glycosylation and phosphorylation might affect the conformational properties of the peptide. The native conformations of the modified peptides in buffer solution have been compared with that of the wild-type peptide by nuclear magnetic resonance spectroscopy. Circular dichroism spectroscopy was used to probe the effects of an O-linked beta-GlcNAc and a phosphate group on the overall folding stability of the peptide. Finally, the rate of fibrillogenesis was used to infer the effects of these chemical modifications on the alpha-to-beta transition as well as the rate of nucleation of amyloidogenesis.

We present here the results of density functional theory (DFT) calculations directed toward elucidation of the C H bond activation mechanism that might be adopted by the particulate methane monooxygenase (pMMO) in the hydroxylation of methane and related small alkanes. In these calculations, we considered three of the most probable models for the transition metal active site mediating the “oxo-transfer”: (i) the trinuclear copper cluster bis(μ 3 -oxo)trinuclear copper(II, II, III) complex 1 , recently proposed by Chan et al. [S.I. Chan, K.H.-C. Chen, S.S.-F. Yu, C.-L. Chen, S.S.-J. Kuo, Biochemistry 43 (2004) 4421–4430.]; (ii) the most frequently used model complex, bis(μ-oxo)Cu(III) 2 complex 2 ; and (iii) the mixed-valence bis(μ-oxo)Cu(II)Cu(III) complex 3 . The results obtained indicate that the methane hydroxylation chemistry mediated by the trinuclear copper cluster bis(μ 3 -oxo)trinuclear copper(II, II, III) complex 1 offers the most facile pathway for methane hydroxylation, and this model yields KIE values that are in good agreement with experiment. In this mechanism, the reaction proceeds along a “singlet” potential surface and a “singlet oxene” is directly inserted across a C H bond in a concerted manner. Kinetic isotope effects ( k H / k D or KIE) associated with the concerted oxene insertion process mediated by complex 1 are calculated to be 5.2 at 300 K when tunneling effects are included. Overall rate constants for the methane hydroxylation by the three models have been calculated as a function of temperature, and the rates are at least 5–6 orders of magnitude more facile when the chemistry is mediated by complex 1 compared to complex 2 or complex 3 .

As part of our continuing study of the effects of the turn sequence on the conformational stability as well as the mechanism of folding of a beta-sheet structure, we have undertaken a parallel investigation of the solution structure, conformational stability, and kinetics of refolding of the beta-sheet VFIVDGOTYTEV(D)PGOKILQ. The latter peptide is an analogue of the original Gellman beta-sheet VFITS(D)PGKTYTEV(D)PGOKILQ, wherein the TS(D)PGK turn sequence in the first hairpin has been replaced by VDGO. Thermodynamics studies revealed comparable conformational stability of the two peptides. However, unlike the Gellman peptide, which showed extremely rapid refolding of the first hairpin, early kinetic events associated with the refolding of the corresponding hairpin in the VDGO mutant were found to be significantly slower. A detailed study of the conformation of the modified peptide suggested that hydrophobic interactions might be contributing to its stability. Accordingly, we surmise that the early kinetic events are sensitive to whether the formation of the hairpin is nucleated at the turn or by sequestering of the hydrophobic residues across the strand, before structural rearrangements to produce the nativelike topology. Nucleation of the hairpin at the turn is expected to be intrinsically rapid for a strong turn. However, if the process must involve collapse of hydrophobic side chains, the nucleation should be slower as solvent molecules must be displaced to sequester the hydrophobic residues. These findings reflect the contribution of different forces toward nucleation of hairpins in the mechanism of folding of beta-sheets.