Modulation of the Redox Potential and Electron/Proton Transfer Mechanisms in the Outer Membrane Cytochrome OmcF From Geobacter sulfurreducens

PD/00193/2012 UID/FIS/00068/2019 PTDC/BBBBQB/3554/2014 PTDC/BIA-BQM/31981/2017 PD/BD/114445/2016 UID/Multi/04378/2019 ROTEIRO/0031/2013 -PINFRA/22161/2016The monoheme outer membrane cytochrome F (OmcF) from Geobacter sulfurreducens plays an important role in Fe(III) reduction and electric current production. The electrochemical characterization of this cytochrome has shown that its redox potential is modulated by the solution pH (redox-Bohr effect) endowing the protein with the necessary properties to couple electron and proton transfer in the physiological range. The analysis of the OmcF structures in the reduced and oxidized states showed that with the exception of the side chain of histidine 47 (His47), all other residues with protonatable side chains are distant from the heme iron and, therefore, are unlikely to affect the redox potential of the protein. The protonatable site at the imidazole ring of His47 is in the close proximity to the heme and, therefore, this residue was suggested as the redox-Bohr center. In the present work, we tested this hypothesis by replacing the His47 with non-protonatable residues (isoleucine – OmcFH47I and phenylalanine – OmcFH47F). The structure of the mutant OmcFH47I was determined by X-ray crystallography to 1.13 Å resolution and showed only minimal changes at the site of the mutation. Both mutants were 15N-labeled and their overall folding was confirmed to be the same as the wild-type by NMR spectroscopy. The pH dependence of the redox potential of the mutants was measured by cyclic voltammetry. Compared to the wild-type protein, the magnitude of the redox-Bohr effect in the mutants was smaller, but not fully abolished, confirming the role of His47 on the pH modulation of OmcF’s redox potential. However, the pH effect on the heme substituents’ NMR chemical shifts suggested that the heme propionate P13 also contributes to the overall redox-Bohr effect in OmcF. In physiological terms, the contribution of two independent acid–base centers to the observed redox-Bohr effect confers OmcF a higher versatility to environmental changes by coupling electron/proton transfer within a wider pH range.publishersversionpublishe

Protein Expression, Characterization and Activity Comparisons of Wild Type and Mutant DUSP5 Proteins

Background The mitogen-activated protein kinases (MAPKs) pathway is critical for cellular signaling, and proteins such as phosphatases that regulate this pathway are important for normal tissue development. Based on our previous work on dual specificity phosphatase-5 (DUSP5), and its role in embryonic vascular development and disease, we hypothesized that mutations in DUSP5 will affect its function. Results In this study, we tested this hypothesis by generating full-length glutathione-S-transferase-tagged DUSP5 and serine 147 proline mutant (S147P) proteins from bacteria. Light scattering analysis, circular dichroism, enzymatic assays and molecular modeling approaches have been performed to extensively characterize the protein form and function. We demonstrate that both proteins are active and, interestingly, the S147P protein is hypoactive as compared to the DUSP5 WT protein in two distinct biochemical substrate assays. Furthermore, due to the novel positioning of the S147P mutation, we utilize computational modeling to reconstruct full-length DUSP5 and S147P to predict a possible mechanism for the reduced activity of S147P. Conclusion Taken together, this is the first evidence of the generation and characterization of an active, full-length, mutant DUSP5 protein which will facilitate future structure-function and drug development-based studies

Protochemical and crystallographic studies on Dimethyl 9,10-Dihydro-9-Methyl-9,10-Ethenoanthracene-11,12-Dicarbosylate

The photochemistry of dimethyl 9,10-dihydro-9-methyl-9,10-etheno-anthracene-11,12-dicarboxylate (5) was studied in solution as well as in the solid state. Upon direct irradiation in solution, three products were obtained, two of which were identified as regioisomeric products of the di-π-methane rearrangement (derivatives of semibull-valene) and the other a derivative of dibenzocyclooctatetraene. When sensitized (by acetone, xanthone or benzophenone) in solution, only the di-π-methane rearrangement products were obtained, suggesting that the other photoproduct obtained in direct irradiation might be a singlet-derived product. In acetonitrile approximately 65% of the photochemical reaction observed was di-π-methane rearrangement. Solid state irradiations mainly resulted in di-π-methane rearrangement but with a reversal of product selectivity from that observed in solution. The X-ray crystal structure of the starting material indicates that one of the ester groups is conjugated to the central double bond while the other is non-conjugated. Radical stabilization through conjugation with the ester carbonyl group is consistent with the major product formed in the solid state. A regular decrease in the photoproduct selectivity was observed with the extent of grinding of the crystals, and this may be attributed to a lower regioselectivity at the surface than that within the bulk of the crystal. Irradiation in a KBr matrix resulted not only in producing more presumed singlet product, but also in the enhancement of the rate of the reaction. Also the singlet photoproduct was found to be produced more when pressure was applied in the solid state. Thus, the photochemical reaction of 5 was found to be sensitive to the environment in which the reaction is taking place. Irradiation of a solid solution of 1% xanthone and the starting material demonstrated the possibility of solid-state sensitization. The sensitized irradiations in the solid state were found to produce more of the presumed singlet product, and triplet-triplet annihilation was suggested as one of the possible explanations.Science, Faculty ofChemistry, Department ofGraduat

Solution and solid state photochemistry of some bridgehead substituted dibenzobarrelene diesters : x-ray crystallography of starting materials and photoproducts

The solid state and solution phase photochemistry of three bridgehead-substituted dibenzobarrelene-11,12-diesters and a 2,3-naphthobarrelene diester derivative were investigated. These compounds were expected to undergo the di-π-methane rearrangement via their triplet excited states, and a rearrangement to a cyclooctatetraene (COT) derivative via their singlet excited states. All compounds investigated underwent smooth photoreactions in the solid state to produce the same products as observed in the corresponding solution phase photolyses. One exception to this was a bridgehead dimethyl- substituted dibenzobarrelene diester. In this case an unusual photo-product which was characterized as a dibenzopentalene derivative, was obtained in the solid state along with lesser amounts of the normal-solution products. The mechanism proposed for the formation of this product involves a 1,4-biradical intermediate which undergoes a novel double 1,2-ester migration. It was recognized that this biradical intermediate could also undergo fragmentation to produce a cyclooctatetraene (COT) derivative which differs in its symmetry from that of the COT expected based on the mechanism proposed by H. E. Zimmerman for similar transformations observed in the cases of benzo- and naphthobarrelenes. Thus, there are two structures possible for the COT formed which cannot be distinguished based on their spectral properties. For this reason, single crystal X-ray diffraction analysis of the COTs formed in each case was performed. Of the four COT structures determined by X-ray crystallography, three COTs had structures that were consistent with the fragmentation mechanism, while one had a structure consistent with the Zimmerman mechanism. In light of the possible unusual photorearrangements observed, it was thought desirable to establish the molecular structures of all photo-products obtained. To this end, crystal and molecular structures of 11 photoproducts were determined. Also, in an attempt to establish structure-reactivity relationships, crystal and molecular structures of four starting materials were determined. A bridgehead chloromethyl-substituted dibenzobarrelene diester was also found to produce dibenzopenatalene-like photoproducts in the solid state or in chloroform solution; these photoproducts were also characterized based mainly on X-ray crystallography. These results add to the generality of the unusual photobehavior of some dibenzobarrelene derivatives. In the solution phase photolysis of a bridgehead dichloro-substituted dibenzobarrelene diester, a novel cyclic peroxide product was obtained. This was rationalized as being derived from photolysis of the primary di-π-methane photoproduct followed by trapping of the resulting 1,3-biradical by traces of molecular oxygen present in the reaction mixture. Thus, in the present study it was found that bridgehead substituted dibenzobarrelene derivatives undergo di-π-methane rearrangement via their T₁ states as expected, but that their S₁ states may undergo unusual rearrangements to produce cyclooctatetraene derivatives with unexpected structures, and dibenzopentalene derivatives in some cases.Science, Faculty ofChemistry, Department ofGraduat

Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA. Crystal structures of native Fab and three Fab-mononucleotide complexes

NRC publication: Ye

Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA. Crystal structures of native Fab and three Fab-mononucleotide complexes

NRC publication: Ye

Mimicking Natural Photosynthesis: Designing Ultrafast Photosensitized Electron Transfer into Multiheme Cytochrome Protein Nanowires

Efficient nanomaterials for artificial photosynthesis require fast and robust unidirectional electron transfer (ET) from photosensitizers through charge-separation and accumulation units to redox-active catalytic sites. We explored the ultrafast time-scale limits of photo-induced charge transfer between a Ru(II)tris(bipyridine) derivative photosensitizer and PpcA, a 3-heme c-type cytochrome serving as a nanoscale biological wire. Four covalent attachment sites (K28C, K29C, K52C, and G53C) were engineered in PpcA enabling site-specific covalent labeling with expected donor-acceptor (DA) distances of 4–8 Å. X-ray scattering results demonstrated that mutations and chemical labeling did not disrupt the structure of the proteins. Time-resolved spectroscopy revealed three orders of magnitude difference in charge transfer rates for the systems with otherwise similar DA distances and the same number of covalent bonds separating donors and acceptors. All-atom molecular dynamics simulations provided additional insight into the structure-function requirements for ultrafast charge transfer and the requirement of van der Waals contact between aromatic atoms of photosensitizers and hemes in order to observe sub-nanosecond ET. This work demonstrates opportunities to utilize multi-heme c-cytochromes as frameworks for designing ultrafast light-driven ET into charge-accumulating biohybrid model systems, and ultimately for mimicking the photosynthetic paradigm of efficiently coupling ultrafast, light-driven electron transfer chemistry to multi-step catalysis within small, experimentally versatile photosynthetic biohybrid assemblies