CMR2009: 5.04: Post-mortem analysis of gadolinium distribution in NSF subjects

No Abstract.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/64915/1/323_ftp.pd

Grazing‐angle characterization of photosynthetic oxygen evolution protein monolayers

Variable‐period x‐ray standing wave (XSW) spectroscopy has been shown to be a practical probe for studying metalloproteins. The photosynthetic oxygen evolving complex (OEC) is a transmembrane multipolypeptide complex that catalyzes the oxidation of water to dioxygen. The OEC contains Mn, Ca, and Cl and is potentially amenable to study by XSW. In this feasibility study, preliminary results on OEC samples deposited on Au mirrors are discussed. First XSW measurements from the SSRL grazing‐incidence setup are presented. © 1996 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70867/2/RSINAK-67-9-3364-5.pd

Making or Breaking Metal- Dependent Catalytic Activity: The Role of Stammers in Designed Three- Stranded Coiled Coils

While many life- critical reactions would be infeasibly slow without metal cofactors, a detailed understanding of how protein structure can influence catalytic activity remains elusive. Using de novo designed three- stranded coiled coils (TRI and Grand peptides formed using a heptad repeat approach), we examine how the insertion of a three residue discontinuity, known as a stammer insert, directly adjacent to a (His)3 metal binding site alters catalytic activity. The stammer, which locally alters the twist of the helix, significantly increases copper- catalyzed nitrite reductase activity (CuNiR). In contrast, the well- established zinc- catalyzed carbonic anhydrase activity (p- nitrophenyl acetate, pNPA) is effectively ablated. This study illustrates how the perturbation of the protein sequence using non- coordinating and non- acid base residues in the helical core can perturb metalloenzyme activity through the simple expedient of modifying the helical pitch adjacent to the catalytic center.The addition of a stammer discontinuity within a de novo designed 3SCC containing a symmetric (His)3 metal binding site enhances copper nitrite reductase activity and ablates zinc esterase activity. These results suggest catalytic activity of designed α- helical systems can be modulated by inclusion of discontinuity insertions and deletions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/163447/3/anie202008356-sup-0001-misc_information.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163447/2/anie202008356_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163447/1/anie202008356.pd

XAS of the MerR metalloregulatory protein

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27900/1/0000320.pd

Structural characterization of reduced and chemically substituted derivatives of the MN cluster in the photosynthetic oxygen evolving complex

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30718/1/0000364.pd

Modifying the Steric Properties in the Second Coordination Sphere of Designed Peptides Leads to Enhancement of Nitrite Reductase Activity

Protein design is a useful strategy to interrogate the protein structureâ function relationship. We demonstrate using a highly modular 3â stranded coiled coil (TRIâ peptide system) that a functional typeâ 2 copper center exhibiting copper nitrite reductase (NiR) activity exhibits the highest homogeneous catalytic efficiency under aqueous conditions for the reduction of nitrite to NO and H2O. Modification of the amino acids in the second coordination sphere of the copper center increases the nitrite reductase activity up to 75â fold compared to previously reported systems. We find also that steric bulk can be used to enforce a threeâ coordinate CuI in a site, which tends toward twoâ coordination with decreased steric bulk. This study demonstrates the importance of the second coordination sphere environment both for controlling metalâ center ligation and enhancing the catalytic efficiency of metalloenzymes and their analogues.Erstklassiges aus der zweiten Reihe: Die Aktivität der Nitritreduktase kann durch Modifikation der sterischen Eigenschaften in der zweiten Koordinationssphäre eines Typâ 2â Kupferzentrums deutlich erhöht werden. à ber die Sterik lassen sich die Koordination und Reaktivität des Metalls in einem dreisträngigen â Coiledâ coilâ â TRIâ Peptidgerüst (TRIWâ H) vorgeben.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142882/1/ange201712757_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142882/2/ange201712757-sup-0001-misc_information.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142882/3/ange201712757.pd

Modifying the Steric Properties in the Second Coordination Sphere of Designed Peptides Leads to Enhancement of Nitrite Reductase Activity

Protein design is a useful strategy to interrogate the protein structureâ function relationship. We demonstrate using a highly modular 3â stranded coiled coil (TRIâ peptide system) that a functional typeâ 2 copper center exhibiting copper nitrite reductase (NiR) activity exhibits the highest homogeneous catalytic efficiency under aqueous conditions for the reduction of nitrite to NO and H2O. Modification of the amino acids in the second coordination sphere of the copper center increases the nitrite reductase activity up to 75â fold compared to previously reported systems. We find also that steric bulk can be used to enforce a threeâ coordinate CuI in a site, which tends toward twoâ coordination with decreased steric bulk. This study demonstrates the importance of the second coordination sphere environment both for controlling metalâ center ligation and enhancing the catalytic efficiency of metalloenzymes and their analogues.Second is best: A significant increase in nitrite reductase activity is achieved by modification of the steric properties of the second coordination sphere of a typeâ 2 copper center. The steric properties can be harnessed to control metal coordination and reactivity in a 3â stranded coiled coil TRI peptide scaffold (TRIWâ H).Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142897/1/anie201712757.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142897/2/anie201712757-sup-0001-misc_information.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142897/3/anie201712757_am.pd

XAS investigation of the Fe sites in phthalate dioxygenase

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27899/1/0000319.pd

Structural characterization of the mononuclear iron site in Pseudomonas cepacia phthalate DB01 dioxygenase using X-ray absorption spectroscopy

 Phthalate dioxygenase (PDO) from Pseudomonas cepacia contains a Rieske-like [2Fe-2S] cluster and a mononuclear non-heme Fe(II) site. The mononuclear iron can be replaced by a variety of divalent metal ions, although only Fe(II) permits catalytic activity. We used X-ray absorption spectroscopy to characterize the structural properties of the mononuclear iron site and to follow the structural changes in this site as a function both of Rieske site oxidation state and of phthalate binding. Data for the mononuclear site have been measured directly for PDO substituted with Co or Zn in the mononuclear site, and by difference for the native 3-Fe protein. The mononuclear site was modeled well by low Z-ligation (oxygen or nitrogen) and showed no evidence for high-Z ligands (e.g., sulfur). The relatively short average first shell bond lengths and the absence of significant outer shell scattering suggest that the mononuclear site has several oxygen ligands. With Zn in the mononuclear site, the average bond length (2.00 Å) suggests a 5-coordinate site under all conditions. In contrast, the Co- or Fe-containing mononuclear site appeared to be 6-coordinate and changed to 5-coordinate when substrate was bound, since the first shell bond length changed from 2.08 to 2.02 Å (Co) or 2.10 to 2.06 Å (Fe). The implications of these findings for the PDO mechanism are discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42321/1/775-1-1-24_60010024.pd

Sulfur speciation in heavy petroleums: Information from X-ray absorption near-edge structure

The chemical speciation of sulfur in heavy petroleums, petroleum source rock extracts, and source rock pyrolysis products was studied using X-ray absorption near-edge structure (XANES) spectroscopy. The good energy resolution (ca. 0.5 eV) at the sulfur K edge and the strong dependence of XANES on the sulfur environment combine to give excellent sensitivity to changes in the electronic and structural environment of the sulfur. This has permitted identification and approximate quantitation of different classes of sulfur-containing compounds (e.g., sulfur, sulfides (including disulfides and polysulfides as a group), thiophenes, sulfoxides, sulfones, sulfinic acids, sulfonic acids, and sulfate) in a series of petroleums and petroleum source rocks. Our results indicate that the sulfur speciation of geological samples can be correlated with differences in source depositional environment, thermal maturity, and aromaticity. We report organosulfur compositions for the asphaltene, maltene, and liquid Chromatographie fractions of two sulfur-rich oils. In addition, we find that the organosulfur species in some, but not all, oils are subject to oxidation upon storage and thus may also be susceptible to oxidation in shallow reservoirs exposed to oxic waters. This work illustrates the utility of XANES as a direct spectroscopic probe for the quantitative determination of sulfur species in geological samples.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29445/1/0000527.pd