Structure and mechanism of the iron‐sulfur flavoprotein phthalate dioxygenase reductase

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154520/1/fsb2009014006.pd

Crystallization and preliminary X-ray diffraction studies of the cobalamin-binding domain of methionine synthase from Escherichia coli

Crystals of a cobalamin-binding domain (Mr = 28,000) have been grown in polyethylene glycol 6000 at pH 7.5, starting from solutions of intact (Mr = 133,000) cobalamin-dependent methionine synthase. The crystals are orthorhombic in space group P212121, with cell dimensions a = 96.9 A, B = 55.4 A, C = 103.8 A. For two molecules per asymmetric unit, the calculated Vm value is 2.45 A3/Da. A native data set has been collected to 3 A resolution.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30045/1/0000413.pd

Damage Detection and Verification System (DDVS) for In-Situ Health Monitoring

Project presentation for Game Changing Program Smart Book Release. Detection and Verification System (DDVS) expands the Flat Surface Damage Detection System (FSDDS) sensory panels damage detection capabilities and includes an autonomous inspection capability utilizing cameras and dynamic computer vision algorithms to verify system health. Objectives of this formulation task are to establish the concept of operations, formulate the system requirements for a potential ISS flight experiment, and develop a preliminary design of an autonomous inspection capability system that will be demonstrated as a proof-of-concept ground based damage detection and inspection system

Structure of the semiquinone form of flavodoxin from Clostridium MP : Extension of 1.8 A resolution and some comparisons with the oxidized state

As part of a series of comparisons of the structures of the three oxidation states of flavodoxin from Clostridium MP, phases for the semiquinono form were determined to 2.0 A resolution by isomorphous replacement (m > = 0.725). Subsequently, the structure was refined at 1.8 A resolution by a combination of difference Fourier, real space and reciprocal space methods. After refining to an R of 0.194, we explored the conformation of the FMN binding site by real space refinement versus maps with Fourier coefficients of the form (2|Fo|- |Fc|) exp (i[alpha]c). To minimize bias in the fitting, groups of atoms were systematically omitted from the structure factors used in computation of the (2|Fo - |Fc|) maps.One-electron reduction of oxidized flavodoxin is accompanied by several changes at the FMN binding site: the conformation of residues in the reverse bend formed by Met56-Gly57-Asp58-Glu59 differs in the crystal structures of the oxidized and semiquinone species; further, backbone atoms in residues 55 and 89 shift by more than 0.5 A and the indole ring of Trp90 undergoes a significant displacement. The orientation of the peptide unit connecting Gly57 and Asp58 is consistent with the presence of a hydrogen bond between the carbonyl oxygen of Gly57 and the flavin N(5) in flavodoxin semiquinone. No equivalent bond is found in oxidized flavodoxin. In both the oxidized and semiquinone species of clostridial flavodoxin, the isoalloxazine ring is essentially planar : the bending angles about N(5)---N(10) are ~2.5 [deg] for the semiquinone structure and ~0 [deg] in oxidized flavodoxin.The intensity changes resulting from the oxidized agsemiquinone conversion (RI = 0.33) arise in part from changes in molecular packing. Intermolecular contacts, including neighbors of the prosthetic group, are altered in the repacking. Maps or models of the two oxidation states can be brought into approximate coincidence by a rigid body motion. The required transformation, determined for the isomorphous replacement maps by the method of Cox (1967), is equivalent to a screw motion with a rotation of 1.18 [deg] and a translation of -0.34 A. The molecular structures of oxidized and semiquinone flavodoxins have been compared after superposition of models with idealized co-ordinates and discrepancy indices Rox = 0.213 and Rsq = 0.200. The root-mean-square distance between 523 backbone atoms (excluding sequences 56 to 59 and 89 to 91) is 0.308 A.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/22809/1/0000366.pd

A method for the preparation of heavy-atom derivatives of yeast cytochrome c peroxidase

This Letter describes a strategy for preparation of heavy-atom derivatives which has succeeded with yeast cytochrome c peroxidase and which may be useful for other crystalline proteins. Transfer of the crystals from methylpentanediol solutions, in which they were grown, to solutions of polyethylene glycol (Mr 6000) maintains the crystal structure so that crystals tolerate heavy-atom concentrations at least ten times larger than could be attained in methylpentanediol mother liquors.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/23653/1/0000619.pd

Characterization of the manganese sites in manganese redox enzymes: Catalase and superoxide dismutase.

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30701/1/0000346.pd

Cobalamin-Independent Methionine Synthase (MetE): A Face-to-Face Double Barrel That Evolved by Gene Duplication

Cobalamin-independent methionine synthase (MetE) catalyzes the transfer of a methyl group from methyltetrahydrofolate to L-homocysteine (Hcy) without using an intermediate methyl carrier. Although MetE displays no detectable sequence homology with cobalamin-dependent methionine synthase (MetH), both enzymes require zinc for activation and binding of Hcy. Crystallographic analyses of MetE from T. maritima reveal an unusual dual-barrel structure in which the active site lies between the tops of the two (βα)(8) barrels. The fold of the N-terminal barrel confirms that it has evolved from the C-terminal polypeptide by gene duplication; comparisons of the barrels provide an intriguing example of homologous domain evolution in which binding sites are obliterated. The C-terminal barrel incorporates the zinc ion that binds and activates Hcy. The zinc-binding site in MetE is distinguished from the (Cys)(3)Zn site in the related enzymes, MetH and betaine–homocysteine methyltransferase, by its position in the barrel and by the metal ligands, which are histidine, cysteine, glutamate, and cysteine in the resting form of MetE. Hcy associates at the face of the metal opposite glutamate, which moves away from the zinc in the binary E·Hcy complex. The folate substrate is not intimately associated with the N-terminal barrel; instead, elements from both barrels contribute binding determinants in a binary complex in which the folate substrate is incorrectly oriented for methyl transfer. Atypical locations of the Hcy and folate sites in the C-terminal barrel presumably permit direct interaction of the substrates in a ternary complex. Structures of the binary substrate complexes imply that rearrangement of folate, perhaps accompanied by domain rearrangement, must occur before formation of a ternary complex that is competent for methyl transfer

Pennsylvania Folklife Vol. 9, No. 4

• Dry Houses • Harvest Home • Golden Fields in the Golden Years • Illuminators, Scribes and Printers • John Drissel and His Boxes • Tick-Tock Time in Old Pennsylvania • About the Authors • Present Day Food Habits of the Pennsylvania Dutch • The Attitude of the Early Reformed Church Fathers Toward Worldly Amusementshttps://digitalcommons.ursinus.edu/pafolklifemag/1003/thumbnail.jp

Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing

Biogas production from renewable resources is attracting increased attention as an alternative energy source due to the limited availability of traditional fossil fuels. Many countries are promoting the use of alternative energy sources for sustainable energy production. In this study, a metagenome from a production-scale biogas fermenter was analysed employing Roche's GS FLX Titanium technology and compared to a previous dataset obtained from the same community DNA sample that was sequenced on the GS FLX platform. Taxonomic profiling based on 16S rRNA-specific sequences and an Environmental Gene Tag (EGT) analysis employing CARMA demonstrated that both approaches benefit from the longer read lengths obtained on the Titanium platform. Results confirmed Clostridia as the most prevalent taxonomic class, whereas species of the order Methanomicrobiales are dominant among methanogenic Archaea. However, the analyses also identified additional taxa that were missed by the previous study, including members of the genera Streptococcus, Acetivibrio, Garciella, Tissierella, and Gelria, which might also play a role in the fermentation process leading to the formation of methane. Taking advantage of the CARMA feature to correlate taxonomic information of sequences with their assigned functions, it appeared that Firmicutes, followed by Bacteroidetes and Proteobacteria, dominate within the functional context of polysaccharide degradation whereas Methanomicrobiales represent the most abundant taxonomic group responsible for methane production. Clostridia is the most important class involved in the reductive CoA pathway (Wood-Ljungdahl pathway) that is characteristic for acetogenesis. Based on binning of 16S rRNA-specific sequences allocated to the dominant genus Methanoculleus, it could be shown that this genus is represented by several different species. Phylogenetic analysis of these sequences placed them in close proximity to the hydrogenotrophic methanogen Methanoculleus bourgensis. While rarefaction analyses still indicate incomplete coverage, examination of the GS FLX Titanium dataset resulted in the identification of additional genera and functional elements, providing a far more complete coverage of the community involved in anaerobic fermentative pathways leading to methane formation

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms