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Articles 1 - 24 of 24

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Clinical Light Exposure, Photoreceptor Degeneration, And Ap-1 Activation: A Cell Death Or Cell Survival Signal In The Rhodopsin Mutant Retina?, Danian Gu, William Beltran, Zexiao Li, Gregory M. Acland, Gustavo D. Aguirre Nov 2007

Clinical Light Exposure, Photoreceptor Degeneration, And Ap-1 Activation: A Cell Death Or Cell Survival Signal In The Rhodopsin Mutant Retina?, Danian Gu, William Beltran, Zexiao Li, Gregory M. Acland, Gustavo D. Aguirre

Departmental Papers (Vet)

PURPOSE. The T4R RHO mutant dog retina shows retinal degeneration with exposures to light comparable to those used in clinical eye examinations of patients. To define the molecular mechanisms of the degeneration, AP-1 DNA-binding activity, composition, posttranslational modification of the protein complex, and modulation of ERK/MAPK signaling pathways were examined in light-exposed mutant retinas.

METHODS. Dark-adapted retinas were exposed to short-duration light flashes from a retinal camera used clinically for retinal photography and were collected at different time points after exposure. Electrophoretic mobility shift assay (EMSA), supershift EMSA, Western blot analysis, and immunocytochemistry were used to examine AP-1 signaling ...


Characterization And Structure Of A Zn2+ And [2fe-2s]-Containing Copper Chaperone From Archaeoglobus Fulgidus, Matthew H. Sazinsky, Benjamin Lemoine, Maria Orofino, Roman Davydov, Krisztina Z. Bencze, Timothy L. Stemmler, Brian M. Hoffman, José M. Argüello, Amy C. Rosenzweig Jul 2007

Characterization And Structure Of A Zn2+ And [2fe-2s]-Containing Copper Chaperone From Archaeoglobus Fulgidus, Matthew H. Sazinsky, Benjamin Lemoine, Maria Orofino, Roman Davydov, Krisztina Z. Bencze, Timothy L. Stemmler, Brian M. Hoffman, José M. Argüello, Amy C. Rosenzweig

Biochemistry and Molecular Biology Faculty Publications

Bacterial CopZ proteins deliver copper to P1B-type Cu+-ATPases that are homologous to the human Wilson and Menkes disease proteins. The genome of the hyperthermophile Archaeoglobus fulgidus encodes a putative CopZ copper chaperone that contains an unusual cysteine rich N-terminal domain of 130 amino acids in addition to a C-terminal copper-binding domain with a conserved CXXC motif. The N-terminal domain (CopZ-NT) is homologous to proteins found only in extremophiles and is the only such protein that is fused to a copper chaperone. Surprisingly, optical, electron paramagnetic resonance, and X-ray absorption spectroscopic data indicate the presence of a [2Fe-2S] cluster in ...


Human Frataxin: Iron And Ferrochelatase Binding Surface, Krisztina Z. Bencze, Taejin Yoon, CéSar MilláN-Pacheco, Patrick B. Bradley, Nina Pastor, J. A. Cowan, Timothy L. Stemmler May 2007

Human Frataxin: Iron And Ferrochelatase Binding Surface, Krisztina Z. Bencze, Taejin Yoon, CéSar MilláN-Pacheco, Patrick B. Bradley, Nina Pastor, J. A. Cowan, Timothy L. Stemmler

Biochemistry and Molecular Biology Faculty Publications

The coordinated iron structure and ferrochelatase binding surface of human frataxin have been characterized to provide insight into the protein’s ability to serve as the iron chaperone during heme biosynthesis.


Bestrophin Gene Mutations Cause Canine Multifocal Retinopathy: A Novel Animal Model For Best Disease, Karina E. Guziewicz, Barbara Zangerl, Sarah J. Lindauer, Robert F. Mullins, Lynne S. Sandmeyer, Bruce H. Grahn, Edwin M. Stone, Gregory M. Acland, Gustavo D. Aguirre May 2007

Bestrophin Gene Mutations Cause Canine Multifocal Retinopathy: A Novel Animal Model For Best Disease, Karina E. Guziewicz, Barbara Zangerl, Sarah J. Lindauer, Robert F. Mullins, Lynne S. Sandmeyer, Bruce H. Grahn, Edwin M. Stone, Gregory M. Acland, Gustavo D. Aguirre

Departmental Papers (Vet)

PURPOSE. Canine multifocal retinopathy (cmr) is an autosomal recessive disorder of multiple dog breeds. The disease shares a number of clinical and pathologic similarities with Best macular dystrophy (BMD), and cmr is proposed as a new large animal model for Best disease.

METHODS. cmr was characterized by ophthalmoscopy and histopathology and compared with BMD-affected patients. BEST1 (alias VMD2), the bestrophin gene causally associated with BMD, was evaluated in the dog. Canine ortholog cDNA sequence was cloned and verified using RPE/choroid 5′- and 3′-RACE. Expression of the canine gene transcripts and protein was analyzed by Northern and Western blotting ...


Biochemical Studies Of Mms6--A Biomineralization Protein, Lijun Wang Jan 2007

Biochemical Studies Of Mms6--A Biomineralization Protein, Lijun Wang

Retrospective Theses and Dissertations

Magnetotactic bacteria are aquatic prokaryotes that can move under the direction of a local geomagnetic field. The magnetosomes found in magnetotactic bacteria are arranged in a single chain or chains, which is the physics basis of magnetotaxis trait. It is believed that with the trait of magnetotaxis, magnetotactic bacteria can simplify their search for the optimal oxygen environments.;Mms6 is a magnetosome membrane-associated protein in Magnetospirillum magneticum strain AMB-1. It has 59 amino acids with a hydrophobic N-terminal and a hydrophilic C-terminal region. Magnetite nanoparticles with similar size and shape to bacterial magnetite can be synthesized in vitro in the ...


Kinetic Studies Of Escherichia Coli And Human Saicar Synthetase, Daniel Joseph Binkowski Jan 2007

Kinetic Studies Of Escherichia Coli And Human Saicar Synthetase, Daniel Joseph Binkowski

Retrospective Theses and Dissertations

Phosphoribosyl-aminoimidazole-succinocarboxamide synthetase (SAICAR synthetase) catalyzes the eighth step of de novo IMP biosynthesis in bacteria, and the seventh step in humans. The SAICAR synthetase reaction is analogous to that of adenylosuccinate synthetase (first committed step of AMP biosynthesis), using ATP to ligate 5-amino-imidazole-4-carboxy ribonucleotide and L-aspartate to produce 5-aminoimidazole-4(N-succinylcarboxamide) ribonucleotide (SAICAR). SAICAR synthetase and other enzymes of purine nucleotide biosynthesis are targets of natural products that impair cell growth. Prior to these studies, the kinetic mechanism of any SAICAR synthetase was unknown. Herein are reported the kinetic mechanisms of bacterial and human SAICAR synthetase activities, the structure of the ...


Investigating Reactions Catalyzed By Terpene Synthases In A Novel Model System, Paul Ross Wilderman Jan 2007

Investigating Reactions Catalyzed By Terpene Synthases In A Novel Model System, Paul Ross Wilderman

Retrospective Theses and Dissertations

Terpene synthases are a set of enzymes that initiate the biosynthetic production of the largest class of known natural products. However, not much is known about how these enzymes carry out their complex cyclization reactions to form polycyclic olefins from linear hydrocarbon diphosphates such as geranylgeranyl diphosphate.;Since rice is known to produce many diterpenoid natural products and the rice genome was recently published, sequence information for many putative diterpene synthases was available. This provided the basis for functional characterization of the diterpene synthases from rice (Oryza sativa ssp. Indica). An enzyme producing syn-pimaradiene was identified, followed by those producing ...


Characterization Of The Starch Branching Enzymes In Arabidopsis Thaliana, Qinglei Gan Jan 2007

Characterization Of The Starch Branching Enzymes In Arabidopsis Thaliana, Qinglei Gan

Retrospective Theses and Dissertations

The roles of three starch branching enzyme isoforms, BE1, BE2 and BE3, in Arabidopsis leaf starch metabolism were investigated by AtBE mutant analysis. We also determined the expression patterns of BEs in Arabidopsis by GUS staining and microarray experiments. The possible correlation of BE gene expression with other genes in the Arabidopsis genome was analyzed to identify putative genes that are functionally correlated with BEs. Motifs in the promoters of the Arabidopsis BE genes were identified to better understand their expression differences. BE2 and BE3 expression levels during a diurnal cycle were evaluated with isoform specific antibodies. Meantime, the in ...


Crystallographic Analysis Of Parasponia Andersonii Hemoglobin, Andrea Savage Jan 2007

Crystallographic Analysis Of Parasponia Andersonii Hemoglobin, Andrea Savage

Retrospective Theses and Dissertations

The x-ray crystal structure of ferric Parasponia andersonii hemoglobin has been determined to 2.3 A resolution by molecular replacement with Rice hemoglobin 1 (rHb1). By means of absorbance spectroscopy, electrochemistry and x-ray crystallography, it has been revealed that depending on the oxidation state, the heme iron can exsist in either the pentacoordinate or hexacoordinate form. Pentacoordination of the heme iron is found primarily in the deoxy ferrous (2+) form, whereas the ferric (3+) form is exhibited predominantly in bis-histidine coordination. This is unique among known forms of hemoglobins. Furthermore, the crystallographic data has provided evidence which supports previous works ...


Characterization Of Rns2, An S-Like Rnase In Arabidopsis Thaliana Suggests Role In Phosphate Recycling, Saralyn Ohanian Jan 2007

Characterization Of Rns2, An S-Like Rnase In Arabidopsis Thaliana Suggests Role In Phosphate Recycling, Saralyn Ohanian

Retrospective Theses and Dissertations

Ribonucleases play important biological roles within all organisms but many have not been well characterized. The family of T2 RNases is well-conserved throughout the kingdoms of life and yet their properties and functions are not well understood. RNS2 is one of five such RNases found in Arabidopsis, and preliminary evidence shows that it may be involved in phosphate recycling and localized to an intracellular compartment. Using rns2 knock-out mutant plants, I showed that RNS2 has an effect on flowering time during times of phosphate starvation. I also showed that RNS2 is localized to the ER, more specifically, to ER-bodies. To ...


Biophysical Characterization Of The 117 Amino Acids Long N-Terminal Segment Of D-Raf (Isoform A), Oren Tchaicheeyan Jan 2007

Biophysical Characterization Of The 117 Amino Acids Long N-Terminal Segment Of D-Raf (Isoform A), Oren Tchaicheeyan

Retrospective Theses and Dissertations

Drosophila Raf (D-Raf) is an orthologue of Human B-Raf. D-Raf may have two splice variants, a short (Isoform A, I-A) and a long one (Isoform B, I-B). Protocols for over-expression (E. Coli) and purification of 117 amino acids (aa) N-terminal segment (NTS) of D-Raf protein (I-A), both WT and Mutant (T60E) were established. These protein constructs were also biophysically characterized. Thrombin cleavage conditions were optimized, as monitored by 5 amino acid NTS sequencing, mass spectroscopy and SDS-PAGE electrophoresis. An attempt to purify the 160 aa D-Raf (I-B) NTS failed. NMR characterization in a 700 MHz magnet employing three experiments (HSQC ...


The Role Of Tyr61 In Synechocystis Hemoglobin In Regulating E-Helix Movement, Anand Venugopal Jan 2007

The Role Of Tyr61 In Synechocystis Hemoglobin In Regulating E-Helix Movement, Anand Venugopal

Retrospective Theses and Dissertations

Hexacoordinate hemoglobins have been discovered that have yet to have a functional role confidently assigned to them. The eubacteria synechocystis sp. PCC 6803 has been found to have a truncated hemoglobin which is hexacoordinated. The structures of the hexacoordinated and cyanide bound forms of synechocystis hemoglobin have been solved, and a large shift in the E-helix has been seen upon ligand binding. Also, the loop connecting the E and F helix contains residues Tyr61 and Asp62 that are involved in hydrogen bonding networks in the cyanide-bound and hexacoordinate states respectively. A mutation was made to the Y61 residue to make ...


Biophysical And Biochemical Characterization Of Hexacoordinate Hemoglobins, Benoit Joel Smagghe Jan 2007

Biophysical And Biochemical Characterization Of Hexacoordinate Hemoglobins, Benoit Joel Smagghe

Retrospective Theses and Dissertations

Within the hemoglobin (Hb) superfamily, an unusual group called hexacoordinate hemoglobin (hxHbs) whose members are found in all living organisms is the subject of exciting studies since their discovery. They are named "hexacoordinate" because of reversible coordination of the sixth coordination site of the heme iron by a histidine side chain located in the heme distal pocket. Interestingly, hxHbs share high degree of similarity in their primary sequence and a common globin fold indicating that they might share a common role and that endogenous coordination might be an important part of their not yet characterized physiological function. The characterization of ...


Allosteric Regulation Of Mammalian And Bacterial Fructose-1,6-Bisphosphatases, Justin Keith Hines Jan 2007

Allosteric Regulation Of Mammalian And Bacterial Fructose-1,6-Bisphosphatases, Justin Keith Hines

Retrospective Theses and Dissertations

Fructose-1,6-bisphosphatase (FBPase) is a critical regulatory enzyme in gluconeogenesis. In mammals, the enzyme is subject to metabolic regulation; the hormones insulin and glucagon reciprocally regulate the enzyme in the liver through the controlled production and degradation of the inhibitor fructose-2,6-bisphosphate (Fru-2,6-P2) and hence control hepatic glucose production. FBPase is nearly ubiquitous in living organisms and in the bacterium Escherichia coli , the homologous enzyme is imperative for growth on gluconeogenic substrates. How does this organism regulate FBPase without the use of exogenous hormones or Fru-2,6-P2? Investigations reported herein describe high resolution crystal structures of the enzyme from ...


Production Of 3-Hydroxypropionate From Biomass, Netra Rajguru Agarkar Jan 2007

Production Of 3-Hydroxypropionate From Biomass, Netra Rajguru Agarkar

Retrospective Theses and Dissertations

Biorenewable technology is a developing field of science that researches alternative sources for petroleum products like fuels, plastics, paints, etc. The DoE biomass program has identified the 12 top chemicals that can be produced from biomass and further processed to replace many petroleum products; 3-hydroxypropionate (3HP) is a top 12 chemical that can be used to produce plastics, paints, tires, and other consumer products. This thesis describes the attempts to produce 3HP from glucose in E. coli and from syngas in R. rubrum. Malonyl CoA reductase from C. aurantiacus and R. castenholzii was cloned and expressed in E. coli and ...


The Roles Of Lcn2 In The Inflammatory Lung And Liver, Yinghua Liu Jan 2007

The Roles Of Lcn2 In The Inflammatory Lung And Liver, Yinghua Liu

Retrospective Theses and Dissertations

Uterocalin (Lcn2; also called 24p3, SIP24, or siderocalin and abbreviated as Utc) is an acute phase protein, for which the physiological function remains to be determined. Basal Utc expression is highest in the uterus, mammary gland and lung, which are three tissues with direct exposure to the diverse bacterial flora of the external environment. The demonstrated ability to bind siderophores is one means by which Utc can provide protection against pathogenic bacteria. However, its specificity for siderophores limits the ability of Utc to ward off pathogens. Epithelial tissues that interact with the external environment are exposed to many different nonpathogenic ...


Structural And Functional Studies On Membrane Fusion Proteins-Snares, Yibin Xu Jan 2007

Structural And Functional Studies On Membrane Fusion Proteins-Snares, Yibin Xu

Retrospective Theses and Dissertations

Membrane fusion is a ubiquitous and essential intracellular function. Membrane fusion is mediated by a protein superfamily known as N-ethymaleimide-sensitive fusion protein attachment protein receptors (SNAREs). From plant to mammal, there is a remarkable sequence similarity among the SNARE-family related to the conserved function of this family. The function of SNAREs has been proposed to be the key to membrane fusion as minimal fusion machinery. Depending on their distinct membrane distribution, SNAREs were classified into v (vesicle)-SNAREs and t (target)-SNAREs. It is widely believed that SNARE complex assembly by v- and t-SNAREs on opposite membranes offers the ultimate ...


Biotechnological Improvements Of Bio-Based Fuels And Lubricants: Characterization Of Genes For Branched Chain Fatty Acids And Mono-Acyl Esters, Yuqin Jin Jan 2007

Biotechnological Improvements Of Bio-Based Fuels And Lubricants: Characterization Of Genes For Branched Chain Fatty Acids And Mono-Acyl Esters, Yuqin Jin

Retrospective Theses and Dissertations

The goals of the research in this dissertation are to generate the fundamental technologies that can be used to improve the production and quality of vegetable-oil based biodiesel and biolubricants. Specifically, we sought to test the hypothesis that branched chain fatty acids (BCFAs) can substitute for unsaturated fatty acids in maintaining fluidityin an organism. Toward this goal, we examined the utility of two Bacillus keto-acyl synthase III (KASIII) coding genes (yhfB and yjaX) in producing BCFAs. In conducting this research it was necessary to examine if the E. coli KASIII gene (fabH) was essential for initiating fatty acid biosynthesis and ...


Determinants Of Substrate Recognition And Mechanisms Of Subunit Exchange, Yang Zhou Jan 2007

Determinants Of Substrate Recognition And Mechanisms Of Subunit Exchange, Yang Zhou

Retrospective Theses and Dissertations

Adenylosuccinate synthetase (ADSS) offers a good opportunity to measure the effect of non-bonded interactions. Both IMP and 2'-deoxy-IMP are good substrates supporting identical binding affinities and maximal velocities; however, L-aspartate exhibits significant differences in binding affinities depending on which nucleotide is used as a substrate. Crystal structures of both complexes were identical except for the absence of the 2'-OH group in the dexoy-nucleotide complex. The decrease in energy (∼2 kcal/mole) in non-bonded interactions due to the loss of one atom explains the nearly 40-fold difference in the binding affinity of L-aspartate and an analog of L-aspartate called ...


Structural Study Of Yeast Snare Proteins On Membrane By Epr, Yinghui Zhang Jan 2007

Structural Study Of Yeast Snare Proteins On Membrane By Epr, Yinghui Zhang

Retrospective Theses and Dissertations

Membrane fusion is a basic biophysical process involved in cell's physiological activities. The value of studying the exocytosis of mammalian cells and yeast cells lies in that a highly conserved SNARE (Soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein super family mediates this process and is proposed to be the core protein machinery for the membrane. The SNARE proteins located on plasma membrane and vesicle membrane are assembled together to form a trans-SNARE bridging two separate membranes and initiating membrane.;My research centers on how SNARE assembly involved in yeast cells' exocytosis promotes membrane fusion between yeast vesicle and plasma ...


Methanobactin And The Membrane-Associated Methane Monooxygenase In Methanotrophy: A Tale Of Two Proteins, Dongwon Choi Jan 2007

Methanobactin And The Membrane-Associated Methane Monooxygenase In Methanotrophy: A Tale Of Two Proteins, Dongwon Choi

Retrospective Theses and Dissertations

No abstract provided.


Investigation Of Allosteric Regulation Of Porcine Fructose-1,6-Bisphosphatase, Jian Lu Jan 2007

Investigation Of Allosteric Regulation Of Porcine Fructose-1,6-Bisphosphatase, Jian Lu

Retrospective Theses and Dissertations

Porcine Fructose-1,6-bisphosphatase is a homotetramer with four identical subunits. It plays a central role in gluconeogenesis and is tightly regulated by metabolites fructose 2,6-bisphosphate (F26P2) and AMP. Loop 52-72, loop 182-194 and residues 7-11 of the N-terminal segment play important role in the mechanism of catalysis and allosteric inhibition by AMP by retaining a structural hydrophobic region. Disruption of the hydrophobic region will evidently affect the catalysis and regulation of FBPase. Mutation of Thr53 reduced the catalysis activity of FBPase, mutation of Thr194 eliminated inhibition of AMP due to its low affinity to the enzyme, while double mutation ...


Role Of Leu[Superscript B 10] In Cytoglobin And Comparison Of Direct And Indirect Measurements Of Hexacoordinate Hemoglobin Ligand Affinity, Jordan Richard Witmer Jan 2007

Role Of Leu[Superscript B 10] In Cytoglobin And Comparison Of Direct And Indirect Measurements Of Hexacoordinate Hemoglobin Ligand Affinity, Jordan Richard Witmer

Retrospective Theses and Dissertations

Hexacoordinate hemoglobins (HxHbs) have recently been discovered and have been found in nearly all living organisms. In humans, hxHbs are represented by neuroglobin (Ngb) and cytoglobin (Cgb). While Ngb is principally found in the brain, Cgb is ubiquitously expressed in all tissues. Ligand binding in hexacoordinate hemoglobins is complex due to the reversible coordination of the heme iron by the distal histidine. Hexacoordination regulates ligand binding and is regulated by specific residues in the heme pocket including the B10 position. Therefore, we investigated the influence of LeuB10 on hexacoordination and ligand binding in Cgb. Ligand binding was analyzed for recombinant ...


Characterization Of Three Spindle Matrix Proteins, Megator, East And Asator, In Drosophila, Hongying Qi Jan 2007

Characterization Of Three Spindle Matrix Proteins, Megator, East And Asator, In Drosophila, Hongying Qi

Retrospective Theses and Dissertations

Two previously identified proteins Skeletor and Chromator provide the molecular evidence for the existence of a spindle matrix complex in Drosophila. The spindle matrix has been proposed to be a macromolecular complex, which plays a role in organization and stabilization of the mitotic spindle as well as in providing structural support for counterbalancing force production.;In this dissertation, I present the identification and characterization of three more putative spindle matrix candidate proteins, Megator, EAST and Asator. Megator, an ortholog of the mammalian TPR protein, contains a large coiled-coil domain at its NH2-terminus and an acidic, non-structural COOH-terminus. Immunohistochemistry studies show ...