Biochemistry, Biophysics, and Structural Biology Commons^™

Welcome To The Journal Of Evolution And Health, Aaron Blaisdell, Paul Jaminet, David C. Pendergrass

Aaron P Blaisdell

Welcome to the first issue of the Journal of Evolution and Health! The Journal of Evolution and Health is the peer-reviewed, open-access journal of the Ancestral Health Society, a community of scientists, healthcare professionals, and laypersons who collaborate to understand health challenges from an evolutionary perspective.

Characterizing The Promiscuity Of Ligab, A Lignin Catabolite Degrading Extradiol Dioxygenase From Sphingomonas Paucimobilis Syk-6, Kevin P. Barry, Erika A. Taylor

Erika A. Taylor, Ph.D.

LigAB from Sphingomonas paucimobilis SYK-6 is the only structurally characterized dioxygenase of the largely uncharacterized superfamily of Type II extradiol dioxygenases (EDO). This enzyme catalyzes the oxidative ring-opening of protocatechuate (3,4-dihydroxybenzoic acid or PCA) in a pathway allowing the degradation of lignin derived aromatic compounds (LDACs). LigAB has also been shown to utilize two other LDACs from the same metabolic pathway as substrates, gallate, and 3-O-methyl gallate; however, kcat/KM had not been reported for any of these compounds. In order to assess the catalytic efficiency and get insights into the observed promiscuity of this enzyme, steady-state kinetic analyses were performed …

Comparative Metabolism Of Phenanthro[3,4-B]Thiophene And Benzo[C]Phenanthrene, Jaquan M. Williams

Jaquan M Williams

ABSTRACT OF THESIS Comparative Metabolism of Phenanthro[3,4-b]Thiophene And Benzo[c]Phenanthrene Polycyclic aromatic hydrocarbons (PAHs) and their sulfur-heterocyclic analogs (thia-PAHs) are commonly occurring persistent environmental contaminants formed by incomplete combustion of organic matter. A number of thia-PAHs have shown significant mutagenic and carcinogenic activities. As noted with PAHs, these chemical contaminants also require metabolic activation in order to exhibit their mutagenic and carcinogenic effects. In the present study, a comparison of the metabolism of highly mutagenic phenanthro[3,4-b]thiophene (P[3,4-b]T) and its weakly mutagenic carbon analogue, benzo[c]phenanthrene (B[c]P), was investigated. Metabolism studies were conducted using liver microsomes from induced rats, un-induced rats, as well …

Escherichia Coli Heptosyltransferase I: Investigation Of Protein Dynamics Of A Gt-B Structural Enzyme, Erika A. Taylor, Daniel J. Czyzyk, Shreya S. Sawant, Carlos A. Ramirez-Mondragon

Erika A. Taylor, Ph.D.

Heptosyltransferase I (HepI), the enzyme responsible for the transfer of l-glycero-d-manno-heptose to a 3-deoxy-α-d-manno-oct-2-ulopyranosonic acid (Kdo) of the growing core region of lipopolysaccharide, is a member of the GT-B structural class of enzymes. Crystal structures have revealed open and closed conformations of apo and ligand-bound GT-B enzymes, implying that large-scale protein conformational dynamics play a role in their reaction mechanism. Here we report transient kinetic analysis of conformational changes in HepI reported by intrinsic tryptophan fluorescence and present the first real-time evidence of a GT-B enzyme undergoing a substrate binding-induced transition from an open to closed state prior to catalysis.

Function And X-Ray Crystal Structure Of Escherichia Coli Yfde, Elwood A. Mullins, Kelly L. Sullivan, T. Joseph Kappock

T. Joseph Kappock

Many food plants accumulate oxalate, which humans absorb but do not metabolize, leading to the formation of urinary stones. The commensal bacterium Oxalobacter formigenes consumes oxalate by converting it to oxalyl-CoA, which is decarboxylated by oxalyl-CoA decarboxylase (OXC). OXC and the class III CoA-transferase formyl-CoA:oxalate CoA-transferase (FCOCT) are widespread among bacteria, including many that have no apparent ability to degrade or to resist external oxalate. The EvgA acid response regulator activates transcription of the Escherichia coli yfdXWUVE operon encoding YfdW (FCOCT), YfdU (OXC), and YfdE, a class III CoA-transferase that is ~30% identical to YfdW. YfdW and YfdU are necessary …

Global Analysis Of Gene Expression Changes During Retinoic Acid-Induced Growth Arrest And Differentiation Of Melanoma: Comparison To Differentially Expressed Genes In Melanocytes Vs Melanoma, Mary H. Estler, Goran Boskovic, James Denvir, Sarah Miles, Donald A. Primerano, Richard M. Niles

Goran Boskovic

BACKGROUND: The incidence of malignant melanoma has significantly increased over the last decade. Some of these malignancies are susceptible to the growth inhibitory and pro-differentiating effects of all-trans-retinoic acid (RA). The molecular changes responsible for the biological activity of RA in melanoma are not well understood. RESULTS: In an analysis of sequential global gene expression changes during a 4-48 h RA treatment of B16 mouse melanoma cells, we found that RA increased the expression of 757 genes and decreased the expression of 737 genes. We also compared the gene expression profile (no RA treatment) between non-malignant melan-a mouse melanocytes and …

Current State Of Food Security: Research, Education And Outreach In Burkina Universities, Mamoudou H. Dicko Prof.

Pr. Mamoudou H. DICKO, PhD

Burkina Faso is a Sahelian West African country. Current population is about 16 millions and 43.9 % live below the poverty line. Burkina Faso is classified as both a least developed country and a low-income, food-deficit country. The nutritional quality is poor (1830 against 2000 Kcal/person/day). Food insecurity affects 50 % of households, and is increasing in the urban areas. However, Burkina Faso is one of the country that respect the 2003 Maputo’s declaration’s call to invest at least 10 percent of the budget in agriculture, in order to increase agricultural production and attain food self-sufficiency. Several training programs dealing …

Genetic Parameters For Concentrations Of Minerals In Longissimus Muscle And Their Associations With Palatability Traits In Angus Cattle, R. G. Mateescu, A. J. Garmyn, Richard G. Tait Jr., Qing Duan, Q. Liu, Mary S. Mayes, Dorian J. Garrick, A. L. Van Eenennaam, D. L. Vanoverbeke, G. G. Hilton, Donald C. Beitz, James M. Reecy

Richard G. Tait Jr.

The objective of this study was to estimate genetic parameters for concentrations of minerals in LM and to evaluate their associations with beef palatability traits. Samples of LM from 2,285 Angus cattle were obtained and fabricated into steaks for analysis of mineral concentrations and for trained sensory panel assessments. Nine minerals, including calcium, copper, iron, magnesium, manganese, phosphorus, potassium, sodium, and zinc, were quantified. Restricted maximum likelihood procedures were used to obtain estimates of variance and covariance components under a multiple-trait animal model. Estimates of heritability for mineral concentrations in LM varied from 0.01 to 0.54. Iron and sodium were …

Genetic Parameters For Carnitine, Creatine, Creatinine, Carnosine, And Anserine Concentration In Longissimus Muscle And Their Association With Palatability Traits In Angus Cattle, R. G. Mateescu, A. J. Garmyn, M. A. O'Neil, Richard G. Tait Jr., Almass A. Abuzaid, Mary S. Mayes, Dorian J. Garrick, A. L. Van Eenennaam, D. L. Vanoverbeke, G. G. Hilton, Donald C. Beitz, James M. Reecy

Richard G. Tait Jr.

The objective of this study was to estimate genetic parameters for carnitine, creatine, creatinine, carnosine, and anserine concentration in LM and to evaluate their associations with Warner-Bratzler shear force (WBSF) and beef palatability traits. Longissimus muscle samples from 2,285 Angus cattle were obtained and fabricated into steaks for analysis of carnitine, creatine, creatinine, carnosine, anserine, and other nutrients, and for trained sensory panel and WBSF assessments. Restricted maximum likelihood procedures were used to obtain estimates of variance and covariance components under a multiple-trait animal model. Estimates of heritability for carnitine, creatine, creatinine, carnosine, and anserine concentrations in LM from Angus …

Proximate Composition Of Traditional Local Sorghum Beer “ Dolo ” Manufactured In Ouagadougou, Fatouma Mohamed Abdoul-Latif, Mamoudou H. Dicko Prof.

Pr. Mamoudou H. DICKO, PhD

Dolo is a local beer manufactured from malted red sorghum grains. It is the most commonly consumed alcoholic beverage in Burkina Faso. Thirty samples of dolo, were collected from local markets in Ouagadougou and analyzed with respect to their proximate compositions and pH values. The average values of pH, dry matter and insoluble matter among samples were 3.5, 5.90 % and 0.85 %, respectively. Alcohol content of dolo samples was on average 2.3 % (v/v). The content of total proteins, carbohydrates and reducing sugars were 26, 38 and 10 µg/ml, respectively. Only traces of lipids were detected in all dolo …

Characterization Of Myxococcus Xanthus Mazf And Implications For A New Point Of Regulation, Tye O. Boynton, Jonathan L. Mcmurry, Lawrence J. Shimkets

Jonathan McMurry

During development, Myxococcus xanthus cells undergo programmed cell death (PCD) whereby 80% of vegetative cells die. Previously, the MazF RNA interferase has been implicated in this role. Recently, it was shown that deletion of the mazF gene does not eliminate PCD in wild-type strain DK1622 as originally seen in DZF1. To clarify the role of MazF, recombinant enzyme was characterized using a highly sensitive assay in the presence and absence of the proposed antitoxin MrpC. In contrast to previous reports that MrpC inhibits MazF activity, the hydrolysis rate was enhanced in a concentration-dependent manner with MrpC or MrpC2, an N-terminally …

Dna Damage Repair Genes Controlling Human Papillomavirus (Hpv) Episome Levels Under Conditions Of Stability And Extreme Instability, Terri G. Edwards, Thomas J. Vidmar, Kevin Koeller, James K. Bashkin, Chris Fisher

James Bashkin

Psychosine, The Cytotoxic Sphingolipid That Accumulates In Globoid Cell Leukodystrophy, Alters Membrane Architecture, Jacqueline A. Hawkins-Salsbury, Archana R. Parameswar, Xuntian Jiang, Paul H. Schlesinger, Ernesto Bongarzone, Daniel S. Ory, Alexei V. Demchenko, Mark S. Sands

Alexei Demchenko

Inhibition Of Bacillus Cereus Growth By Bacteriocin Producing Bacillus Subtilis Isolated From Fermented Baobab Seeds (Maari) Is Substrate Dependent, Donatien Kaboré, Dennis S. Nielsen, Hagrétoui Sawadogo-Lingan, Bréhima Diawara, Mamoudou H. Dicko Prof., Mogens Jakobsen, Line Thorsen

Pr. Mamoudou H. DICKO, PhD

Quantitative Non-Isotopic Nitrocellulose Filter Binding Assays: Bacterial Mnsod-Dna Interactions, Joshua D. Czerwinski, David P. Mascotti

David P. Mascotti

No abstract provided.

Thermal And Sodium Dodecylsulfate Induced Transitions Of Streptavidin, Mark J. Waner, Irina Navrotskaya, Amanda Bain, Edward D. Oldham, David P. Mascotti

Mark J. Waner

The strong specific binding of streptavidin (SA) to biotin is utilized in numerous biotechnological applications. The SA tetramer is also known to exhibit significant stability, even in the presence of sodium dodecylsulfate (SDS). Despite its importance, relatively little is known about the nature of the thermal denaturation pathway for SA. This work uses a homogeneous SA preparation to expand on the data of previous literature reports, leading to the proposal of a model for temperature induced structural changes in SA. Temperature dependent data were obtained by SDS and native polyacrylamide gel electrophoresis (PAGE), differential scanning calorimetry (DSC), and fluorescence and …

The Effect Of Oxidant And The Non-Oxidant Alteration Of Cellular Thiol Concentration On The Formation Of Protein Mixed-Disulfides In Hek 293 Cells, Jasen Lee Gilge, Michael Fisher, Yuh-Cherng Chai

Yuh-Cherng Chai

Cellular molecules possess various mechanisms in responding to oxidant stress. In terms of protein responses, protein S-glutathionylation is a unique post-translational modification of protein reactive cysteines forming disulfides with glutathione molecules. This modification has been proposed to play roles in antioxidant, regulatory and signaling in cells under oxidant stress. Recently, the increased level of protein S-glutathionylation has been linked with the development of diseases. In this report, specific S-glutathionylated proteins were demonstrated in human embryonic kidney 293 cells treated with two different oxidative reagents: diamide and hydrogen peroxide. Diamide is a chemical oxidizing agent whereas hydrogen peroxide is a physiological …

Structural Adaptations Of Proteins To Different Biological Membranes, Prof. Stephanie Tristram-Nagle, Irina Pogozheva, Harold Mosberg, Andrei Lomize

Prof. Stephanie Tristram-Nagle Ph.D.

To gain insight into adaptations of proteins to their membranes, intrinsic hydrophobic thicknesses, distributions of different chemical groups and profiles of hydrogen-bonding capacities (α and β) and the dipolarity/ polarizability parameter (π*) were calculated for lipid-facing surfaces of 460 integral α-helical, β-barrel and peripheral proteins from eight types of biomembranes. For comparison, polarity profiles were also calculated for ten artificial lipid bilayers that have been previously studied by neutron and X-ray scattering. Estimated hydrophobic thicknesses are 30–31 Å for proteins from endoplasmic reticulum, thylakoid, and various bacterial plasma membranes, but differ for proteins from outer bacterial, inner mitochondrial and eukaryotic …

Membrane Structure Correlates To Function Of Llp2 On The Cytoplasmic Tail Of Hiv-1 Gp41 Protein, Alexander Boscia, Zachary Benamram, Jonathan Michel, Michael Jablin, Jonathan D. Steckbeck, Ronald C. Montelaro, John F. Nagle, Prof. Stephanie Tristram-Nagle Ph.D.

Prof. Stephanie Tristram-Nagle Ph.D.

Mutation studies previously showed that the lentivirus lytic peptide (LLP2) sequence of the cytoplasmic C-terminal tail of the HIV-1 gp41 envelope protein inhibited viral-initiated T-cell death and T-cell syncytium formation, at which time in the HIV life cycle the gp41 protein is embedded in the T-cell membrane. In striking contrast, the mutants did not affect virion infectivity, during which time the gp41 protein is embedded in the HIV envelope membrane. To examine the role of LLP2/membrane interactions, we applied synchrotron X-radiation to determine structure of hydrated membranes. We focused on WT LLP2 peptide (þlus three charge) and MX2 mutant (negative …

Ahsg-Fetuin Blocks The Metabolic Arm Of Insulin Action Through Its Interaction With The 95-Kd Beta-Subunit Of The Insulin Receptor, Anton Scott Goustin

Anton Scott Goustin

We previously have shown that Ahsg, a liver glycoprotein, inhibits insulin receptor (InsR) tyrosine kinase (TK) activity and the ERK1/2 mitogenic signaling arm of insulin signaling. Here we show that Ahsg blocks insulin-stimulated GLUT4 translocation and Akt activation in intact cells (mouse myoblasts). Furthermore, Ahsg inhibits InsR autophosphorylation of highly-purified insulin holoreceptors in a cell-free, ATP-dependent system,with an IC50within the range of single-chain Ahsg concentrations in human serum. Binding of 125I-insulin to living cells overexpressing the InsR shows a dissociation constant (KD) of 250 pM, unaltered in the presence of 300 nMAhsg. Amutant InsR cDNA encoding the signal peptide, the …

Conditional Knockdown Of Dna Methyltransferase-1 (Dnmt1) Reveals A Key Role Of Retinal Pigment Epithelium In Mammalian Photoreceptor Differentiation, I. O. Nasonkin, S. L. Merbs, K. Lazo, V. F. Oliver, M. Brooks, K. Patel, Raymond Enke, J. Nellissery, M. Jamrich, Y. Z. Le, K. Bharti, R. N. Fariss, R. A. Rachel, D. J. Zack, E. Rodriguez-Boulan, A. Swaroop

Ray Enke Ph.D.

No abstract provided.

Determination Of Dosage Compensation Of The Mammalian X Chromosome By Rna-Seq Is Dependent On Analytical Approach, Nathaniel K. Jue, Michael B. Murphy, Seth D. Kasowitz, Sohaib M. Qureshi, Craig J. Obergfell, Sahar Elsisi, Robert J. Foley, Rachel J. O’Neill, Michael J. O’Neill

Nathaniel Jue