Open Access. Powered by Scholars. Published by Universities.®

Biochemistry Commons

Open Access. Powered by Scholars. Published by Universities.®

7,167 Full-Text Articles 15,898 Authors 1,409,441 Downloads 230 Institutions

All Articles in Biochemistry

Faceted Search

7,167 full-text articles. Page 245 of 254.

Selection For Non-Amyloidogenic Mutants Of Islet Amyloid Polypeptide (Iapp) Identifies An Extended Region For Amyloidogenicity, Ayano Fox, Thibaut Snollaerts, Camille Errecart Casanova, Anastasia Calciano, Luiza A. Nogaj, David A. Moffet 2010 Loyola Marymount University

Selection For Non-Amyloidogenic Mutants Of Islet Amyloid Polypeptide (Iapp) Identifies An Extended Region For Amyloidogenicity, Ayano Fox, Thibaut Snollaerts, Camille Errecart Casanova, Anastasia Calciano, Luiza A. Nogaj, David A. Moffet

Chemistry and Biochemistry Faculty Works

The aggregation of the 37-residue polypeptide IAPP, as either insoluble amyloid or as small oligomers, appears to play a direct role in the death of pancreatic β-islet cells in type II diabetes. While IAPP has been known to be the primary component of type II diabetes amyloid, the molecular interactions responsible for this aggregation have not been identified. To identify the aggregation-prone region(s), we constructed a library of randomly generated point mutants of IAPP. This mutant IAPP library was expressed in E. coli as genetic fusions to the reporter protein enhanced green fluorescent protein (EGFP). Because IAPP aggregates rapidly ...


Kinetic Characterization Of Salmonella Flik-Flhb Interactions Demonstrates Complexity Of The Type Iii Secretion Substrate-Specificity Switch, Daniel P. Morris, Eric D. Roush, J. Will Thompson, M. Arthur Moseley, James W. Murphy, Jonathan L. McMurry 2010 Duke University

Kinetic Characterization Of Salmonella Flik-Flhb Interactions Demonstrates Complexity Of The Type Iii Secretion Substrate-Specificity Switch, Daniel P. Morris, Eric D. Roush, J. Will Thompson, M. Arthur Moseley, James W. Murphy, Jonathan L. Mcmurry

Faculty Publications

The bacterial flagellum is a complex macromolecular machine consisting of more than 20000 proteins, most of which must be exported from the cell via a dedicated Type III secretion apparatus. At a defined point in flagellar morphogenesis, hook completion is sensed and the apparatus switches substrate specificity type from rod and hook proteins to filament ones. How the switch works is a subject of intense interest. FIiK and F1hBs play central roles. In the present study, two optical biosensing methods were used to characterize FIiK-F1hB interactions using wild-type and two variant FlhBs from mutants with severe flagellar structural defects. Binding ...


Frataxin And Mitochondrial Fes Cluster Biogenesis, Timothy L. Stemmler, Emmanuel Lesuisse, Debumar Pain, Andrew Dancis 2010 Wayne State University

Frataxin And Mitochondrial Fes Cluster Biogenesis, Timothy L. Stemmler, Emmanuel Lesuisse, Debumar Pain, Andrew Dancis

Biochemistry and Molecular Biology Faculty Publications

Friedreich’s ataxia is an inherited neurodegenerative disease caused by frataxin deficiency. Frataxin is a conserved mitochondrial protein that plays a role in Fe-S cluster assembly in mitochondria. Fe-S clusters are modular cofactors that perform essential functions throughout the cell. They are synthesized by a multi-step and multi-subunit mitochondrial machinery that includes a scaffold protein Isu for assembling a protein bound Fe-S cluster intermediate. Frataxin interacts with Isu, iron, and with the cysteine desulfurase Nfs1 that supplies sulfur, thus placing it at the center of mitochondrial Fe-S cluster biosynthesis.


Novel Polymer Coupling Chemistry Based Upon Latent Cysteine-Like Residues And Thiazolidine Chemistry, Jospeh S. Carlson, Megan R. Hill, Taiga Young, Philip Costanzo 2010 California Polytechnic State University - San Luis Obispo

Novel Polymer Coupling Chemistry Based Upon Latent Cysteine-Like Residues And Thiazolidine Chemistry, Jospeh S. Carlson, Megan R. Hill, Taiga Young, Philip Costanzo

Chemistry and Biochemistry

Chain end functional polymers were prepared via reversible addition–fragmentation transfer (RAFT) polymerization techniques that were further chain extended with acrylonitrile. Under reducing conditions, latent cysteine-like residues were exposed at the chain ends. A variety of reduction conditions were explored and base polymers were then tethered together via thiazolidine chemistry.


Studies On Antidyslipidemic Effects Of Morinda Citrifolia (Noni) Fruit, Leaves And Root Extracts., Saf-ur Rehman Mandukhail, Nauman Aziz, Anwar Gilani 2010 Aga Khan University

Studies On Antidyslipidemic Effects Of Morinda Citrifolia (Noni) Fruit, Leaves And Root Extracts., Saf-Ur Rehman Mandukhail, Nauman Aziz, Anwar Gilani

Department of Biological & Biomedical Sciences

Background: The objective of present study was to provide the pharmacological basis for the medicinal use of Morinda citrifolia Linn in dyslipidemia using the aqueous-ethanolic extracts of its fruits (Mc.Cr.F), leaves (Mc.Cr.L) and roots (Mc.Cr.R). Results: Mc.Cr.F, Mc.Cr.L and Mc.Cr.R showed antidyslipidemic effects in both triton (WR-1339) and high fat diet-induced dyslipidemic rat models to variable extents. All three extracts caused reduction in total cholesterol and triglyceride levels in triton-induced dyslipidemia. In high fat diet-induced dyslipidemia all these extracts caused significant reduction in total cholesterol, triglyceride, low density ...


Integrated Affinity Column Capillary Electrophoresis Microdevices For Biomarker Analysis, Weichun Yang 2010 Brigham Young University - Provo

Integrated Affinity Column Capillary Electrophoresis Microdevices For Biomarker Analysis, Weichun Yang

Theses and Dissertations

In this dissertation, microfluidic systems that integrate antibody-based sample preparation methods with electrophoretic separation are developed to analyze multiple biomarkers in a point-of-care setting. To form an affinity column, both monolith materials and wall-coated channels were explored. I successfully demonstrated that monolith columns can be prepared in microfluidic devices via photopolymerization. The selectivity of monolith columns was improved by immobilizing antibodies on the surface. These affinity columns can selectively enrich target analytes and reduce the signal of contaminant proteins up to 25,000 fold after immunoaffinity extraction. These results clearly demonstrate that microchip affinity monoliths can selectively concentrate and purify ...


Mechanisms Of Oxidant Generation By Catalase, Diane E. Heck, Michael Shakarjian, Hong-Duck Kim, Jeffrey Laskin, Anna M. Vetrano 2010 New York Medical College

Mechanisms Of Oxidant Generation By Catalase, Diane E. Heck, Michael Shakarjian, Hong-Duck Kim, Jeffrey Laskin, Anna M. Vetrano

NYMC Faculty Publications

The enzyme catalase converts solar radiation into reactive oxidant species (ROS). In this study, we report that several bacterial catalases (hydroperoxidases, HP), including Escherichia coli HP-I and HP-II also generate reactive oxidants in response to ultraviolet B light (UVB). HP-I and HP-II are identical except for the presence of NADPH. We found that only one of the catalases, HPI, produces oxidants in response to UVB light, indicating a potential role for the nucleotide in ROS production. This prompts us to speculate that NADPH may act as a cofactor regulating ROS generation by mammalian catalases. Structural analysis of the NADPH domains ...


Lipid Profiling Reveals Tissue-Specific Differences For Ethanolamide Lipids In Mice Lacking Fatty Acid Amide Hydrolase, Aruna Kilaru, Giorgis Isaac, Pamela Tamura, David Baxter, Scott R. Duncan, Barney J. Venables, Ruth Welti, Peter Koulen, Kent D. Chapman 2010 University of North Texas

Lipid Profiling Reveals Tissue-Specific Differences For Ethanolamide Lipids In Mice Lacking Fatty Acid Amide Hydrolase, Aruna Kilaru, Giorgis Isaac, Pamela Tamura, David Baxter, Scott R. Duncan, Barney J. Venables, Ruth Welti, Peter Koulen, Kent D. Chapman

Aruna Kilaru

N‐Acylethanolamines (NAE) are fatty acid derivatives, some of which function as endocannabinoids in mammals. NAE metabolism involves common (phosphatidylethanolamines, PEs) and uncommon (N‐acylphosphatidylethanolamines, NAPEs) membrane phospholipids. Here we have identified and quantified more than a hundred metabolites in the NAE/endocannabinoid pathway in mouse brain and heart tissues, including many previously unreported molecular species of NAPE. We found that brain tissue of mice lacking fatty acid amide hydrolase (FAAH−/−) had elevated PE and NAPE molecular species in addition to elevated NAEs, suggesting that FAAH activity participates in the overall regulation of this pathway. This perturbation of the NAE ...


The Marine Sponge Metabolite Mycothiazole: A Novel Prototype Mitochondrial Complex I Inhibitor., J Brian Morgan, Fakhri Mahdi, Yang Liu, Veena Coothankandaswamy, Mika B. Jekabsons, Tyler A. Johnson, Koneni V. Sashidhara, Phillip Crews, Dale G. Nagle, Yu-Dong Zhou 2010 University of Mississippi, Mississippi, USA

The Marine Sponge Metabolite Mycothiazole: A Novel Prototype Mitochondrial Complex I Inhibitor., J Brian Morgan, Fakhri Mahdi, Yang Liu, Veena Coothankandaswamy, Mika B. Jekabsons, Tyler A. Johnson, Koneni V. Sashidhara, Phillip Crews, Dale G. Nagle, Yu-Dong Zhou

Natural Sciences and Mathematics | Faculty Scholarship

A natural product chemistry-based approach was applied to discover small-molecule inhibitors of hypoxia-inducible factor-1 (HIF-1). A Petrosaspongia mycofijiensis marine sponge extract yielded mycothiazole (1), a solid tumor selective compound with no known mechanism for its cell line-dependent cytotoxic activity. Compound 1 inhibited hypoxic HIF-1 signaling in tumor cells (IC(50) 1nM) that correlated with the suppression of hypoxia-stimulated tumor angiogenesis in vitro. However, 1 exhibited pronounced neurotoxicity in vitro. Mechanistic studies revealed that 1 selectively suppresses mitochondrial respiration at complex I (NADH-ubiquinone oxidoreductase). Unlike rotenone, MPP(+), annonaceous acetogenins, piericidin A, and other complex I inhibitors, mycothiazole is a mixed polyketide ...


Antibodies Directed Against The Extracellular Region Of The Epidermal Growth Factor Receptor Adopt Distinct Modes Of Binding And Inhibition, Karl R. Schmitz 2010 University of Pennsylvania

Antibodies Directed Against The Extracellular Region Of The Epidermal Growth Factor Receptor Adopt Distinct Modes Of Binding And Inhibition, Karl R. Schmitz

Publicly Accessible Penn Dissertations

The work described in this dissertation comprises two distinct projects. In the first, we describe the structural and functional characterization of a family of Golgi associated cytosolic proteins, represented by Vps74 in fungi and GOLPH3 in animals, by X-ray crystallography, biophysical assays, and cellular techniques. We find that Vps74 is required for the proper steady state localization of a subset of Golgi enzymes in yeast, and that disruption of vps74 results in incomplete protein glycosylation. We further describe the crystal structures of Vps74 and GOLPH3, identifying structural motifs required both for oligomer formation and protein function. Finally, we find that ...


The Evolution Of Platelet Responses To Collagen Under Conditions Of Hemodynamic Flow, Alec A. Schmaier 2010 Univresity of Pennsylvania

The Evolution Of Platelet Responses To Collagen Under Conditions Of Hemodynamic Flow, Alec A. Schmaier

Publicly Accessible Penn Dissertations

Collagen activates platelets through the immune-type GPVI receptor, but the mechanism by which this receptor has adapted to function in platelets under conditions of rapid blood flow is unclear. Additionally, it is unknown if responses to collagen are conserved in nucleated thrombocytes found in non-mammalian vertebrates, which do not express GPVI. Here we show that the GPVI proline-rich domain accelerates GPVI signaling kinetics and is required for maximal adhesion to collagen under flow. The proline-rich domain accelerates signaling through binding and directly activating the Src-family kinase Lyn. Chicken thrombocytes are potently activated by collagen but do not form 3-dimensional aggregates ...


On The Nature Of The Hydrogen Bond And Biomolecular Solvation, James N. Scott 2010 University of Pennsylvania

On The Nature Of The Hydrogen Bond And Biomolecular Solvation, James N. Scott

Publicly Accessible Penn Dissertations

Water is the most studied molecule in the history of scientific research, and yet much remains unknown about this structurally simple but functionally complex molecule. There is ample evidence that understanding the fundamental nature of the hydrogen bond and its response to changing chemical and thermodynamic conditions is the key to understanding water’s many properties and functions. The goal of this work was to examine the H-bond in the context of its bond angle and bond distance, and furthermore to investigate the impact that alteration of water’s bulk structure can have on biomolecules and vice versa. A two-dimensional ...


Measures Of The Dynamics Of G Protein Interaction With The Ribosome With Applications To Antibiotic Screening, Haiou Qin 2010 University of Pennsylvania

Measures Of The Dynamics Of G Protein Interaction With The Ribosome With Applications To Antibiotic Screening, Haiou Qin

Publicly Accessible Penn Dissertations

Ribosomes catalyze protein synthesis via the translation cycle, in which the translation initiation is recognized as a key step to regulate the process. The functional complexes of the bacterial ribosome undergo large conformational changes during the initiation of protein synthesis. Dramatic progress in the elucidation of ribosome structure by both X-ray crystallography and cryoelectron microscopy (cryo-EM) has provided some of the best evidence for such changes. At the same time, detailed rate studies of initiation, even though for the most part incomplete, have shown this process to be complex, multistep reactions, raising the question of the extent to which specific ...


Synthesis And Characterization Of An Oligothiophene-Ruthenium Complex And Synthesis And Optical Properties Of Oligothiophene-Ruthenium Complexes Bound To Cdse Nanoparticles, Nathan A. Bair 2010 Brigham Young University - Provo

Synthesis And Characterization Of An Oligothiophene-Ruthenium Complex And Synthesis And Optical Properties Of Oligothiophene-Ruthenium Complexes Bound To Cdse Nanoparticles, Nathan A. Bair

Theses and Dissertations

Oligothiophenes are of increasing interest in organic based electronic devices in part due to their high electron and hole mobilities. In an organic photovoltaic (OPV) device, the electronic properties of oligothiophenes make them advantageous as charge transfer junctions. To serve as charge transfer junctions, oligothiophenes must be functionalized to bind to the donor and acceptor parts of the device. The donor and acceptor parts are different materials and the synthesis of asymmetric oligothiophenes is of great interest. Previous researchers in our lab synthesized four asymmetric oligothiophenes, two with two thiophene subunits and two with four. Each set of oligothiophenes contained ...


Aryl Boronic Acid Inhibition Of Synthetic Melanin Polymerization, Jason M. Belitsky 2010 Oberlin College

Aryl Boronic Acid Inhibition Of Synthetic Melanin Polymerization, Jason M. Belitsky

Faculty & Staff Scholarship

Inhibitors of melanin formation are sought after for a range of applications. Boronophenylalanine is known to inhibit melanogenesis via boronic acid-catechol interactions. A spectroscopic assay was developed to study the polymerization of L-dopa to synthetic melanin in the presence of para-substituted aryl boronic acids. The best inhibition was observed for aryl boronic acids with electron-withdrawing substituents. The IC50 values exhibit a correlation with the Hammett sigma(p) parameter (rho = 0.97, r(2) = 0.92).


Properties Of Microbes In Natural Fire Burn Soils, Holly Anderson 2010 Utah State University

Properties Of Microbes In Natural Fire Burn Soils, Holly Anderson

Undergraduate Honors Capstone Projects

Soil underlying a natural fire develops a hydrophobic soil sub-layer. This hydrophobicity decreases with time although the mechanisms are unresolved, but are thought to be biotic and abiotic. Some of the compounds accounting for hydrophobicity are polycyclic aromatic hydrocarbons (PAHs) of which pyrene is an example.

Bacteria that grew on pyrene were isolated from burned soils at two sites in Utah in order to analyze the biotic microbial degradation of the hydrophobic soil sub-layer. The two sites were Wood Camp (Logan, UT) and Milford Flats (Central UT). Identifications of the genera of nine isolated bacteria were made through l6S rRNA ...


Study Of The Efficacy, Biodistribution, And Safety Profile Of Therapeutic Gutless Adenovirus Vectors As A Prelude To A Phase I Clinical Trial For Glioblastoma, AKM Ghulam Muhammad, Mariana Puntel, Marianela Candolfi, A Salem, Kader Yagiz, C Farrokhi, Kurt Kroeger, Weidong Xiong, James Curtin, Chunyan Liu, K Lawrence, Niyati Bondale, Jonathan Lerner, G Baker, David Foulad, Robert Pechnick, Donna Palmer, Philip Ng, Pedro Lowenstein, Maria Castro 2010 Cedars-Sinai Medical Center

Study Of The Efficacy, Biodistribution, And Safety Profile Of Therapeutic Gutless Adenovirus Vectors As A Prelude To A Phase I Clinical Trial For Glioblastoma, Akm Ghulam Muhammad, Mariana Puntel, Marianela Candolfi, A Salem, Kader Yagiz, C Farrokhi, Kurt Kroeger, Weidong Xiong, James Curtin, Chunyan Liu, K Lawrence, Niyati Bondale, Jonathan Lerner, G Baker, David Foulad, Robert Pechnick, Donna Palmer, Philip Ng, Pedro Lowenstein, Maria Castro

Articles

Glioblastoma multiforme (GBM) is the most common and most aggressive primary brain tumor in humans. Systemic immunity against gene therapy vectors has been shown to hamper therapeutic efficacy; however, helper-dependent high-capacity adenovirus (HC-Ad) vectors elicit sustained transgene expression, even in the presence of systemic anti-adenoviral immunity. We engineered HC-Ads encoding the conditional cytotoxic herpes simplex type 1 thymidine kinase (TK) and the immunostimulatory cytokine fms-like tyrosine kinase ligand 3 (Flt3L). Flt3L expression is under the control of the regulatable Tet-ON system. In anticipation of a phase I clinical trial for GBM, we assessed the therapeutic efficacy, biodistribution, and clinical and ...


Design And Synthesis Of A Boronic Acid Sensor To Study Carbohydrate Binding Using Sers, Paul Russell Petersen 2010 University of Tennessee, Knoxville

Design And Synthesis Of A Boronic Acid Sensor To Study Carbohydrate Binding Using Sers, Paul Russell Petersen

Masters Theses

Carbohydrates are known to play a large number of significant roles in various biological and pathological processes such as cancer metastasis and cellular communication. This is because of their ability to bind a wide range of hosts within the human body such as proteins and viruses. Due to these important interactions, carbohydrate sensing has long been a main focus of research. These research strategies have included the use of aptamers, non-covalent interactions, and boronic acid-based receptors. Boronic acid-based sensors are of particular interest due to their selectivity for 1,2- or 1,3-diols. Within these boronic acid-based studies, a large ...


Exploring Zirconia As A Column Packing Material, Tushar Ghugare 2010 Western Kentucky University

Exploring Zirconia As A Column Packing Material, Tushar Ghugare

Masters Theses & Specialist Projects

Zirconia is one of the most promising column packing materials for High Performance Liquid Chromatography (HPLC). The perfect HPLC support material should be energetically homogenous, have a high surface area on which different chemical species can reversibly attach and be physically and chemically stable over a wide range of pH, temperature and solvent conditions. Most existing supports do not have all of these properties. This project is also focused on a proteomics study. Zirconia, hafnium oxide and titanium oxide which are some of the more promising materials currently available, can be used for the separation and analysis of phosphorylated proteins ...


Poxa, Yjek And Elongation Factor P Coordinately Modulate Virulence And Drug Resistance In Salmonella Enterica, William Wiley Navarre, Shicong Zou, Hervé Roy, Jinglin Lucy Xie, Alexei Savchenko, Alexander Singer, Elena Edvokimova, Lynne R. Prost, Runjun Kumar, Michael Ibba, Ferric C. Fang 2010 University of Toronto

Poxa, Yjek And Elongation Factor P Coordinately Modulate Virulence And Drug Resistance In Salmonella Enterica, William Wiley Navarre, Shicong Zou, Hervé Roy, Jinglin Lucy Xie, Alexei Savchenko, Alexander Singer, Elena Edvokimova, Lynne R. Prost, Runjun Kumar, Michael Ibba, Ferric C. Fang

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We report an interaction between poxA, encoding a paralog of lysyl tRNA-synthetase, and the closely linked yjeK gene, encoding a putative 2,3-β-lysine aminomutase, that is critical for virulence and stress resistance in Salmonella enterica. Salmonella poxA and yjeK mutants share extensive phenotypic pleiotropy, including attenuated virulence in mice, an increased ability to respire under nutrient-limiting conditions, hypersusceptibility to a variety of diverse growth inhibitors, and altered expression of multiple proteins, including several encoded on the SPI-1 pathogenicity island. PoxA mediates posttranslational modification of bacterial elongation factor P (EF-P), analogous to the modification of the eukaryotic EF-P homolog, eIF5A, with ...


Digital Commons powered by bepress