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Functional Analysis Of The Extended N-Terminus For The Drosophila Raf Protein And Initial Characterization Of The Arl1 Gene, Jian Ding 2010 Iowa State University

Functional Analysis Of The Extended N-Terminus For The Drosophila Raf Protein And Initial Characterization Of The Arl1 Gene, Jian Ding

Graduate Theses and Dissertations

The Raf serine/ threonine kinases play a key role(s) in receptor tyrosine kinase (RTK) signaling. However, the mechanisms that modulate Raf activity are complicated and remain elusive. Clues to Raf regulation were derived from the identification of conserved regions/motifs/sites. Drosophila Raf (DRaf) has an extended N-terminus. We show this N-terminal segment contains a novel region (CRN) that is conserved in BRaf proteins of vertebrates. The extended N-terminus can contribute to Torso RTK signaling during embryogenesis in both loss and gain-of-function genetic backgrounds. Furthermore, stronger interactions between DRaf's RBD (Ras Binding Domain) and the small GTPase Ras1 ...


Plasminogen Activator Inhibitor 1: Mechanisms Of Its Synergistic Regulation By Growth Factors, Xiaoling Song 2010 Iowa State University

Plasminogen Activator Inhibitor 1: Mechanisms Of Its Synergistic Regulation By Growth Factors, Xiaoling Song

Graduate Theses and Dissertations

As the major physiological inhibitor of plasminogen activator (PA), the type I plasminogen activator inhibitor (PAI-1) is important for controlling blood clotting and tissue remodeling events such as those that involve cell migration. The changing needs for protease activity under various physiological conditions necessitates a tight cellular control of gene expression to enable rapid changes in the levels of PAI-1 and PA activity. Cooperation between epidermal growth factor (EGF) and transforming growth factor-β (TGF-β) dramatically increase PAI-1 protein level. In this study, we found activators of tyrosine kinase (EGF, FGF, IGF-I and TNF α) or an activator of PKC (PMA ...


Patterns Of Apoptotic Poly(Adp-Ribose) Polymerase Cleavage Induced By Laromustine And Its Analogs, Adam N. Paine 2010 Colby College

Patterns Of Apoptotic Poly(Adp-Ribose) Polymerase Cleavage Induced By Laromustine And Its Analogs, Adam N. Paine

Honors Theses

The anticancer prodrug Laromustine (VNP40101M) has produced promising remission rates in clinical trials among leukemic patients relative to currently available chemotherapeutics. Such improvements demand that the agent’s mechanism of action be elucidated. This study aimed to determine the role of poly(ADP-ribose) polymerase (PARP) in Laromustine-induced cell death. Previous studies indicated that the methyl isocyanate produced upon activation of Laromustine is largely responsible for its effective induction of apoptosis. Results reported herein strongly support the activation of a PARP-dependent apoptotic pathway by Laromustine’s carbamoylating and chlorethylating subspecies. Furthermore, it is evident that the Laromustine-induced PARP-dependent apoptosis is primarily ...


Purification And Properties Of Amycolatopsis Mediterranei Dsm 43304 Lipase And Its Potential In Flavour Ester Synthesis, Dharmendra Dheeman, Gary Henehan, Jesus Maria Frias 2010 Technological University Dublin

Purification And Properties Of Amycolatopsis Mediterranei Dsm 43304 Lipase And Its Potential In Flavour Ester Synthesis, Dharmendra Dheeman, Gary Henehan, Jesus Maria Frias

Articles

An extracellular thermostable lipase from Amycolatopsis mediterranei DSM 43304 has been purified to homogeneity using ammonium sulphate precipitation followed by anion exchange chromatography and hydrophobic interaction chromatography. This protocol resulted in 398 fold purification with 36% final recovery. The purified A. mediterranei DSM 43304 lipase (AML) has an apparent molecular mass of 33 kDa. The N-terminal sequence, AANPYERGPDPTTASIEATR, showed highest similarity to a lipase from Streptomyces exfoliatus. The values of and for p-nitrophenyl palmitate (p-NPP) under optimal temperature (60°C) and pH (8.0) conditions were 0.10 ± 0.01 mM and 2.53 ± 0.06 mmol/minmg ...


Structure And Reactivity Of Hexacoordinate Hemoglobins, Smita Kakar 2010 Iowa State University

Structure And Reactivity Of Hexacoordinate Hemoglobins, Smita Kakar

Graduate Theses and Dissertations

The heme prosthetic group in hemoglobins is most often attached to the globin through coordination of either one or two histidine side chains. Those proteins with one histidine coordinating the heme iron are called “pentacoordinate” hemoglobins, a group represented by red blood cell hemoglobin and most other oxygen transporters. Those with two histidines are called “hexacoordinate hemoglobins”, which have broad representation among eukaryotes. Coordination of the second histidine in hexacoordinate Hbs is reversible, allowing for binding of exogenous ligands like oxygen, carbon monoxide, and nitric oxide. Research over the past several years has produced a fairly detailed picture of the ...


Recycling Of Vitamin B12 And Nad+ Within The Pdu Microcompartment Of Salmonella Enterica, Shouqiang Cheng 2010 Iowa State University

Recycling Of Vitamin B12 And Nad+ Within The Pdu Microcompartment Of Salmonella Enterica, Shouqiang Cheng

Graduate Theses and Dissertations

Salmonella enterica is capable of utilizing 1,2-propanediol (1,2-PD) as a sole carbon and energy source in a coenzyme B12 (Adenosylcobalamin, AdoCbl) -dependent fashion that involves a bacterial microcompartment (MCP), the Pdu MCP. Pdu MCP is a polyhedral organelle composed entirely of protein subunits and its function is to sequester the intermediate propionaldehyde formed in the first step of 1,2-PD degradation in order to mitigate its toxicity and prevent DNA damage. Several sequentially-acting metabolic enzymes, including the diol dehydratase PduCDE and the propionaldehyde dehydrogenase PduP that respectively use AdoCbl and NAD+ as cofactors, are encapsulated within the ...


Interaction Between The Saga Complex And Chromatin Regulates Nucleosome Acetylation And Inducible Gene Transcription, Shanshan Li 2010 Iowa State University

Interaction Between The Saga Complex And Chromatin Regulates Nucleosome Acetylation And Inducible Gene Transcription, Shanshan Li

Graduate Theses and Dissertations

The SAGA family of coactivators is a group of highly conserved histone acetyltransferases that is essential for transcription of genes participating in stress adaptation and developemental processes. Misregulation of SAGA function can lead to developmental diseases and cancer. One important function of SAGA in regulating gene expression is to acetylate nucleosomes at both gene promoters and coding regions. To understand the molecular mechanism of nucleosome acetylation, much work has been done using recombinant Gcn5, the catalytic subunit of SAGA, and histone proteins or peptides. However, little is known about how histones are acetylated by full SAGA complex in the context ...


Evolution Of New Enzymatic Function By Structural Modulation Of Cysteine Reactivity In Pseudomonas Fluorescens Isocyanide Hydratase, Mahadevan Lakshminarasimhan, Peter Madzelan, Ruth Nan, Nicole Marie Milkovic, Mark A. Wilson 2010 University of Nebraska - Lincoln

Evolution Of New Enzymatic Function By Structural Modulation Of Cysteine Reactivity In Pseudomonas Fluorescens Isocyanide Hydratase, Mahadevan Lakshminarasimhan, Peter Madzelan, Ruth Nan, Nicole Marie Milkovic, Mark A. Wilson

Biochemistry -- Faculty Publications

Isocyanide (formerly isonitrile) hydratase (EC 4.2.1.103) is an enzyme of the DJ-1 superfamily that hydrates isocyanides to yield the corresponding N-formamide. In order to understand the structural basis for isocyanide hydratase (ICH) catalysis, we determined the crystal structures of wild-type and several site-directed mutants of Pseudomonas fluorescens ICH at resolutions ranging from 1.0 to 1.9 Å. We also developed a simple UV-visible spectrophotometric assay for ICH activity using 2-naphthyl isocyanide as a substrate. ICH contains a highly conserved cysteine residue (Cys101) that is required for catalysis and interacts with Asp17, Thr102, and an ordered ...


Quantitative Nuclear Proteomics Identifies Mtor Regulation Of Dna Damage Response, Sricharan Bandhakavi, Young-Mi Kim, Seung-Hyun Ro, Hongwei Xie, Getiria Onsongo, Chang-Bong Jun, Do-Hyung Kim, Timothy J. Griffin 2010 University of Minnesota

Quantitative Nuclear Proteomics Identifies Mtor Regulation Of Dna Damage Response, Sricharan Bandhakavi, Young-Mi Kim, Seung-Hyun Ro, Hongwei Xie, Getiria Onsongo, Chang-Bong Jun, Do-Hyung Kim, Timothy J. Griffin

Biochemistry -- Faculty Publications

Cellular nutritional and energy status regulates a wide range of nuclear processes important for cell growth, survival, and metabolic homeostasis. Mammalian target of rapamycin (mTOR) plays a key role in the cellular responses to nutrients. However, the nuclear processes governed by mTOR have not been clearly defined. Using isobaric peptide tagging coupled with linear ion trap mass spectrometry, we performed quantitative proteomics analysis to identify nuclear processes in human cells under control of mTOR. Within 3 h of inhibiting mTOR with rapamycin in HeLa cells, we observed downregulation of nuclear abundance of many proteins involved in translation and RNA modification ...


The Role Of Copepods And Heterotrophic Dinoflagellates In The Production Of Dissolved Organic Matter And Inorganic Nutrients, Grace Kathleen Saba 2010 College of William and Mary - Virginia Institute of Marine Science

The Role Of Copepods And Heterotrophic Dinoflagellates In The Production Of Dissolved Organic Matter And Inorganic Nutrients, Grace Kathleen Saba

Dissertations, Theses, and Masters Projects

Zooplankton play a key role in the cycling of dissolved organic matter (DOM) and inorganic nutrients. The factors that affect these processes, however, are not fully understood. I measured the effects of various diets on DOM and inorganic nutrient production by the copepod Acartia tonsa and the heterotrophic dinoflagellate Oxyrrhis marina, and explored the mechanisms of nutrient release from copepods. Copepods feeding on a mixed diet, the preferred diet of most copepods, had significantly lower dissolved organic carbon (DOC), ammonium (NH4+), and total dissolved nitrogen (TDN) release rates compared to feeding on a carnivorous or herbivorous diet. Thus, copepod feeding ...


In Vivo Labeling Of A Model Β-Clam Protein With A Fluorescent Amino Acid, Mangayarkarasi Periasamy 2010 University of Massachusetts Amherst

In Vivo Labeling Of A Model Β-Clam Protein With A Fluorescent Amino Acid, Mangayarkarasi Periasamy

Masters Theses 1911 - February 2014

Proteins can be labeled with different tags to enable their structural and functional investigations. In addition, labeling proteins at specific sites helps in studying the conformational dynamics of these molecules. A plethora of methods is available to facilitate labeling, choice of which largely depends on the requirements and the anticipated end results. In general, the various labeling methods can be classified into four different classes based on the stage at which labeling is performed, namely post translational labeling, non-ribosomal synthesis, in vitro translation and in vivo translation. Interestingly all these techniques use different unnatural amino acids for this purpose.

Protein ...


Interconversion Of The Specificities Of Human Lysosomal Enzymes, Ivan B. Tomasic 2010 University of Massachusetts Amherst

Interconversion Of The Specificities Of Human Lysosomal Enzymes, Ivan B. Tomasic

Masters Theses 1911 - February 2014

Fabry disease (FD) is an X-linked recessive lysosomal storage disorder (LSD) known to affect approximately 1 in every 40,000 males, and a smaller number of females. FD results from a deficiency of functional α-galactosidase (α-GAL), which leads to the accumulation of terminally α-galactosylated substrates in the lysosome. The predominant treatment is Enzyme Replacement Therapy (ERT), requiring the regular infusion of recombinant human α-GAL. More than half of individuals receiving ERT experience a range of adverse infusion reactions, and it has been reported that as many as 88% of patients receiving ERT develop neutralizing IgG antibodies against the drug.

In ...


Anti-Diabetic Potentials Of Phenolic Enriched Chilean Potato And Select Herbs Of Apiaceae And Lamiaceae Families, Fahad Saleem 2010 University of Massachusetts Amherst

Anti-Diabetic Potentials Of Phenolic Enriched Chilean Potato And Select Herbs Of Apiaceae And Lamiaceae Families, Fahad Saleem

Masters Theses 1911 - February 2014

The incidence of diabetes mellitus and cardiovascular diseases is increasing at a worrisome rate globally. Diabetes mellitus is known to occur due to high blood glucose levels, caused by defects in insulin levels. Adult on-set type II diabetes, which is closely associated with obesity, is reported to be 90-95% of all diabetic cases and linked to diet and lifestyle factors. A large population of the developed and developing countries is now being effected by this epidemic. Natural sources of phenolic antioxidants and inhibitors of digestive enzymes from food sources have potential for low cost dietary management of type II diabetes ...


Induction Of Interferon And Interferon Signaling Pathways By Replication Of Defective Interfering Particle Rna In Cells Constitutively Expressing Vesicular Stomatitis Virus Replication Proteins, Debasis Panda, Phat X. Dinh, Lalit Beura, Asit K. Pattnaik 2010 University of Nebraska - Lincoln

Induction Of Interferon And Interferon Signaling Pathways By Replication Of Defective Interfering Particle Rna In Cells Constitutively Expressing Vesicular Stomatitis Virus Replication Proteins, Debasis Panda, Phat X. Dinh, Lalit Beura, Asit K. Pattnaik

Papers in Veterinary and Biomedical Science

We show here that replication of defective interfering (DI) particle RNA in HEK293 cells stably expressing vesicular stomatitis virus (VSV) replication proteins potently activates interferon (IFN) and IFN signaling pathways through upregulation of IFN- promoter, IFN-stimulated response element (ISRE) promoter, and NF-κB promoter activities. Replication of DI particle RNA, not mere expression of the viral replication proteins, was found to be critical for induction of IFN and IFN signaling. The stable cells supporting replication of DI RNA described in this report will be useful in further examining the innate immune signaling pathways and the host cell functions in viral genome ...


Towards An Understanding Of The Herpes Simplex Virus Type 1 Latency-Reactivation Cycle, Guey-Chuen Perng, Clinton Jones 2010 Emory University School of Medicine

Towards An Understanding Of The Herpes Simplex Virus Type 1 Latency-Reactivation Cycle, Guey-Chuen Perng, Clinton Jones

Papers in Veterinary and Biomedical Science

Infection by herpes simplex virus type 1 (HSV-1) can cause clinical symptoms in the peripheral and central nervous system. Recurrent ocular shedding can lead to corneal scarring and vision loss making HSV-1 a leading cause of corneal blindness due to an infectious agent. The primary site of HSV-1 latency is sensory neurons within trigeminal ganglia. Periodically, reactivation from latency occurs resulting in virus transmission and recurrent disease. During latency, the latency-associated transcript (LAT) is abundantly expressed. LAT expression is important for the latency-reactivation cycle in animal models, in part, because it inhibits apoptosis, viral gene expression, and productive infection. A ...


Regulation Of Sealing Ring Formation By L-Plastin And Cortactin In Osteoclasts, Tao Ma, Kavitha Sadashivalah, Nandakumar Madayiputhiya, Meenakshi A. Chellaia 2010 Dental School, University of Maryland

Regulation Of Sealing Ring Formation By L-Plastin And Cortactin In Osteoclasts, Tao Ma, Kavitha Sadashivalah, Nandakumar Madayiputhiya, Meenakshi A. Chellaia

Biochemistry -- Faculty Publications

The aim of this study is to identify the exact mechanism(s) by which cytoskeletal structures are modulated during bone resorption. In this study, we have shown the possible role of different actin-binding and signaling proteins in the regulation of sealing ring formation. Our analyses have demonstrated a significant increase in cortactin and a corresponding decrease in L-plastin protein levels in osteoclasts subjected to bone resorption for 18 h in the presence of RANKL, M-CSF, and native bone particles. Time-dependent changes in the localization of L-plastin (in actin aggregates) and cortactin (in the sealing ring) suggest that these proteins may ...


Morphological Changes And Immunohistochemical Expression Of Rage And Its Ligands In The Sciatic Nerve Of Hyperglycemic Pig (Sus Scrofa), Judyta K. Juranek, Alexey Aleshin, Eileen M. Rattigan, Lynne Johnson, Wu Qu, Fei Song, Radha Ananthakrishnan, Nosirudeen Quadri, Shi Du Yan, Ravichandran Ramasamy, Ann Marie Schmidt, Matthew S. Geddis 2010 Columbia University

Morphological Changes And Immunohistochemical Expression Of Rage And Its Ligands In The Sciatic Nerve Of Hyperglycemic Pig (Sus Scrofa), Judyta K. Juranek, Alexey Aleshin, Eileen M. Rattigan, Lynne Johnson, Wu Qu, Fei Song, Radha Ananthakrishnan, Nosirudeen Quadri, Shi Du Yan, Ravichandran Ramasamy, Ann Marie Schmidt, Matthew S. Geddis

Publications and Research

The aim of our project was to study the effect of streptozotocin (STZ)—induced hyperglycemia on sciatic nerve morphology, blood plasma markers and immunohistochemical expression of RAGE (the Receptor for Advanced Glycation End-products), and its ligands—S100B and Carboxymethyl Lysine (CML)-advanced glycation endproduct (AGE) in the laboratory pig. Six months after STZ—injections, blood plasma measurements, morphometric analysis of sciatic nerve fiber density, immunofluorescent distribution of potential molecular neuropathy contributors, ELISA measurement of plasma AGE level and HPLC analysis of sciatic nerve levels of one of the pre-AGE and the glycolysis intermediate products—methyl-glyoxal (MG) were performed. The results ...


Prospects And Pits On The Path Of Biomimetics: The Case Of Tooth Enamel, Vuk Uskoković 2010 Chapman University

Prospects And Pits On The Path Of Biomimetics: The Case Of Tooth Enamel, Vuk Uskoković

Pharmacy Faculty Articles and Research

This review presents a discourse on challenges in understanding and imitating the process of amelogenesis in vitro on the molecular scale. In light of the analysis of imitation of the growth of dental enamel, it also impends on the prospects and potential drawbacks of the biomimetic approach in general. As the formation of enamel proceeds with the protein matrix guiding the crystal growth, while at the same time conducting its own degradation and removal, it is argued that three aspects of amelogenesis need to be induced in parallel: a) crystal growth; b) protein assembly; c) proteolytic degradation. A particular emphasis ...


Crystal Structures Of The Cusa Efflux Pump Suggest Methionine-Mediated Metal Transport, Feng Long, Chih-Chia Su, Michael T. Zimmermann, Scott E. Boyken, Kanagalaghatta R. Rajashankar, Robert L. Jernigan, Edward W. Yu 2010 Iowa State University

Crystal Structures Of The Cusa Efflux Pump Suggest Methionine-Mediated Metal Transport, Feng Long, Chih-Chia Su, Michael T. Zimmermann, Scott E. Boyken, Kanagalaghatta R. Rajashankar, Robert L. Jernigan, Edward W. Yu

Biochemistry, Biophysics and Molecular Biology Publications

Gram-negative bacteria, such as Escherichia coli, frequently utilize tripartite efflux complexes in the resistance-nodulation-cell division (RND) family to expel diverse toxic compounds from the cell.1,2 The efflux system CusCBA is responsible for extruding biocidal Cu(I) and Ag(I) ions.3,4 No prior structural information was available for the heavy-metal efflux (HME) subfamily of the RND efflux pumps. Here we describe the crystal structures of the inner membrane transporter CusA in the absence and presence of bound Cu(I) or Ag(I). These CusA structures provide important new structural information about the HME sub-family of RND efflux ...


Potentials 'R'Us Web-Server For Protein Energy Estimations With Coarse-Grained Knowledge-Based Potentials, Yaping Feng, Andrzej Kloczkowski, Robert L. Jernigan 2010 Iowa State University

Potentials 'R'Us Web-Server For Protein Energy Estimations With Coarse-Grained Knowledge-Based Potentials, Yaping Feng, Andrzej Kloczkowski, Robert L. Jernigan

Biochemistry, Biophysics and Molecular Biology Publications

Background

Knowledge-based potentials have been widely used in the last 20 years for fold recognition, protein structure prediction from amino acid sequence, ligand binding, protein design, and many other purposes. However generally these are not readily accessible online.

Results

Our new knowledge-based potential server makes available many of these potentials for easy use to automatically compute the energies of protein structures or models supplied. Our web server for protein energy estimation uses four-body potentials, short-range potentials, and 23 different two-body potentials. Users can select potentials according to their needs and preferences. Files containing the coordinates of protein atoms in the ...


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