Biochemistry Commons^™

Investigating Structures And Functions Of Apoptotic Caspases, Ishankumar V. Soni

Doctoral Dissertations

Caspases are cysteine aspartate proteases involved in various cellular pathways including apoptosis, inflammation, and neurodegeneration. Caspase-9 is classified as an initiator apoptotic caspase that is activated upon intrinsic stress. Caspase-9 is composed of two domains: an N- terminal CARD domain and a catalytic core domain. We have employed hydrogen deuterium exchange mass spectrometry (H/DX-MS) to determine the 1) dynamics of the full-length caspase- 9, 2) dynamic impacts on caspase-9 upon substrate-induced dimerization, and 3) regions involved in the CARD: catalytic core domains interactions. Upon intrinsic stress, caspase-9 activates executioners, procaspase-3 and -7 but not procaspase-6. We have employed site-directed mutagenesis …

Site-Specific Effects Of Lysine Acetylation On Aminoacyl-Trna Synthetase, Hao Chen

Graduate Theses and Dissertations

Aminoacyl-tRNA synthetases (AARSs) are an ancient and highly conserved family of enzymes which can catalyze a two-steps aminoacylation reaction to charge tRNAs with their cognate amino acids, thus playing crucial roles in ribosomal protein synthesis. Naturally, the accurate amino acids and tRNA recognition of these synthetases are essential to the fidelity of translation process. To assure the correct recognition, some of these synthetases have evolved with an editing function to help remove the mischarged tRNAs. In addition to these functions, AARSs are also involved in various biological processes ranging from transcription to translation. Currently, a series of proteomic studies have …

Enzymatic Degradation Of Microcystin-Lr By Microcystinase (Mlra), Faisal Alqhtani

Graduate Theses and Dissertations

Microcystin-LR (MC-LR) is affecting the water supply worldwide. Hence, a way to eliminate this toxin is an essential target. In this study, successful cloning of the mlrA gene and producing MlrA enzyme that can degrade the cyclic MC-LR to linearized MC-LR was done. MlrA protein was expressed in Escherichia coli BL-21 (E. coli). Also, enhancing the MlrA yield by adding nickel to LB media was a success in producing more MlrA enzyme from the same volume. Even though the enzyme showed no activity after adding Ni, the enzyme was expressed at a higher yield. Furthermore, it was to investigate adding …

Machine Learning And Bioinformatic Insights Into Key Enzymes For A Bio-Based Circular Economy, Japheth E. Gado

Theses and Dissertations--Chemical and Materials Engineering

The world is presently faced with a sustainability crisis; it is becoming increasingly difficult to meet the energy and material needs of a growing global population without depleting and polluting our planet. Greenhouse gases released from the continuous combustion of fossil fuels engender accelerated climate change, and plastic waste accumulates in the environment. There is need for a circular economy, where energy and materials are renewably derived from waste items, rather than by consuming limited resources. Deconstruction of the recalcitrant linkages in natural and synthetic polymers is crucial for a circular economy, as deconstructed monomers can be used to manufacture …

Development Of Fluorescence Microscopy Approaches To Study Subcellular Protein Transport And Enzymatic Activity, Anchal Singh

Masters Theses

Understanding the subcellular localization of proteins and their activity is important in understanding their normal function in eukaryotic cells. Fluorescence cellular imaging techniques can selectively and sensitively visualize subcellular biochemistry. Using this approach, two different methods were employed in this thesis. The first focused on studying protein import into peroxisome and the other on monitoring the activity of an endoplasmic reticulum (ER)-localized enzyme, human carboxylesterase 1 (CES1).

Peroxisomes are mainly known as the center for long chain fatty acid b-oxidation as well as the production and detoxification of hydrogen peroxide. Proteins which are needed in the peroxisomes are encoded in …

Initial Characterization Of A Conserved Active Site Residue For The Cdc34 Ubiquitin Conjugating Enzyme, Arvin Akoopie

Honors College Theses

Ubiquitin-conjugating enzymes (E2s) covalently modify protein substrates with ubiquitins. The active site cysteine residues on E2s are essential for catalyzing the transfer of ubiquitin from the E2 active site onto the protein substrate, however there is a limited amount of information available concerning additional active site residues for E2s that may also participate in catalysis. Cdc34 is an essential E2 that has merited the lion’s share of attention for biochemical analysis of the E2 family. Previous phylogenetic analysis of Cdc34 amino acid sequences has identified an invariably conserved histidine residue close to the active site cysteine in the primary structure, …

Synthesis Of Fluorogenic Substrates For The Enzymatic Characterization Of Rv0045c From M. Tuberculosis, Kelly Jo Mckenna

Undergraduate Honors Thesis Collection

Mycobacterium tuberculosis is the pathogenic bacterial agent commonly responsible for tuberculosis, or TB. Although treatment exists for the active form of tuberculosis, no method has been developed for eliminating M tuberculosis in its dormant state. One hypothesized method for the elimination of dormant TB is to develop an inhibitor specific for M tuberculosis esterases and lipases, as these esterases and lipases are essential to the survival of dormant TB infection. In this research, the substrate specificity of the Rv0045c esterase from M tuberculosis was studied due to the essential role of Rv0045c in TB metabolism and its dissimilarity to other …

Determination Of Pancreatic And Salivary Amylase By Enzyme Immunoassay And Their Prevalence In Hyperamylasemic Patients, Sabdra Borgens Ward

Theses and Dissertations in Biomedical Sciences

Currently, amylase determinations are nonspecific for the organ source and are based entirely on the enzymatic properties of amylase to produce a measurable product or byproduct. The determination of pancreatic amylase is important in the diagnosis of acute pancreatitis. Most commercially available tests for amylase employ the measurement of the change in NADH absorbance at 280 nm or of the p-nitrophenol released from a maltotetrose substrate. These are nonspecific measurements of pancreatic amylase and often necessitate other tests to be run such as a serum lipase.

The two predominant isoenzymes of amylase are pancreatic (p-amylase) and salivary (s-amylase); the most …

Activation In Vitro Of Transfer Rna-Guanine Ribosyltransferase By Protein Kinase C, Panayota Eriotou

Chemistry & Biochemistry Theses & Dissertations

The purpose of this study was to isolate and purify the enzymes, transfer RNA-guanine ribosyltrasferase and protein kinase C, and to determine whether the phosphorylating enzyme activates the insertion enzyme in vitro. Transfer RNA-guanine ribosyltransferase lost activity within several days after isolation and total, complete reactivation was accomplished in the presence of protein kinase C. This demonstrated that ribosyltransferase's instability is related to the degree of its phosphorylation. It is proposed that modification of tRNA is controlled by protein kinase C. Deactivation of the insertion enzyme leads to hypomodified tRNA which in turn is associated with neoplasia. Potential use …

Determination Of Human Sperm Cell Acrosin Activity From Normal And Subfertile Men, Dilrowshan H. Haque

Chemistry & Biochemistry Theses & Dissertations

Acrosin is an acrosomal enzyme which is reported to be involved in sperm penetration through cumulus, zona, and ooplasma. This enzyme has been reported to be significantly lower in sperm of infertile men compared to sperm of fertile men. The acrosin assay which has been developed can be used for studies in patients with suspected infertility and may be used on a fraction of most semen specimens being evaluated in a clinical andrology laboratory.

Within-run precision studies yielded coefficients of variation of 11% for a low-activity pool and 9% for normalactivity pool specimens. Between-run precision studies using a single donor …

The Synthesis And Biochemical Evaluation Of Potential Acetylcholinesterase Reactivators, Andrea Mcdearmid Lunsford

Chemistry & Biochemistry Theses & Dissertations

Objectives of this research were to (1) synthesize, and (2) evaluate new compounds which would be potential reactivators of organophosphate-inhibited acetylcholinesterase.

A series of 1,8-diazafluorenone and 2,2'bipyridylketone oximes and oxime methiodides were synthesized (11, 13, 14, 22, 24). These compounds were developed as structural analogs of 2-PAM (2-Pyridinealdoxime methiodide) and TMB-4 (1,1Trimethylene-Bis(4-formylpyridinium bromide)dioxime), the current drugs of choice for treatment of organophosphorous poisoning.

Acetylcholinesterase from electric eel was inhibited with DFP (diisopropylfluorophosphate), an irreversible-type inhibitor, and the inhibited enzyme was treated with the various reactivator compounds. The reactivation assays were monitored with pH stat apparatus, and the data were evaluated …

Multiple Forms Of Nicotinamide Adenine Dinucleotide Glycohydrolase From Bull Semen, Stanley D. Yeatts Ii

Chemistry & Biochemistry Theses & Dissertations

Nicotinamide adenine dinucleotide glycohydrolase (NADase) of bull semen is an extracellular, soluble enzyme capable of catalyzing the hydrolysis of the nicotinamide N-ribosidic linkage of NAD⁺. In search for a rapid, simple procedure for the preparation of this enzyme, it was found that Matrex Gel Red A (Amicon) column packing served very well as an affinity gel for NADase. The enzyme was applied to the Matrex Red A column (21 cm x 1.5 cm) in 10 mM sodium phosphate buffer, pH 6.0. Surprisingly, two fractions of NADase activity were obtained when the column was eluted with a sodium chloride …

Enzymatic Synthesis Of Oligoribonucleotides Of Defined Base Sequence, Bronwyn Geraldine Hughes

Theses and Dissertations

A possible method for the synthesis of ordered oligoribonucleotides involves primer-dependent polynucleotide phosphorylase (PNPase) synthesis using the RNase A or T1 resistant N-cyclohexyl-N'-β(4-methylmorpholinium)ethylcarbodiimide chloride (CMC-Cl) derivatives of uridine or guanosine containing primers. Thus, CMC-UpA, CMC-GpA, CMC-UpCpC, CMC-GpApC, and ApApApApU-CMC were prepared and studied as primers for PNPase in 15 min 14C-ADP polymerization reactions and also in 6-10 hr synthesis reactions. The CMC-primers were not suitable primers for PNPase catalyzed synthesis reactions for either time. The PNPases used in such studies were contaminated with nuclease that showed the following order of susceptibility: UpA > CpC, GpA > ApU, ApA. Even a highly purified …

Studies Of Rat Brain Thiamine Pyrophosphokinase, Lavell Rolfson Johnson

Theses and Dissertations

The enzyme ATP:thiamine pyrophosphotransferase (thiamine pyrophosphokinaseJ was purified from acetone powders which were prepared from rat brains up to the chromatography on alumina C_γ step by a modified procedure that Mano (Y. Mano, J. Biochem., 42, 283 (1960)] developed for the purification of the rat liver thiamine pyrophosphokinase. The enzyme was purified 12 fold over that in the original extract of the acetone powder. A spectrophotometric assay for the brain thiamine pyrophosphokinase was developed utilizing brewer's yeast apotransketolase. The transketolase assay was able to detect less than 10^-11 moles of thiamine diphosphate, which was synthesized by the kinase, in the …