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Articles 1 - 7 of 7
Full-Text Articles in Life Sciences
Computer Simulations Of Enzymes, Jianzhuang Yao
Computer Simulations Of Enzymes, Jianzhuang Yao
Doctoral Dissertations
Enzymes are important catalysts in living systems, and understanding catalytic mechanisms of enzymes is an important task for modern biophysics and biochemistry. Computer simulations have emerged as very useful tools for understanding how enzymes work. In this dissertation, QM/MM MD simulations were applied to study the catalytic mechanisms of several enzymes, including sedolisin, S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases, and salicylic acid binding protein 2. For sedolisin, we focus on the acylation and deacylation reactions catalyzed by the enzymes. We proposed a general acid/base mechanism involving the Glu/Asp residues at the active site. MD and QM/MM free energy simulations on pro-kumamolisin show that …
The Role Of Biotin And Oxamate In The Carboxyltransferase Reaction Of Pyruvate Carboxylase, Adam D. Lietzan, Yi Lin, Martin St. Maurice
The Role Of Biotin And Oxamate In The Carboxyltransferase Reaction Of Pyruvate Carboxylase, Adam D. Lietzan, Yi Lin, Martin St. Maurice
Biological Sciences Faculty Research and Publications
Pyruvate carboxylase (PC) is a biotin-dependent enzyme that catalyzes the MgATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in central metabolism. During catalysis, carboxybiotin is translocated to the carboxyltransferase domain where the carboxyl group is transferred to the acceptor substrate, pyruvate. Many studies on the carboxyltransferase domain of PC have demonstrated an enhanced oxaloacetate decarboxylation activity in the presence of oxamate and it has been shown that oxamate accepts a carboxyl group from carboxybiotin during oxaloacetate decarboxylation. The X-ray crystal structure of the carboxyltransferase domain from Rhizobium etli PC reveals that oxamate is positioned in the active site …
Synthesis, Characterization And Mechanistic Studies Of Biomolecules@Mesomofs, Yao Chen
Synthesis, Characterization And Mechanistic Studies Of Biomolecules@Mesomofs, Yao Chen
USF Tampa Graduate Theses and Dissertations
Encapsulation of biomolecules is of great interest to research advances related to biology, physiology, immunology, and biochemistry, as well as industrial and biomedical applications such as drug delivery, biocatalysis, biofuel, food and cosmetics. Encapsulation provides functional characteristics that are not fulfilled by free biomolecules and stabilizes the fragile biomolecules. In terms of biocatalysis, solid support can often enhance the stability of enzymes, as well as facilitate separation and recovery for reuse while maintaining activity and selectivity. Various kinds of materials have been used for encapsulation of biomolecules, among which, porous materials are an important group. Metal-organic frameworks (MOFs) have attracted …
Amino Acid Racemase Enzyme Assays, Atanas D. Radkov, Luke A. Moe
Amino Acid Racemase Enzyme Assays, Atanas D. Radkov, Luke A. Moe
Plant and Soil Sciences Faculty Publications
Amino acid racemases are enzymes that invert the α-carbon stereochemistry of amino acids (AAs), interconverting amino acids between their L- and D-enantiomers in a reversible reaction. In bacteria, they are known to have catabolic physiological functions but are also involved in the synthesis of many D-AAs, including D-glutamate and D-alanine, which are necessary components of the peptidoglycan layer of the bacterial cell wall. As such, amino acid racemases represent significant targets for the development of bactericidal compounds. Amino acid racemases are also regarded by the biotechnological industry as important catalysts for the production of economically relevant D-AAs. Here, we provide …
B. Braunii, Race B Gene For A Triterpene Methyltransferase Enzyme And Uses Thereof, Joe Chappell, Okada Shigeru, Scott Kinison, Tom Niehaus
B. Braunii, Race B Gene For A Triterpene Methyltransferase Enzyme And Uses Thereof, Joe Chappell, Okada Shigeru, Scott Kinison, Tom Niehaus
Plant and Soil Sciences Faculty Patents
Provided is an isolated polypeptide having triterpene methyltransferase activity. Also provided is an isolated nucleic acid molecule that encodes the triterpene methyltransferase polypeptides; a vector comprising the nucleic acid molecules that encode the triterpene methyltransferase polypeptides; and a host cell(s) transfected with the aforementioned nucleic acid molecule or vector. In another aspect, a method of producing a methylated triterpene is provided. The method comprises providing a metabolizable carbon source to a host cell transfected with a nucleic acid molecule that encodes a triterpene methyltransferase under conditions sufficient for production of a methylated triterpene. The method optionally further comprises isolating the …
Functionally Diverse Biotin-Dependent Enzymes With Oxaloacetate Decarboxylase Activity, Adam D. Lietzan, Martin St. Maurice
Functionally Diverse Biotin-Dependent Enzymes With Oxaloacetate Decarboxylase Activity, Adam D. Lietzan, Martin St. Maurice
Biological Sciences Faculty Research and Publications
Biotin-dependent enzymes catalyze carboxylation, decarboxylation and transcarboxylation reactions that participate in the primary metabolism of a wide range of organisms. In all cases, the overall reaction proceeds via two half reactions that take place in physically distinct active sites. In the first half-reaction, a carboxyl group is transferred to the 1-N′ of a covalently tethered biotin cofactor. The tethered carboxybiotin intermediate subsequently translocates to a second active site where the carboxyl group is either transferred to an acceptor substrate or, in some bacteria and archaea, is decarboxylated to biotin and CO2 in order to power the export of sodium …
Distribution Of Extracellular Enzyme-Producing Bacteria In The Digestive Tracts Of 4 Brackish Water Fish Species, Paramita Das, Sudipta Mandal, Argha Khan, Sanjib Kumar Manna, Koushik Ghosh
Distribution Of Extracellular Enzyme-Producing Bacteria In The Digestive Tracts Of 4 Brackish Water Fish Species, Paramita Das, Sudipta Mandal, Argha Khan, Sanjib Kumar Manna, Koushik Ghosh
Turkish Journal of Zoology
Occurrence and distribution of enzyme-producing bacteria in the proximal (PI), middle (MI), and distal (DI) segments of the gastrointestinal tracts of 4 brackish water teleosts (Scatophagus argus, Terapon jarbua, Mystus gulio, and Etroplus suratensis) have been investigated. Data were presented as log viable counts g^{-1} intestine (LVC). The heterotrophic bacterial population had the highest occurrence in the DI regions of all fish species studied except M. gulio. Proteolytic and amylolytic bacteria had the highest occurrence in the DI of M. gulio (LVC = 5.50 and 5.93, respectively), while cellulolytic and lipolytic populations exhibited highest occurrences in the DI regions of …