Open Access. Powered by Scholars. Published by Universities.®
Biochemistry, Biophysics, and Structural Biology Commons™
Open Access. Powered by Scholars. Published by Universities.®
- Keyword
-
- Molecular dynamics (3)
- Glycosaminoglycan (2)
- Protein engineering (2)
- 2′-hydroxybiphenyl-2-sulfinate desulfinase (1)
- Aspergillus (1)
-
- Biodesulfurization (1)
- Bioenergy (1)
- Biotechnology (1)
- CO2 Reduction Reaction (1)
- Carbohydrate recognition (1)
- Cellobiohydrolase (1)
- Cellulase (1)
- Chitinase (1)
- Collagen (1)
- Crystal structure (1)
- Cysteine-27 proton (1)
- Desulfination (1)
- Directed evolution (1)
- Diterpene (1)
- DszB (1)
- Electrochemical Treatment (1)
- Electrophilic aromatic substitution (1)
- Free energy perturbation (1)
- Glassy Carbon (1)
- Glycoside hydrolace (1)
- Lectin (1)
- Molecular modeling (1)
- Monoterpene (1)
- Nitrogen-Doped Carbon Nano-Onion (1)
- Oxygen Reduction Reaction (1)
- Publication
- Publication Type
Articles 1 - 7 of 7
Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
Impact Of Conformational Change, Solvation Environment, And Post-Translational Modification On Desulfurization Enzyme 2'-Hydroxybiphenyl-2-Sulfinate Desulfinase (Dszb) Stability And Activity, Landon C. Mills
Theses and Dissertations--Chemical and Materials Engineering
Naturally occurring enzymatic pathways enable highly specific, rapid thiophenic sulfur cleavage occurring at ambient temperature and pressure, which may be harnessed for the desulfurization of petroleum-based fuel. One pathway found in bacteria is a four-step catabolic pathway (the 4S pathway) converting dibenzothiophene (DBT), a common crude oil contaminant, into 2-hydroxybiphenyl (HBP) without disrupting the carbon-carbon bonds. 2’-Hydroxybiphenyl-2-sulfinate desulfinase (DszB), the rate-limiting enzyme in the enzyme cascade, is capable of selectively cleaving carbon-sulfur bonds. Accordingly, understanding the molecular mechanisms of DszB activity may enable development of the cascade as industrial biotechnology. Based on crystallographic evidence, we hypothesized that DszB …
Surface And Structural Modification Of Carbon Electrodes For Electroanalysis And Electrochemical Conversion, Yan Zhang
Theses and Dissertations--Chemistry
Electrocatalysis is key to both sensitive electrochemical sensing and efficient electrochemical energy conversion. Despite high catalytic activity, traditional metal catalysts have poor stability, low selectivity, and high cost. Metal-free, carbon-based materials are emerging as alternatives to metal-based catalysts because of their attractive features including natural abundance, environmental friendliness, high electrical conductivity, and large surface area. Altering surface functionalities and heteroatom doping are effective ways to promote catalytic performance of carbon-based catalysts. The first chapter of this dissertation focuses on developing electrode modification methods for electrochemical sensing of biomolecules. After electrochemical pretreatment, glassy carbon demonstrates impressive figures-of-merit in detecting small, redox-active …
Understanding Carbohydrate Recognition Mechanisms In Non-Catalytic Proteins Through Molecular Simulations, Abhishek A. Kognole
Understanding Carbohydrate Recognition Mechanisms In Non-Catalytic Proteins Through Molecular Simulations, Abhishek A. Kognole
Theses and Dissertations--Chemical and Materials Engineering
Non-catalytic protein-carbohydrate interactions are an essential element of various biological events. This dissertation presents the work on understanding carbohydrate recognition mechanisms and their physical significance in two groups of non-catalytic proteins, also called lectins, which play key roles in major applications such as cellulosic biofuel production and drug delivery pathways. A computational approach using molecular modeling, molecular dynamic simulations and free energy calculations was used to study molecular-level protein-carbohydrate and protein-protein interactions. Various microorganisms like bacteria and fungi secret multi-modular enzymes to deconstruct cellulosic biomass into fermentable sugars. The carbohydrate binding modules (CBM) are non-catalytic domains of such enzymes that …
Improving The Thermal Stability Of Cellobiohydrolase Cel7a From Hypocrea Jecorina By Directed Evolution, Frits Goedegebuur, Lydia Dankmeyer, Peter Gualfetti, Saeid Karkehabadi, Henrik Hansson, Suvamay Jana, Vicky Huynh, Bradley R. Kelemen, Paulien Kruithof, Edmund A. Larenas, Pauline J. M. Teunissen, Jerry Ståhlberg, Christina M. Payne, Colin Mitchinson, Mats Sandgren
Improving The Thermal Stability Of Cellobiohydrolase Cel7a From Hypocrea Jecorina By Directed Evolution, Frits Goedegebuur, Lydia Dankmeyer, Peter Gualfetti, Saeid Karkehabadi, Henrik Hansson, Suvamay Jana, Vicky Huynh, Bradley R. Kelemen, Paulien Kruithof, Edmund A. Larenas, Pauline J. M. Teunissen, Jerry Ståhlberg, Christina M. Payne, Colin Mitchinson, Mats Sandgren
Chemical and Materials Engineering Faculty Publications
Secreted mixtures of Hypocrea jecorina cellulases are able to efficiently degrade cellulosic biomass to fermentable sugars at large, commercially relevant scales. H. jecorina Cel7A, cellobiohydrolase I, from glycoside hydrolase family 7, is the workhorse enzyme of the process. However, the thermal stability of Cel7A limits its use to processes where temperatures are no higher than 50 °C. Enhanced thermal stability is desirable to enable the use of higher processing temperatures and to improve the economic feasibility of industrial biomass conversion. Here, we enhanced the thermal stability of Cel7A through directed evolution. Sites with increased thermal stability properties were combined, and …
Desulfination By 2′-Hydroxybiphenyl-2-Sulfinate Desulfinase Proceeds Via Electrophilic Aromatic Substitution By The Cysteine-27 Proton, Inacrist Geronimo, Shawn R. Nigam, Christina M. Payne
Desulfination By 2′-Hydroxybiphenyl-2-Sulfinate Desulfinase Proceeds Via Electrophilic Aromatic Substitution By The Cysteine-27 Proton, Inacrist Geronimo, Shawn R. Nigam, Christina M. Payne
Chemical and Materials Engineering Faculty Publications
Biodesulfurization is an attractive option for enzymatically removing sulfur from the recalcitrant thiophenic derivatives that comprise the majority of organosulfur compounds remaining in hydrotreated petroleum products. Desulfurization in the bacteria Rhodococcus erythropolis follows a four-step pathway culminating in C–S bond cleavage in the 2′-hydroxybiphenyl-2-sulfinate (HBPS) intermediate to yield 2-hydroxybiphenyl and bisulfite. The reaction, catalyzed by 2′-hydroxybiphenyl-2-sulfinate desulfinase (DszB), is the rate-limiting step and also the least understood, as experimental evidence points to a mechanism unlike that of other desulfinases. On the basis of structural and biochemical evidence, two possible mechanisms have been proposed: nucleophilic addition and electrophilic aromatic substitution. Density …
Inhibition Of Mammalian Glycoprotein Ykl-40 Identification Of The Physiological Ligand, Abhishek A. Kognole, Christina M. Payne
Inhibition Of Mammalian Glycoprotein Ykl-40 Identification Of The Physiological Ligand, Abhishek A. Kognole, Christina M. Payne
Chemical and Materials Engineering Faculty Publications
YKL-40 is a mammalian glycoprotein associated with progression, severity, and prognosis of chronic inflammatory diseases and a multitude of cancers. Despite this well documented association, identification of the lectin′s physiological ligand and, accordingly, biological function has proven experimentally difficult. YKL-40 has been shown to bind chito-oligosaccharides; however, the production of chitin by the human body has not yet been documented. Possible alternative ligands include proteoglycans, polysaccharides, and fibers like collagen, all of which makeup the extracellular matrix. It is likely that YKL-40 is interacting with these alternative polysaccharides or proteins within the body, extending its function to cell biological roles …
Engineering Novel Terpene Production Platforms In The Yeast Saccharomyces Cerevisiae, Xun Zhuang
Engineering Novel Terpene Production Platforms In The Yeast Saccharomyces Cerevisiae, Xun Zhuang
Theses and Dissertations--Plant and Soil Sciences
The chemical diversity and biological activities of terpene and terpenoids have served in the development of new flavors, fragrances, medicines and pesticides. While terpenes are made predominantly by plants and microbes in small amounts and as components of complex mixtures, chemical synthesis of terpenes remains technically challenging, costly and inefficient. In this dissertation, methods to create new yeast lines possessing a dispensable mevalonate biosynthetic pathway wherein carbon flux can be diverted to build any chemical class of terpene product are described. The ability of this line to generate diterpenes was next investigated. Using a 5.5 L fed bath fermentation system, …