Open Access. Powered by Scholars. Published by Universities.®
Biochemistry, Biophysics, and Structural Biology Commons™
Open Access. Powered by Scholars. Published by Universities.®
- Discipline
-
- Biochemistry (10)
- Molecular Biology (6)
- Biophysics (5)
- Cell and Developmental Biology (3)
- Physical Sciences and Mathematics (3)
-
- Bioinformatics (2)
- Biology (2)
- Cell Biology (2)
- Developmental Biology (2)
- Genetics and Genomics (2)
- Plant Sciences (2)
- Structural Biology (2)
- Agriculture (1)
- Amino Acids, Peptides, and Proteins (1)
- Analytical, Diagnostic and Therapeutic Techniques and Equipment (1)
- Animal Sciences (1)
- Biodiversity (1)
- Biogeochemistry (1)
- Biotechnology (1)
- Cardiovascular Diseases (1)
- Cellular and Molecular Physiology (1)
- Chemicals and Drugs (1)
- Chemistry (1)
- Diagnosis (1)
- Diseases (1)
- Earth Sciences (1)
- Ecology and Evolutionary Biology (1)
- Entomology (1)
- Keyword
-
- Arabidopsis thaliana (2)
- Activation energy (1)
- Aminoglycoside Antibiotics (1)
- Aminoglycoside modifying enzyme (1)
- Aminoglycoside modifying enzymes (1)
-
- Anaerobic stress (1)
- And in vivo (1)
- Anion-pi interactions (1)
- Arylphorin (1)
- Bio Energy (1)
- Broiler chickens (1)
- Calcium (1)
- Cohen's effect sizes (1)
- Cry1Ac (1)
- Cytochrome (1)
- Diet manipulation (1)
- Directed evolution (1)
- Drug discovery (1)
- Dynamics (1)
- Ethylene (1)
- Fatty acid oxidation (1)
- Flooding (1)
- Folate Metabolism (1)
- Functional analysis (1)
- GPCR (1)
- GPRC6A (1)
- Heliothis virescens (1)
- Heparan sulfate proteoglycans (1)
- Homology Modeling (1)
- Homology modeling (1)
- Publication
- Publication Type
Articles 1 - 18 of 18
Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
Mechanism Of Lignin Inhibition Of Enzymatic Biomass Deconstruction, Josh V. Vermaas, Loukas Petridis, Xianghong Qi, Roland Schulz, Benjamin Lindner, Jeremy C. Smith
Mechanism Of Lignin Inhibition Of Enzymatic Biomass Deconstruction, Josh V. Vermaas, Loukas Petridis, Xianghong Qi, Roland Schulz, Benjamin Lindner, Jeremy C. Smith
Faculty Publications and Other Works -- Biochemistry, Cellular and Molecular Biology
Background
The conversion of plant biomass to ethanol via enzymatic cellulose hydrolysis offers a potentially sustainable route to biofuel production. However, the inhibition of enzymatic activity in pretreated biomass by lignin severely limits the efficiency of this process.
Results
By performing atomic-detail molecular dynamics simulation of a biomass model containing cellulose, lignin, and cellulases (TrCel7A), we elucidate detailed lignin inhibition mechanisms. We find that lignin binds preferentially both to the elements of cellulose to which the cellulases also preferentially bind (the hydrophobic faces) and also to the specific residues on the cellulose-binding module of the cellulase that are …
Environmental Controls On The Diversity And Distribution Of Endosymbionts Associated With Phacoides Pectinatus (Bivalvia: Lucinidae) From Shallow Mangrove And Seagrass Sediments, St. Lucie County, Florida, Thomas Walters Doty
Masters Theses
Lucinid bivalves are capable of colonizing traditionally inhospitable shallow marine sediments due to metabolic functions of bacterial endosymbionts located within their gills. Because lucinids can often be the dominant sediment infauna, defining their roles in sediment and pore fluid geochemical cycling is necessary to address concerns related to changes in coastal biological diversity and to understanding the sensitivity of threatened coastal ecosystems over time. However, there has been limited research done to understand the diversity and distribution of many lucinid chemosymbiotic systems. Therefore, the goals of this thesis were to evaluate the distribution of Phacoides pectinatus and its endosymbiont communities …
Subfunctionalization Of Ethylene Receptors And Homology Modeling Of Cytosolic Domains In Arabidopsis Thaliana, Sai Keerthana Wuppalapati
Subfunctionalization Of Ethylene Receptors And Homology Modeling Of Cytosolic Domains In Arabidopsis Thaliana, Sai Keerthana Wuppalapati
Masters Theses
Ethylene is a gaseous phytohormone that initiates and modulates several mechanisms related to growth and development in plants through a family of five disulphide-linked receptor dimers. Although the ethylene receptors are very similar in their structures, they have diverse functions with both overlapping and non-overlapping roles. Silver ions are able to support ethylene binding to the receptors but it is also interesting to note that ethylene responses are blocked in the presence of silver. A part of the present study identified that ETR1 receiver domain has little or no role in mediating responses to silver ions, supported by data obtained …
Understanding The Molecular Mechanism Underlying The Great Thermal Stability Of Thermophilic Enzymes Using Aminoglycoside Nucleotidyltransferase 4' As A Model, Xiaomin Jing
Doctoral Dissertations
The aminoglycoside nucleotidyltransferase 4' (ANT) is a homodimeric enzyme that detoxifies antibiotics by nucleotidylating at the C4'-OH site. Two thermostable variants T130K and D80Y generated by direct evolution in laboratory differ by only a single residue replacement compared to the wild type mesophilic enzyme. Both variants display enhanced melting temperatures and execute catalysis at temperatures the wild type would be inactive. However, T130K variant still keeps molecular properties of mesophilic enzyme. T130àK130 does not trigger significant change in enzyme’s local flexibility or thermodynamics of ligand binding while D80Y variant has distinct properties in ligand recognition and dynamics. We hypothesize that …
Engineering Photosystem I Complexes For Use In Bio-Hybrid Dye-Sensitized Solar Cells, Richard Franklin Simmerman
Engineering Photosystem I Complexes For Use In Bio-Hybrid Dye-Sensitized Solar Cells, Richard Franklin Simmerman
Doctoral Dissertations
Increasing global population, growing per capita energy needs, diminishing fossil fuels, and climate change collectively will require new, innovative, and sustainable alternatives to meet the world’s growing energy needs. One of the most promising yet simple approaches are dye-sensitized solar cells (DSSCs). However, conventional DSSCs use semi-conductor anodes sensitized with complex synthetic organometallic dyes. Most dyes utilize ruthenium complexes to absorb photons, which upon excitation, inject electrons into the anode, while holes migrate to the cathode via liquid electrolyte. However, these dyes are expensive, difficult to make, and resource-limited. This dissertation focuses on replacing synthetic dyes with the naturally occurring, …
Elucidation Of Conformational Switching Mechanisms Of Sensing Proteins By Molecular Dynamics Perturbation Studies, Quentin Ramon Johnson
Elucidation Of Conformational Switching Mechanisms Of Sensing Proteins By Molecular Dynamics Perturbation Studies, Quentin Ramon Johnson
Doctoral Dissertations
Sensing proteins are a subclass of switchable proteins, which are biologically designed with multiple, purposeful, low-free-energy states and can interconvert between these states in the wake of some environmental perturbation. Note, that this phenomenon is no small feat. This is a preprogrammed response for regulatory purposes that requires no cognitive action and is reversible as the environment returns to normal. Sensing proteins often switch between active and non-active states, closed and open conformations or other particular dichotomous states. Therefore, understanding the mechanism by which these proteins sense a specific perturbation and how they switch between conformations is paramount. Addressing these …
Quantitative And Functional Analysis Pipeline For Label-Free Metaproteomics Data And Its Applications, Lang Ho Lee
Quantitative And Functional Analysis Pipeline For Label-Free Metaproteomics Data And Its Applications, Lang Ho Lee
Doctoral Dissertations
Since the large-scale metaproteome was first reported in 2005, metaproteomics has advanced at a tremendous rate both in its quantitative and qualitative metrics. Furthermore metaproteomics is now being applied as a general tool in microbial ecology in a large variety of environmental studies. Though metaproteomics is becoming a useful and even a standard tool for the microbial ecologist, standardized bioinformatics pipelines are not readily available. Therefore, we developed quantitative and functional analysis pipeline for metaproteomics (QFAM) to help analyze large and complicated metaproteomics data in a robust and timely fashion with outputs designed to be simple and clearly understood by …
Exploring Structure-Dynamics-Function Relationship In Proteins, Protein: Ligand And Protein: Protein Systems Through Computational Methods, Karan Pal Kapoor
Exploring Structure-Dynamics-Function Relationship In Proteins, Protein: Ligand And Protein: Protein Systems Through Computational Methods, Karan Pal Kapoor
Doctoral Dissertations
The study focuses on understanding the dynamic nature of interactions between molecules and macromolecules. Molecular modeling and simulation technologies are employed to understand how the chemical constitution of the protein, specific interactions and dynamics of its structure provide the basis of its mechanism of function. The structure-dynamics-function relationship is investigated from quantum to macromolecular-assembly level, with applications in the field of rationale drug discovery and in improving efficiency of renewable sources of energy. Results presented include investigating the role of dynamics in the following:
1) In interactions between molecules: analyzing dynamic nature of a specific non-covalent interaction known as “anion-π …
Development Of High Performance Molecular Dynamics With Application To Multimillion-Atom Biomass Simulations, Roland Schulz
Development Of High Performance Molecular Dynamics With Application To Multimillion-Atom Biomass Simulations, Roland Schulz
Doctoral Dissertations
An understanding of the recalcitrance of plant biomass is important for efficient economic production of biofuel. Lignins are hydrophobic, branched polymers and form a residual barrier to effective hydrolysis of lignocellulosic biomass. Understanding lignin's structure, dynamics and its interaction and binding to cellulose will help with finding more efficient ways to reduce its contribution to the recalcitrance. Molecular dynamics (MD) using the GROMACS software is employed to study these properties in atomic detail. Studying complex, realistic models of pretreated plant cell walls, requires simulations significantly larger than was possible before. The most challenging part of such large simulations is the …
Calmodulin-Like Protein 38: A Component Of Ribonucleoprotein Particles During Hypoxic Stress Responses In Arabidopsis, Ansul Lokdarshi
Calmodulin-Like Protein 38: A Component Of Ribonucleoprotein Particles During Hypoxic Stress Responses In Arabidopsis, Ansul Lokdarshi
Doctoral Dissertations
Waterlogging stress leads to a crisis in energy metabolism and the accumulation of toxic metabolites due to the hypoxic and/or anoxic environment associated with this condition. To respond and adapt to this situation, higher plants employ an integrated genetic program that leads to the induction of anaerobic response polypeptide genes that encode metabolic and signaling proteins involved in altering metabolic flow and other adaptive responses. The study presented here shows that the Arabidopsis thaliana calmodulin-like protein CML38 is calcium sensor protein that serves as a member of the core anaerobic response gene family and is involved in modulating the survival …
Cellular Localization And Metabolomic Analysis Of The Arabidopsis Thaliana Major Intrinsic Protein Nip2;1: A Root-Specific Lactic Acid Transporter Induced In Response To Hypoxic Stress, Taylor K. Fuller
Chancellor’s Honors Program Projects
No abstract provided.
The In Vivo Effect Of Osmolytes On Folate Metabolism, Timkhite-Kulu Berhane
The In Vivo Effect Of Osmolytes On Folate Metabolism, Timkhite-Kulu Berhane
Masters Theses
Previous studies have found that addition of osmolytes weakens the binding of dihydrofolate (DHF) to R67 dihydrofolate reductase (DHFR), chromosomal DHFR from E. coli and a pteridine reductase. These results support the preferential interaction of DHF with osmolytes compared to water. Thus, a working model where interaction of DHF with osmolytes shifts the binding away from the protein-DHF complex towards the free species was proposed. As tetrahydrofolate and other folate redox states have similar structures to DHF, we predict osmotic stress will lower the catalytic efficiencies of other folate pathway enzymes. In this thesis, we explore the in vivo effects …
Conformational Dynamics Of Cytochrome P450cam Upon Ligand Binding, Ana Virginia Bernal Gomez
Conformational Dynamics Of Cytochrome P450cam Upon Ligand Binding, Ana Virginia Bernal Gomez
Masters Theses
Cytochrome P450s are a superfamily of metalloenzymes that are responsible for the monooxygenation of their hydrophobic substrates. P450’s retain the same general structural scaffold, however are able to bind promiscuously to substrates with distinct physico-chemical properties. It is believed that they possess considerable flexibility in the substrate binding regions as well as their active site to accomplish the diverse binding and catalytic chemistry with high regio- and stereo-specificity. In order to investigate the conformational dynamics inherent in these enzymes, especially in context of binding different ligands, we carried out amide proton exchange studies via NMR spectroscopy on a model P450 …
Comparison Of Activation Enthalpies For Aminoglycoside Modification Reactions, Brittany Sterling Soto
Comparison Of Activation Enthalpies For Aminoglycoside Modification Reactions, Brittany Sterling Soto
Masters Theses
At highly elevated temperatures, many biological reactions can proceed spontaneously from the ground state to the transition state. However, due to the long half-life of these reactions, catalysts are required to catalyze these reactions at modern day temperatures by lowering the activation energy. Wolfenden et al. has previously shown that catalysts enhance the rate of the reaction by reducing the enthalpy of activation. Therefore, the activation energies have been determined for three aminoglycoside modifying enzymes, APH(3’)-IIIa, AAC(3)-IIIb, and AAC(3)-VIa, to determine whether these three enzymes distinguish between the two classes of aminoglycoside antibiotics by reducing the enthalpy of activation during …
Manipulating Adipose Tissue Fatty Acid Oxidation To Reduce Fatness In Broiler Chickens, Tania Emmanuelle Torchon
Manipulating Adipose Tissue Fatty Acid Oxidation To Reduce Fatness In Broiler Chickens, Tania Emmanuelle Torchon
Masters Theses
Compared to rodents, broiler chickens, those reared for meat, are an attractive model for studies of adipose biology, and obesity development in children. The broiler chicken lacks the gene for uncoupling protein 1, the hallmark for brown adipose tissue making them a useful model to study lipid metabolism in white adipocytes. Two studies were performed to investigate if white adipose tissue had the metabolic ability for fatty acid oxidation (FAO), and to investigate the effects of dietary fatty acids on abdominal fat development of young broiler chickens as a model for childhood obesity. In study one, chickens were fasted for …
The Characterization Of Amyloid Fibrils And Novel Synthetic Heparin-Binding Peptides Binding To Cell Surfaces, Nicole Marie Hackenbrack
The Characterization Of Amyloid Fibrils And Novel Synthetic Heparin-Binding Peptides Binding To Cell Surfaces, Nicole Marie Hackenbrack
Chancellor’s Honors Program Projects
No abstract provided.
Characterization Of The Role Of Alpha-Arylphorin In The Heliothis Virescens Midgut Response To Cry1ac Toxin From Bacillus Thuringiensis, Jerreme Jamael Jackson
Characterization Of The Role Of Alpha-Arylphorin In The Heliothis Virescens Midgut Response To Cry1ac Toxin From Bacillus Thuringiensis, Jerreme Jamael Jackson
Doctoral Dissertations
Homeostasis of the intestinal epithelium in Heliothis virescens is mediated by the proliferation and differentiation of multipotent intestinal stem cells (ISCs) that lie adjacent to the basal lamina. In response to extrinsic and intrinsic signals, ISC proliferation and differentiation promotes epithelial growth and regeneration following the loss of integrity. We tested the in vivo effects of the ISC mitogen, a [alpha]-arylphorin, on ISC proliferation and the morphological changes of the midgut during larval development. Additionally, we examined how these changes affected the intestinal epithelium response to Cry1Ac toxin from Bacillus thuringiensis. Histological and in vitro evidence supported two distinct …
Revisiting The Stoichiometry And Binding Sites Of Pai-1 In Complex With Vitronectin: Vn A Potential Mediator Of Pai-1:Pai-1 Interactions?, Sierra M. Sorter
Revisiting The Stoichiometry And Binding Sites Of Pai-1 In Complex With Vitronectin: Vn A Potential Mediator Of Pai-1:Pai-1 Interactions?, Sierra M. Sorter
Chancellor’s Honors Program Projects
No abstract provided.