Enhancing The Interoperability Of Glycan Data Flow Between Chebi, Pubchem, And Glygen.,
2021
George Washington University
Enhancing The Interoperability Of Glycan Data Flow Between Chebi, Pubchem, And Glygen., Rahi Navelkar, Gareth Owen, Venkatesh Mutherkrishnan, Paul Thiessen, Tiejun Cheng, Evan Bolerlton, Nathan Edwards, Michael Tiemeyer, Matthew P Campbell, Maria Martin, Jeet Vora, Robel Kahsay, Raja Mazumder
Biochemistry and Molecular Medicine Faculty Publications
Glycans play a vital role in health, disease, bioenergy, biomaterials, and bio-therapeutics. As a result, there is keen interest to identify and increase glycan data in bioinformatics databases like ChEBI and PubChem, and connecting them to resources at the EMBL-EBI and NCBI to facilitate access to important annotations at a global level. GlyTouCan is a comprehensive archival database that contains glycans obtained primarily through batch upload from glycan repositories, glycoprotein databases, and individual laboratories. In many instances, the glycan structures deposited in GlyTouCan may not be fully defined or have supporting experimental evidence and citations. Databases like ChEBI and PubChem …
Bridging The 12-6-4 Model And The Fluctuating Charge Model,
2021
Loyola University Chicago
Bridging The 12-6-4 Model And The Fluctuating Charge Model, Pengfei Li
Chemistry: Faculty Publications and Other Works
Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable models and parameters. Previously we showed that the 12-6 Lennard-Jones nonbonded model for ions could not reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values simultaneously when ion has a charge of +2 or higher. We discussed that this deficiency arises from the overlook of the ion-induced dipole interaction in the 12-6 model, and this term is proportional to 1/r …
Structure And Function Of An Arabidopsis Thaliana Sulfate Transporter,
2021
The Texas Medical Center Library
Structure And Function Of An Arabidopsis Thaliana Sulfate Transporter, Lie Wang, Kehan Chen, Ming Zhou
Faculty, Staff and Students Publications
Plant sulfate transporters (SULTR) mediate absorption and distribution of sulfate (SO42−) and are essential for plant growth; however, our understanding of their structures and functions remains inadequate. Here we present the structure of a SULTR from Arabidopsis thaliana, AtSULTR4;1, in complex with SO42− at an overall resolution of 2.8 Å. AtSULTR4;1 forms a homodimer and has a structural fold typical of the SLC26 family of anion transporters. The bound SO42− is coordinated by side-chain hydroxyls and backbone amides, and further stabilized electrostatically by the conserved Arg393 and two helix dipoles. Proton and SO42− are co-transported by AtSULTR4;1 and a …
Complexation Of Glycoalkaloid Α- Tomatine With Sterols And Its Potential Application As An Anti-Cancer Drug,
2021
University of Missouri-St. Louis
Complexation Of Glycoalkaloid Α- Tomatine With Sterols And Its Potential Application As An Anti-Cancer Drug, Bishal Nepal
Dissertations
Glycoalkaloids (GAs) are secondary metabolites found mostly in higher plant species and some marine invertebrates. They are known to form complexes with 3β-hydroxy sterols such as cholesterol causing membrane disruption. So far the visual evidence showcasing the complexes formed between glycoalkaloids and sterols has been mainly restricted to some earlier studies using Brewster angle microscopy. This study aimed to develop a method for topographic and morphological analysis of sterol-glycoalkaloid complexes. Langmuir-Blodgett (LB) transfer of monolayers comprising of glycoalkaloid tomatine, sterols, and lipids in varying molar ratios onto mica followed by AFM examination was performed. The AFM method used required minimal …
Overcoming Obstacles In Protein Expression In The Yeast Pichia Pastoris: Interviews Of Leaders In The Pichia Field,
2021
University of the Pacific
Overcoming Obstacles In Protein Expression In The Yeast Pichia Pastoris: Interviews Of Leaders In The Pichia Field, Zoe Ingram, Abha Patkar, Dahoon Oh, Kevin K. Zhang, Christina Chung, Joan Lin-Cereghino, Geoff P. Lin-Cereghino
Pacific Journal of Health
The yeast Pichia pastoris (also known as Komagataella pastoris) has been used for over 30 years to produce thousands of valuable, heterologous proteins, such as insulin to treat diabetes and antibodies to prevent migraine headaches. Despite its success, there are some common, stubborn problems encountered by research scientists when they try to use the yeast to produce their recombinant proteins. In order to provide those working in this field with strategies to overcome these common obstacles, nine experts in P. pastoris protein expression field were interviewed to create a written review and video (https://www.youtube.com/watch?v=FyC9xXVLyD0). This review describes …
Lipoprotein-Induced Increases In Cholesterol And 7-Ketocholesterol Result In Opposite Molecular-Scale Biophysical Effects On Membrane Structure,
2021
Dordt University
Lipoprotein-Induced Increases In Cholesterol And 7-Ketocholesterol Result In Opposite Molecular-Scale Biophysical Effects On Membrane Structure, Manuela A.A. Ayee, Irena Levitan
Faculty Work Comprehensive List
Under hypercholesterolemic conditions, exposure of cells to lipoproteins results in a subtle membrane increase in the levels of cholesterol and 7-ketocholesterol, as compared to normal conditions. The effect of these physiologically relevant concentration increases on multicomponent bilayer membranes was investigated using coarse-grained molecular dynamics simulations. Significant changes in the structural and dynamic properties of the bilayer membranes resulted from these subtle increases in sterol levels, with both sterol species inducing decreases in the lateral area and inhibiting lateral diffusion to varying extents. Cholesterol and 7-ketocholesterol, however, exhibited opposite effects on lipid packing and orientation. The results from this study indicate …
Characterizing Multivalent Interactions Between Folded Protein Domains And Intrinsically Disordered Regions Or Peptide Substrates,
2021
Syracuse University
Characterizing Multivalent Interactions Between Folded Protein Domains And Intrinsically Disordered Regions Or Peptide Substrates, Tongyin Zheng
Dissertations - ALL
Protein-protein interactions (PPIs) play central roles in most biological processes. Studying PPIs is a fundamental step in understanding the molecular basis of cellular processes such as cell-cell contact, enzyme activity, and transient assembly of signaling complexes or cellular structures. In this work, we employed a combination of biophysical and biochemical methods to characterize PPIs, with a focus on interactions between structured domains and intrinsically disordered regions or peptide substrates.The subject of Chapter two is prolyl isomerase Ess1, which is an essential enzyme found in Saccharomyces cerevisiae. Ess1 regulates the transcription and co-transcriptional RNA processing by catalyzing the isomerization of serine-proline …
Coordination Geometries In Metallobundles Enforcing Oxidative And Hydrolytic Catalysis And Designing Biomaterials For Use As Antimicrobials,
2021
Syracuse University
Coordination Geometries In Metallobundles Enforcing Oxidative And Hydrolytic Catalysis And Designing Biomaterials For Use As Antimicrobials, Jennifer Yoon
Dissertations - ALL
De novo protein design permits discovery of intricate folds and functions emulating natural enzymes in simpler, yet robust model constructs. Helical bundles serve as premier scaffolds to incorporate diverse reactivities from oxidative, reductive, to hydrolytic transformations observed in much grander O2-utilizing metalloproteins such as radical-generating ribonucleotide reductases and catalases. One notable family of de novo proteins is the Due Ferri or DF series of four-helix bundles providing a dinuclear site for metal incorporation and are amenable for tailoring active site reactivity. As reactive oxygen species and radical-based intermediates are prevalent and necessary for steering life-essential processes through reactive radicals stabilized …
Late Embryogenesis Abundant Proteins And Mitochondrial Membranes From An Animal Extremophile: Insights Into Severe Water Stress,
2021
Louisiana State University and Agricultural and Mechanical College
Late Embryogenesis Abundant Proteins And Mitochondrial Membranes From An Animal Extremophile: Insights Into Severe Water Stress, John Marcus Anderson
LSU Doctoral Dissertations
This dissertation focuses on two major topics germane to mechanisms by which animals tolerate extreme water stress. First, the impact of transgenic expression of late embryogenesis abundant proteins (LEA) on water stress tolerance of the fruit fly Drosophila melanogaster was investigated. The overall aim was to extend current understanding of the protective properties of LEA proteins documented with isolated cells to a desiccation-sensitive organism during exposure to drying and hyperosmotic stress. Four lines of D. melanogaster were created that expressed transgenes encoding selected LEA proteins originally identified in embryos of the extremophile Artemia franciscana. After 80% tissue water loss, …
Medical Schools Ignore The Nature Of Consciousness At Great Cost,
2021
independent scholar
Medical Schools Ignore The Nature Of Consciousness At Great Cost, Anoop Kumar
Journal of Wellness
The essential question of the relationship between consciousness and matter is ignored in medical school curricula, leading to a machine-like view of the human being that contributes to physician burnout and intellectual dissatisfaction. The evidence suggesting that the brain may not be the seat of consciousness is generally ignored to preserve the worldview of the primacy of matter. By investigating new frameworks detailing the nature of consciousness at different levels of hierarchy, we can bring intellectual rigor to a once opaque subject that supports a fundamental reality about our experience: We are human beings, not only human bodies.
Screening Next-Generation Fluorine-19 Probe And Preparation Of Yeast-Derived G Proteins For Gpcr Conformation And Dynamics Study,
2021
University of South Florida
Screening Next-Generation Fluorine-19 Probe And Preparation Of Yeast-Derived G Proteins For Gpcr Conformation And Dynamics Study, Wenjie Zhao
USF Tampa Graduate Theses and Dissertations
GPCR regulates numerous diverse physiological processes relevant to diabetes, obesity, Alzheimer's diseases, and several central nervous system disorders and targets proteins in signaling pathways. It has created nearly 200 billion profits from its derivative drugs in 2018. There are near 400 structures of over 70 GPCRs have been resolved by X-ray crystallography, cryo-electron microscopy, and NMR spectroscopy. One of the current challenges that remain in the conformational transition and dynamics study using NMR spectroscopy is to obtain sufficient quantities of the G proteins and GPCRs. Pichia pastoris has shown its tremendous promise in expressing the GPCRs in a high yield, …
Fisheries Food Webs: Quantifying Habitat-Use, Trophic Structure, And Energetic Pathways In Coastal Tanzania,
2021
Louisiana State University
Fisheries Food Webs: Quantifying Habitat-Use, Trophic Structure, And Energetic Pathways In Coastal Tanzania, Mario Fernando Hernandez
LSU Doctoral Dissertations
Commercial and recreational fisheries are a valuable resource to millions of people around the world. Developing countries are particularly dependent on the revenue provided by locally harvested fish with total exports from these nations valued at $80 billion USD. For Tanzania, fisheries provide not only a source of revenue but an important source of protein with an estimated 25 to 30kg of fish consumed per person every year. There is no doubt that high fisheries production is critical to the well-being of millions of livelihoods along the Tanzanian coast. An important but poorly understood driver of fisheries production is the …
A Kinetic Model For Blood Biomarker Levels After Mild Traumatic Brain Injury,
2021
Missouri University of Science and Technology
A Kinetic Model For Blood Biomarker Levels After Mild Traumatic Brain Injury, Sima Azizi, Daniel B. Hier, Blaine Allen, Tayo Obafemi-Ajayi, Gayla R. Olbricht, Matthew S. Thimgan, Donald C. Wunsch
Mathematics and Statistics Faculty Research & Creative Works
Traumatic brain injury (TBI) imposes a significant economic and social burden. The diagnosis and prognosis of mild TBI, also called concussion, is challenging. Concussions are common among contact sport athletes. After a blow to the head, it is often difficult to determine who has had a concussion, who should be withheld from play, if a concussed athlete is ready to return to the field, and which concussed athlete will develop a post-concussion syndrome. Biomarkers can be detected in the cerebrospinal fluid and blood after traumatic brain injury and their levels may have prognostic value. Despite significant investigation, questions remain as …
Case 51: Purification Of A Transferase Involved In The Production Of Physiologically Important Glycoproteins,
2021
Providence College
Case 51: Purification Of A Transferase Involved In The Production Of Physiologically Important Glycoproteins, Dr. Kathleen Cornely
Chemistry & Biochemistry Case Studies
A transferase involved in post-translational glycosylation of a physiologically important glycoprotein is purified and characterized.
Case 40: A Collection Of Collagen Cases,
2021
Providence College
Case 40: A Collection Of Collagen Cases, Dr. Kathleen Cornely
Chemistry & Biochemistry Case Studies
Factors important in the stability of collagen are examined.
Case 6: Hemoglobin Providence,
2021
Providence College
Case 6: Hemoglobin Providence, Dr. Kathleen Cornely
Chemistry & Biochemistry Case Studies
A mutant hemoglobin variant, Hemoglobin Providence, exists in two forms in vivo.
Tp-5801 In Vitro Kinase Screen Data,
2021
Brigham Young University
Tp-5801 In Vitro Kinase Screen Data, Joshua Andersen
ScholarsArchive Data
In vitro kinase screen data for TP-5801 to accompany Chan and Egbert et al., Nature Communications, 2021 (in press)
A Synthetic Circuit For Buffering Gene Dosage Variation Between Individual Mammalian Cell,
2021
The Texas Medical Center Library
A Synthetic Circuit For Buffering Gene Dosage Variation Between Individual Mammalian Cell, Jin Yang, Jihwan Lee, Michelle A Land, Shujuan Lai, Oleg A Igoshin, François St-Pierre
Faculty, Staff and Students Publications
Precise control of gene expression is critical for biological research and biotechnology. However, transient plasmid transfections in mammalian cells produce a wide distribution of copy numbers per cell, and consequently, high expression heterogeneity. Here, we report plasmid-based synthetic circuits - Equalizers - that buffer copy-number variation at the single-cell level. Equalizers couple a transcriptional negative feedback loop with post-transcriptional incoherent feedforward control. Computational modeling suggests that the combination of these two topologies enables Equalizers to operate over a wide range of plasmid copy numbers. We demonstrate experimentally that Equalizers outperform other gene dosage compensation topologies and produce as low cell-to-cell …
Novel “Acid Tuned” Deep Eutectic Solvents Based On Protonated L-Proline,
2021
Kettering University
Novel “Acid Tuned” Deep Eutectic Solvents Based On Protonated L-Proline, Patrycja Janicka, Andrzej Przyjazny, Grzegorz Boczkaj
Natural Sciences Publications
The paper presents new types of deep eutectic solvents (DESs) based on L-proline protonated using three different acids (hydrochloric, sulfuric and phosphoric)and playing the role of a hydrogen bond acceptor(HBA). Glucose and xylitol were used as hydrogen bond donors (HBD). A series of deep eutectic solvents with various mole ratios were obtained for the systems L-proline: glucose and L-proline: xylitol. Density, melting point, pH and viscosity of the synthesized DESs were determined along with the effect of water content, mole fraction of the HBA in DES and temperature on properties of the DESs. A wide range of densities (1343–1606 kg/m3), …
Cellular Toxicity Of Malonato (Ethylenediamine) Platinum (Ii) In Models Of Cancer,
2021
Western Kentucky University
Cellular Toxicity Of Malonato (Ethylenediamine) Platinum (Ii) In Models Of Cancer, Sidikat Olanrewaju Olajuwon
Masters Theses & Specialist Projects
Platinum(II) compounds including the three FDA approved drugs, cisplatin, carboplatin, and oxaliplatin, are composed of two structural components, a leaving ligand, and a non-leaving ligand, each attached to a central platinum(II) atom. All bifunctional platinum compounds studied have similar mechanisms of initiating cell death. However, their efficacy as chemotherapeutics depends on the tissues in which the cancer originates. No model has explained these tissue-specific efficacies. We hypothesized that the efficacies of these platinum compounds vary due to structural differences in the leaving ligands. To test the influence of the leaving ligand on cellular survival, novel platinum compounds were synthesized, and …
