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- Thermal analysis (2)
- 4-ethylenedioxythiophene) (PEDOT); Carbon fiber microelectrode; Peroxynitrite detection (1)
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- DNA polymerization;Fidelity;Mutagenesis;Non-natural nucleotides;Hydrogen bonding interactions (1)
- DNA polymerization;Template-independent DNA synthesis;Fidelity;Recombination;Nucleotide analog (1)
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Articles 1 - 18 of 18
Full-Text Articles in Chemistry
[Fe-Fe]-Hydrogenase Reactivated By Residue Mutations As Bridging Carbonyl Rearranges: A Qm/Mm Study, Stefan Motiu, Valentin Gogonea
[Fe-Fe]-Hydrogenase Reactivated By Residue Mutations As Bridging Carbonyl Rearranges: A Qm/Mm Study, Stefan Motiu, Valentin Gogonea
Chemistry Faculty Publications
In this work, we found aqueous enzyme phase reaction pathways for the reactivation of the exogenously inhibited [Fe-Fe]-hydrogenases by O2, or OH−, which metabolizes to H2O (Dogaru et al., Int J Quantum Chem 2008, 108; Motiu et al., Int J Quantum Chem 2007, 107, 1248). We used the hybrid quantum mechanics/molecular mechanics (QM/MM) method to study the reactivation pathways of the exogenously inhibited enzyme matrix. The ONIOM calculations performed on the enzyme agree with experimental results (Liu et al., J Am Chem Soc 2002, 124, 5175), that is, wild-type [Fe-Fe]-hydrogenase H-cluster is inhibited by oxygen metabolites. An enzyme spherical region …
Dnmt1 Stability Is Regulated By Proteins Coordinating Deubiquitination And Acetylation-Driven Ubiquitination, Zhanwen Du, Jing Song, Yong Wang, Yiqing Zhao, Kishore Guda, Shuming Yang, Hung Ying Kao, Yan Xu, Joseph Willis, Sanford D. Markowitz, David Sedwick, Robert M. Ewing, Zhenghe Wang
Dnmt1 Stability Is Regulated By Proteins Coordinating Deubiquitination And Acetylation-Driven Ubiquitination, Zhanwen Du, Jing Song, Yong Wang, Yiqing Zhao, Kishore Guda, Shuming Yang, Hung Ying Kao, Yan Xu, Joseph Willis, Sanford D. Markowitz, David Sedwick, Robert M. Ewing, Zhenghe Wang
Chemistry Faculty Publications
DNA methyltransferase 1 (DNMT1) is the primary enzyme that maintains DNA methylation. We describe a previously unknown mode of regulation of DNMT1 protein stability through the coordinated action of an array of DNMT1-associated proteins. DNMT1 was destabilized by acetylation by the acetyltransferase Tip60, which triggered ubiquitination by the E3 ligase UHRF1, thereby targeting DNMT1 for proteasomal degradation. In contrast, DNMT1 was stabilized by histone deacetylase 1 (HDAC1) and the deubiquitinase HAUSP (herpes virus–associated ubiquitin-specific protease). Analysis of the abundance of DNMT1 and Tip60, as well as the association between HAUSP and DNMT1, suggested that during the cell cycle the initiation …
Cox-2 Inhibitor Nimesulide Analogs Are Aromatase Suppressors In Breast Cancer Cells, Bin Su, Xiaohan Cai, Yanyan Hong, Shiuan Chen
Cox-2 Inhibitor Nimesulide Analogs Are Aromatase Suppressors In Breast Cancer Cells, Bin Su, Xiaohan Cai, Yanyan Hong, Shiuan Chen
Chemistry Faculty Publications
Cyclooxygenase-2 (COX-2) inhibitor nimesulide derivatives compounds A and B decreased aromatase activity in breast cancer cells via a novel mechanism different to aromatase inhibitors (AIs), and were defined as “aromatase suppressors”. Breast carcinoma cells (MCF-7aro and T47Daro) transfected with aromatase full gene were used to explore the mechanisms of the two compounds. They dose and time-dependently suppressed aromatase activity in MCF-7aro and T47Daro cells in the nanomole range. However, they neither directly inhibited aromatase, nor improved aromatase degradation even at much higher concentrations. They could also suppress androgen stimulated cell growth, but did not affect estrogen enhanced cell proliferation. These …
Residue Mutations In [Fe-Fe]-Hydrogenase Impedes O 2 Binding: A Qm/Mm Investigation, Daniela Dogaru, Stefan Motiu, Valentin Gogonea
Residue Mutations In [Fe-Fe]-Hydrogenase Impedes O 2 Binding: A Qm/Mm Investigation, Daniela Dogaru, Stefan Motiu, Valentin Gogonea
Chemistry Faculty Publications
[Fe-Fe]-hydrogenases are enzymes that reversibly catalyze the reaction of protons and electrons to molecular hydrogen, which occurs in anaerobic media. In living systems, [Fe-Fe]-hydrogenases are mostly used for H(2) production. The [Fe-Fe]-hydrogenase H-cluster is the active site, which contains two iron atoms. The latest theoretical investigations1,2 advocate that the structure of di-iron air inhibited species are either Fe(p) (II)-Fe(d) (II)-O-H(-), or Fe(p) (II)-Fe(d) (II)-O-O-H, thus O(2) has to be prevented from binding to Fe(d) in all di-iron subcluster oxidation states in order to retain a catalytically active enzyme. By performing residue mutations on [Fe-Fe]-hydrogenases, we were able to weaken O(2) …
An Antimicrobial Peptide Regulates Tumor-Associated Macrophage Trafficking Via The Chemokine Receptor Ccr2, A Model For Tumorigenesis, Ge Jin, Hameem I. Kawsar, Stanley A. Hirsch, Chun Zeng, Xun Jia, Zhimin Feng, Santosh K. Ghosh, Qing Yin Zheng, Aimin Zhou, Thomas M. Mcintyre, Aaron Weinberg
An Antimicrobial Peptide Regulates Tumor-Associated Macrophage Trafficking Via The Chemokine Receptor Ccr2, A Model For Tumorigenesis, Ge Jin, Hameem I. Kawsar, Stanley A. Hirsch, Chun Zeng, Xun Jia, Zhimin Feng, Santosh K. Ghosh, Qing Yin Zheng, Aimin Zhou, Thomas M. Mcintyre, Aaron Weinberg
Chemistry Faculty Publications
Background: Tumor-associated macrophages (TAMs) constitute a significant part of infiltrating inflammatory cells that are frequently correlated with progression and poor prognosis of a variety of cancers. Tumor cell-produced human β-defensin-3 (hBD-3) has been associated with TAM trafficking in oral cancer; however, its involvement in tumor-related inflammatory processes remains largely unknown. Methodology: The relationship between hBD-3, monocyte chemoattractant protein-1 (MCP-1), TAMs, and CCR2 was examined using immunofluorescence microscopy in normal and oral carcinoma in situ biopsy specimens. The ability of hBD-3 to chemoattract host macrophages in vivo using a nude mouse model and analysis of hBD-3 on monocytic cell migration in …
Dna Polymerases: Perfect Enzymes For An Imperfect World, Anthony J. Berdis
Dna Polymerases: Perfect Enzymes For An Imperfect World, Anthony J. Berdis
Chemistry Faculty Publications
This Special Thematic Issue explores the molecular properties of DNA polymerases as extraordinary biological catalysts. In this short introductory chapter, I briefly highlight some of the most important concepts from the articles contained within this Special Issue. The contents of this Special Issue are arranged into distinct sub-categories corresponding to mechanistic studies of faithful DNA polymerization, studies of "specialized" DNA polymerases that function on damaged DNA, and DNA polymerases that are of therapeutic importance against various diseases. Emphasis is placed on understanding the dynamic cellular roles and biochemical functions of DNA polymerases, and how their structure and mechanism impact their …
Non-Natural Nucleotides As Probes For The Mechanism And Fidelity Of Dna Polymerases, Irene Lee, Anthony J. Berdis
Non-Natural Nucleotides As Probes For The Mechanism And Fidelity Of Dna Polymerases, Irene Lee, Anthony J. Berdis
Chemistry Faculty Publications
DNA is a remarkable macromolecule that functions primarily as the carrier of the genetic information of organisms ranging from viruses to bacteria to eukaryotes. The ability of DNA polymerases to efficiently and accurately replicate genetic material represents one of the most fundamental yet complex biological processes found in nature. The central dogma of DNA polymerization is that the efficiency and fidelity of this biological process is dependent upon proper hydrogen-bonding interactions between an incoming nucleotide and its templating partner. However, the foundation of this dogma has been recently challenged by the demonstration that DNA polymerases can effectively and, in some …
Terminal Deoxynucleotidyl Transferase: The Story Of A Misguided Dna Polymerase, Edward A. Motea, Anthony J. Berdis
Terminal Deoxynucleotidyl Transferase: The Story Of A Misguided Dna Polymerase, Edward A. Motea, Anthony J. Berdis
Chemistry Faculty Publications
Nearly every DNA polymerase characterized to date exclusively catalyzes the incorporation of mononucleotides into a growing primer using a DNA or RNA template as a guide to direct each incorporation event. There is, however, one unique DNA polymerase designated terminal deoxynucleotidyl transferase that performs DNA synthesis using only single-stranded DNA as the nucleic acid substrate. In this chapter, we review the biological role of this enigmatic DNA polymerase and the biochemical mechanism for its ability to perform DNA synthesis in the absence of a templating strand. We compare and contrast the molecular events for template-independent DNA synthesis catalyzed by terminal …
Nanostructured Poly(3,4-Ethylenedioxythiophene)–Metalloporphyrin Films: Improved Catalytic Detection Of Peroxynitrite, Serban Peteu, Pubudu Peiris, Ermias Gebermichael, Mekki Bayachou
Nanostructured Poly(3,4-Ethylenedioxythiophene)–Metalloporphyrin Films: Improved Catalytic Detection Of Peroxynitrite, Serban Peteu, Pubudu Peiris, Ermias Gebermichael, Mekki Bayachou
Chemistry Faculty Publications
We investigated in this paper the sensing performance of inherently conductive polymer, poly(3,4-ethylenedioxythiophene) (PEDOT), functionalized with hemin (iron protoporphyrin) as an electrocatalytic reporter. The sensing platform is prepared by electrodeposition of a composite film of hemin–PEDOT on a 30-μm diameter carbon fiber electrode (CFE). The polymerized films were characterized by field emission scanning electron microscopy (FESEM), which pointed to nanostructured films with tortuous pores. The electrocatalytic oxidation of peroxynitrite was characterized by cyclic voltammetry as well as other electrochemical methods. The catalytic current is proportional to the analyte's concentration. Optimized hemin–PEDOT modified CFEs were utilized for the first time to …
Selective Regulation Of Aromatase Expression For Drug Discovery, Robert W. Brueggemeier, Bin Su, Michael V. Darby, Yasuro Sugimoto
Selective Regulation Of Aromatase Expression For Drug Discovery, Robert W. Brueggemeier, Bin Su, Michael V. Darby, Yasuro Sugimoto
Chemistry Faculty Publications
Aromatase is a particularly attractive drug target in the treatment of hormone-responsive breast cancer, and aromatase activity in breast cancer patients is greater in or near the tumor tissue compared with the normal breast tissue. Complex regulation of aromatase expression in human tissues involves alternative promoter sites that provide tissue-specific control. Previous studies in our laboratories suggested a strong association between aromatase (CYP19) gene expression and the expression of cyclooxygenase (COX) genes. Additionally, COX selective inhibitors can suppress CYP19 gene expression and decrease aromatase activity. Our current hypothesis is that pharmacological regulation of aromatase can act locally to decrease the …
Homozygous Frameshift Mutation In Tmco1 Causes A Syndrome With Craniofacial Dysmorphism, Skeletal Anomalies, And Mental Retardation, Baozhong Xin, Erik G. Puffenberger, Susan Turben, Haiyan Tan, Aimin Zhou, Heng Wang
Homozygous Frameshift Mutation In Tmco1 Causes A Syndrome With Craniofacial Dysmorphism, Skeletal Anomalies, And Mental Retardation, Baozhong Xin, Erik G. Puffenberger, Susan Turben, Haiyan Tan, Aimin Zhou, Heng Wang
Chemistry Faculty Publications
We identified an autosomal recessive condition in 11 individuals in the Old Order Amish of northeastern Ohio. The syndrome was characterized by distinctive craniofacial dysmorphism, skeletal anomalies, and mental retardation. The typical craniofacial dysmorphism included brachycephaly, highly arched bushy eyebrows, synophrys, long eyelashes, low-set ears, microdontism of primary teeth, and generalized gingival hyperplasia, whereas Sprengel deformity of scapula, fusion of spine, rib abnormities, pectus excavatum, and pes planus represented skeletal anomalies. The genome-wide homozygosity mapping using six affected individuals localized the disease gene to a 3.3-Mb region on chromosome 1q23.3-q24.1. Candidate gene sequencing identified a homozygous frameshift mutation, c.139_140delAG, in …
Targeting Base Excision Repair Suggests A New Therapeutic Strategy Of Fludarabine For The Treatment Of Chronic Lymphocytic Leukemia, A. D. Bulgar, M. Snell, J. R. Donze, E. B. Kirkland, Lan Li, Shuming Yang, Yan Xu, S. L. Gerson, Lili Liu
Targeting Base Excision Repair Suggests A New Therapeutic Strategy Of Fludarabine For The Treatment Of Chronic Lymphocytic Leukemia, A. D. Bulgar, M. Snell, J. R. Donze, E. B. Kirkland, Lan Li, Shuming Yang, Yan Xu, S. L. Gerson, Lili Liu
Chemistry Faculty Publications
No abstract provided.
Design, Synthesis And Characterization Of Oriented Glyco-Affinity Macroligands For Glyco-Capturing, Glycomics And Glycoproteomics Applications, Srinivas Chalagalla
Design, Synthesis And Characterization Of Oriented Glyco-Affinity Macroligands For Glyco-Capturing, Glycomics And Glycoproteomics Applications, Srinivas Chalagalla
ETD Archive
Cell surface carbohydrates existing as parts of glycoproteins, glycolipids, and other conjugates present the first information about cell to the outside world and are intimately involved in various biological events such as intercellular communication, and molecular and cellular targeting. However, mechanisms of most processes at the molecular level are still unclear. Therefore, it is very important to develop carbohydrate-specific binding molecules for rapid, efficient, sensitive purification and accurate analysis of complex carbohydrate structures as well as their functions. Furthermore, carbohydrate-specific binding molecules can be expected to be used in medical diagnostic applications for carbohydrate biomarkers. In this thesis study, oriented …
Dna Mutation/Methylation Screening Method For Colon Cancer Screening, Wei Meng
Dna Mutation/Methylation Screening Method For Colon Cancer Screening, Wei Meng
ETD Archive
Cancer is a result of unregulated cell growth. For all types of cancer currently studied, the transition from a healthy cell to a malignant tumor cell is a step-by-step process which requires mutation in at least several oncogenes and tumor suppressor genes together. Another cancer early event is DNA methylation. Cancer-related DNA methylation focuses on promoter hypermethylation of the certain genes. The DNA mutation and methylation profile can serve as biomarkers for diagnosing early stage of cancer. Colorectal cancer is the third most common cancer type in the United States and has been well studied. The essential mechanism of cancer …
Molecular Basis Of The Role Of Kindlin 2 In Cell Adhesion, Hettiarachchige Dhanuja Deepamalee Perera
Molecular Basis Of The Role Of Kindlin 2 In Cell Adhesion, Hettiarachchige Dhanuja Deepamalee Perera
ETD Archive
Kindlins are a novel family of cytoskeleton proteins that plays an important role in the activation of heterodimeric integrin transmembrane receptors. These receptors play a vital role in cell adhesion, cell migration and other cellular processes. The Kindlin protein family consists of three homologous proteins, Kindlin 1, 2 and 3 with differential tissue distribution and varying expression levels in human. Mutations of Kindlin 1 protein are clinically linked to Kindler Syndrome. Kindlin 2 knockdown studies have shown embryonic lethality in mouse, but no diseases have been clinically testified. Kindlin 3 mutations are associated with bleeding disorders, e.g. LADIII. Talin is …
Human Prostate Cancer Cell Apoptosis Induced By Interferon-Y And Double-Stranded Rna And Studies On The Biological Roles Of Transmembrane And Coiled-Coil Domains 1, Haiyan Tan
ETD Archive
No abstract provided.
Study Of Drug Delivery Behavior Through Biomembranes Using Thermal And Bioanalytical Techniques, Hareesha Reddy Venumuddala
Study Of Drug Delivery Behavior Through Biomembranes Using Thermal And Bioanalytical Techniques, Hareesha Reddy Venumuddala
ETD Archive
This Master of Science thesis encompasses two projects in chemical pharmaceuticals. The first is a study of excipients and the added new information collected beyond Thermal Gravimetric Analysis and Differential Scanning Calorimetry from Dielectric Analysis. These new properties enhance our global knowledge of excipients by thermal analytical methods. Excipients, the inactive ingredients in formulated drugs, aid different functions of the active pharmacy ingredient, the drugs. Low temperature transitions, by DEA including melting of frozen solvents, e.g. water, are more definitive than observed by low temperature DSC. Millions of dollars are expended annually on pharmaceutical testing to qualify excipients for fully …
Disintegration Of Tablets And Capsules Measured By Isothermal Thermal Mechanical Analysis And Macrophotography, Visweswararao Badipatla
Disintegration Of Tablets And Capsules Measured By Isothermal Thermal Mechanical Analysis And Macrophotography, Visweswararao Badipatla
ETD Archive
The current United States Pharmacopoeia (USP) test for tablet and encapsulated drug disintegration does not specify the initial disintegration time and provides limited information on the disintegration process itself. An isothermal Thermal Mechanical Analysis (IsoTMA) method is presented to measure the rate and initial time of drug disintegration, that is, the mechanical collapse of the gelatin capsule or the solid tablet. This method monitors changes in the dimensions of the formulated drugs during their disintegration in a liquid. Dimensional changes can be followed as a function of time, temperature, applied stress and pH. Some of the drugs studied were Olanzapine®, …