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Molecular Biosciences: Recent submissions
Now showing items 241-260 of 887
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Identification of Ligand Templates using Local Structure Alignment for Structure-based Drug Design
(American Chemical Society, 2012-10-22)With a rapid increase in the number of high-resolution protein-ligand structures, the known protein-ligand structures can be used to gain insight into ligand-binding modes in a target protein. Based on the fact that the ... -
CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application
(American Chemical Society, 2013-01-28)Advanced free energy perturbation molecular dynamics (FEP/MD) simulation methods are available to accurately calculate absolute binding free energies of protein-ligand complexes. However, these methods rely on several ... -
Application of Binding Free Energy Calculations to Prediction of Binding Modes and Affinities of MDM2 and MDMX Inhibitors
(American Chemical Society, 2012-01-23)Molecular docking is widely used to obtain binding modes and binding affinities of a molecule to a given target protein. Despite considerable efforts, however, prediction of both properties by docking remains challenging ... -
Inhibition and Allosteric Signaling of Transcription Activation by Bacterial AraC Family Activator Proteins
(University of Kansas, 2016-12-31)AraC family transcriptional activators are defined by a 100-amino acid DNA-binding domain (DBD) containing two DNA binding helix-turn-helix (HTH) motifs. My research focused on three AraC family proteins: RhaR (activator ... -
Gene Expression and Introgression of Two Genes Implicated in Behavioral Reproductive Isolation between Drosophila simulans and D. sechellia
(University of Kansas, 2016-12-31)Reproductive isolation maintains species barriers and can cause population divergence. Pre-mating isolation prevents courtship between species and can be caused by changes in gene expression resulting in sex- and ... -
Atomic accuracy in predicting and designing non-canonical RNA structure
(Nature Publishing Group, 2010-02-28)We present a Rosetta full-atom framework for predicting and designing the non-canonical motifs that define RNA tertiary structure, called FARFAR (Fragment Assembly of RNA with Full Atom Refinement). For a test set of ... -
A knock-in mouse model reveals roles for nuclear Apc in cell proliferation, Wnt signal inhibition and tumor suppression
(Nature Publishing Group, 2011-09-26)Mutation of the tumor suppressor adenomatous polyposis coli (APC) is considered an initiating step in the genesis of the vast majority of colorectal cancers. APC inhibits the Wnt signaling pathway by targeting proto-oncogene ... -
Understanding phenotypic variation in rodent models with germline Apc mutations
(AACR, 2013-04-15)Adenomatous Polyposis Coli (APC) is best known for its crucial role in colorectal cancer suppression. Rodent models with various Apc mutations have enabled experimental validation of different Apc functions in tumors and ... -
Expanding the results of a high throughput screen against an isochorismate-pyruvate lyase to enzymes of a similar scaffold or mechanism
(Elsevier, 2014-11-01)Antibiotic resistance is a growing health concern, and new avenues of antimicrobial drug design are being actively sought. One suggested pathway to be targeted for inhibitor design is that of iron scavenging through ... -
A PEG-Fmoc conjugate as a nanocarrier for paclitaxel
(Elsevier, 2014-08)We report here that a simple, well-defined, and easy-to-scale up nanocarrier, PEG5000-lysyl-(α-Fmoc-ε-t-Boc-lysine)2 conjugate (PEG-Fmoc), provides high loading capacity, excellent formulation stability and low systemic ... -
MicroRNA100 Inhibits Self-Renewal of Breast Cancer Stem–like Cells and Breast Tumor Development
(American Association for Cancer Research, 2014-11-15)miRNAs are essential for self-renewal and differentiation of normal and malignant stem cells by regulating the expression of key stem cell regulatory genes. Here, we report evidence implicating the miR100 in self-renewal ... -
Structural and Electrostatic Characterization of Pariacoto Virus: Implications for Viral Asembly
(Wiley, 2009-07)We present the first all-atom model for the structure of a T=3 virus, pariacoto virus (PaV), which is a non-enveloped, icosahedral RNA virus and a member of the Nodaviridae family. The model is an extension of the crystal ... -
Differentiating between models of Epothilone binding to microtubules using tubulin mutagenesis, cytotoxicity, and molecular modeling
(Wiley, 2012-09)Microtubule stabilizers are powerful anti-mitotic compounds and represent a proven cancer treatment strategy. Several classes of compounds in clinical use or trials, such as the taxanes and epothilones, bind to the same ... -
A high-throughput screen for chemical inhibitors of exocytic transport in yeast
(Wiley, 2010-06-14)Most of the components of the membrane and protein traffic machinery were discovered by perturbing their functions, either with bioactive compounds or by mutations. However, the mechanisms responsible for exocytic transport ... -
Structural templates for comparative protein docking
(Wiley, 2015-09)Structural characterization of protein-protein interactions is important for understanding life processes. Because of the inherent limitations of experimental techniques, such characterization requires computational ... -
HSV-1 ICP0-MEDIATED IMPAIRMENT OF HOST INTRINSIC AND INNATE IMMUNE FACTORS
(University of Kansas, 2014-08-31)Understanding mechanisms viruses use to evade the immune system and to persist within its host, is of crucial relevance in controlling, preventing and treating HSV-1-associated diseases. As reviewed in this dissertation, ... -
Computational approaches to identify small-molecule inhibitors of non-traditional drug targets
(University of Kansas, 2015-08-31)Non-traditional targets for therapeutic intervention are those proteins that have not evolved to bind small molecules, but have instead evolved to bind other macromolecules. Such targets include protein–protein interaction ... -
Mining Evolutionary Data to Reveal the Layered Architecture of Protein Function
(University of Kansas, 2014-08-31)Revolutionary advances in sequencing technology have dramatically expanded the set of known, naturally-occurring protein sequences. Protein sequences arise from an evolutionary process and during evolution proteins experience ... -
Cytoplasmic vs. Nuclear RNAi in Caenorhabditis elegans
(University of Kansas, 2014-08-31)ABSTRACT Experimentally and/or intrinsically delivered dsRNAs can trigger complex set of mechanisms, acting in multiple cell compartments and tissues throughout developmental time. Several methods are available for effective ... -
Crosstalk, Network Dynamics, and the Evolution of Signaling
(University of Kansas, 2014-12-31)Cells have developed networks of interacting proteins to process information about their environment and respond appropriately to stimuli. Reversible post-translational modifications alter the functionality of these proteins, ...