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Molecular Biosciences: Recent submissions
Now showing items 221-240 of 887
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A Flow Cytometric Assay for the Study of E3 Ubiquitin Ligase Activityb
(Wiley, 2009-07)BACKGROUND: Current methods for monitoring E3 ubiquitin ligase activity in cell culture or in vivo are limited. As a result, the degradation of cellular targets by many E3 ubiquitin ligases in live cells has not yet been ... -
Protein Structure Prediction: Is It Useful?
(Elsevier, 2009-04)Computationally predicted three-dimensional structure of protein molecules has demonstrated the usefulness in many areas of biomedicine, ranging from approximate family assignments to precise drug screening. For nearly 40 ... -
Low-resolution structural modeling of protein interactome
(Elsevier, 2013-04)Structural characterization of protein–protein interactions across the broad spectrum of scales is key to our understanding of life at the molecular level. Low-resolution approach to protein interactions is needed for ... -
Computational Design of Affinity and Specificity at Protein-Protein Interfaces
(Elsevier, 2009-08)The computer-based design of protein-protein interactions is a rigorous test of our understanding of molecular recognition and an attractive approach for creating novel tools for cell and molecular research. Considerable ... -
Elimination of T cell reactivity to pancreatic β cells and partial preservation of β cell activity by peptide blockade of LFA-1:ICAM-1 interaction in the NOD mouse model
(Elsevier, 2013-08)In insulin dependent diabetes mellitus (T1D), self-reactive T cells infiltrate pancreatic islets and induce beta cell destruction and dysregulation of blood glucose. A goal is to control only the self-reactive T cells, ... -
The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation
(American Chemical Society, 2013-12-18)The ability to selectively activate function of particular proteins via pharmacological agents is a longstanding goal in chemical biology. Recently, we reported an approach for designing a de novo allosteric effector site ... -
Novel Pyrrolopyrimidine-Based α-Helix Mimetics: Cell- Permeable Inhibitors of Protein-Protein Interactions
(American Chemical Society, 2011-02-02)There is considerable interest in developing nonpeptidic, small molecule α-helix mimetics to disrupt α-helix-mediated protein-protein interactions. Herein, we report the design of a novel pyrrolopyrimidine-based scaffold ... -
Illuminating the diversity of aromantic polyketide synthases in Aspergillus nidulans
(American Chemical Society, 2012-05-16)Genome sequencing has revealed that fungi have the ability to synthesize many more natural products (NPs) than are currently known, but methods for obtaining suitable expression of NPs have been inadequate. We have developed ... -
Genome-Based Deletion Analysis Reveals the Prenyl Xanthone Biosynthesis Pathway in Aspergillus nidulans
(American Chemical Society, 2011-03-23)Xanthones are a class of molecules that bind to a number of drug targets and possess a myriad of biological properties. An understanding of xanthone biosynthesis at the genetic level should facilitate engineering of ... -
Entropic and enthalpic components of catalysis in the mutase and lyase activities of Pseudomonas aeruginosa PchB
(American Chemical Society, 2011-05-11)The isochorismate-pyruvate lyase from Pseudomonas aeruginosa (PchB) catalyzes two pericyclic reactions, demonstrating the eponymous activity and also chorismate mutase activity. The thermodynamic parameters for these ... -
An Efficient System for Heterologous Expression of Secondary Metabolite Genes in Aspergillus nidulans
(American Chemical Society, 2013-05-22)Fungal secondary metabolites (SMs) are an important source of medically valuable compounds. Genome projects have revealed that fungi have many SM biosynthetic gene clusters that are not normally expressed. To access these ... -
3-Substituted biquinolinium inhibitors of AraC family transcriptional activator VirF from S. flexneri obtained through in situ chemical ionization of 3,4-disubstituted dihydroquinolines
(Royal Society of Chemistry, 2014-08-18)During a structure–activity relationship optimization campaign to develop an inhibitor of AraC family transcriptional activators, we discovered an unexpected transformation of a previously reported inhibitor that occurs ... -
Role of a cdk5-associated protein, p35, in herpes simplex virus type 1 replication in vivo
(Springer Verlag, 2013-10)Previous studies have shown that herpes simplex virus type 1 (HSV-1) replication is inhibited by the cyclin-dependent kinase (cdk) inhibitor roscovitine. One roscovitine-sensitive cdk that functions in neurons is cdk5, ... -
Web Interface for Brownian Dynamics Simulation of Ion Transport and Its Application to Beta-Barrel Pores
(Wiley, 2012-01-20)Brownian dynamics (BD) in a suitably constructed potential of mean force is an efficient and accurate method for simulating ion transport through wide ion channels. Here, a web-based graphical user interface (GUI) is ... -
Glycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteins
(Wiley, 2011-11-15)Understanding how glycosylation affects protein structure, dynamics, and function is an emerging and challenging problem in biology. As a first step toward glycan modeling in the context of structural glycobiology, we have ... -
CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations
(Wiley, 2014-10-15)CHARMM-GUI Membrane Builder, http://www.charmm-gui.org/input/membrane, is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems for molecular dynamics simulation ... -
Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly
(American Chemical Society, 2013)The method of window exchange umbrella sampling molecular dynamics (WEUSMD) with a pre-optimized parameter set was recently used to obtain the most probable conformations and the energetics of transmembrane (TM) helix ... -
Quantification of Drive-Response Relationships Between Residues During Protein Folding
(American Chemical Society, 2013-08-13)Mutual correlation and cooperativity are commonly used to describe residue-residue interactions in protein folding/function. However, these metrics do not provide any information on the causality relationships between ... -
The structural properties of non-traditional drug targets present new challenges for virtual screening
(American Chemical Society, 2013-08-26)Traditional drug targets have historically included signaling proteins that respond to small-molecules and enzymes that use small-molecules as substrates. Increasing attention is now being directed towards other types of ... -
Ligand Binding Site Detection b Local Structure Alignment and Its Performance Complementarity
(American Chemical Society, 2013-09-23)Accurate determination of potential ligand binding sites (BS) is a key step for protein function characterization and structure-based drug design. Despite promising results of template-based BS prediction methods using ...