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Thomas Kodadek

Publications and source records attributed to Thomas Kodadek.

43 records · Page 3Linked to original sources
PubMed2002

Recruitment of a 19S proteasome subcomplex to an activated promoter.

The 19S proteasome regulatory particle plays a critical role in cellular proteolysis. However, recent reports have demonstrated that 19S proteins play a nonproteolytic role in nucleotide excision repair and transcription elongation. We show by chromatin immunoprecipitation assays that proteins comprising the 19S complex are recruited to the GAL1-10 promoter by the Gal4 transactivator upon induction with galactose. This recruited complex does not contain proteins from the 20S proteolytic particle and includes a subset of the 19S proteins. This subset is also specifically retained from an extract by the Gal4 activation domain. These data indicate that in vivo, the base of the 19S complex functions independently of the larger complex and plays a direct, nonproteolytic role in RNA polymerase II transcription.

Adenosine Triphosphatases↗
PubMed2002

Magnetic resonance imaging detects a specific peptide-protein binding event.

DOTA was conjugated to the N-terminus of a 12-mer peptide by using standard peptide synthesis chemistry. The peptide, first isolated by phage display, maintained a high affinity for its protein-binding target, Gal-80, even with GdDOTA attached. The high affinity constant (KA = 5 x 105 M-1) combined with the high relaxivity of the resulting GdDOTA-peptide.protein complex (r1bound = 44.8 +/- 1.7 mM-1 s-1) allowed detection of Gal-80 at muM levels using a standard magnetic resonance imaging protocol. This novel peptide-based, binding-activated MRI method could potentially be used to screen a wide variety of biomolecules.

Amino Acid Sequence↗
PubMed2002

Toward synthetic transcription activators: recruitment of transcription factors to DNA by a PNA-peptide chimera.

A PNA-peptide chimera designed to mimic the biochemical function of transcription activators has been synthesized and characterized. The bis-PNA segment binds specifically to a DNA site while the 20-residue peptide is capable of binding to the transcription factors Gal11 and Gal80. The PNA-peptide chimera thus mimics one of the central functions of a native transcription activator, recruitment of transcription factors to a specific DNA site.

DNA↗
PubMed2002

Inhibition of proteolysis and other posttranslational modifications with substrate-targeted inhibitors.

This article reviews the concept of developing protease inhibitors that target the substrate polypeptide rather than the enzyme. Substrate-targeted inhibitors have the potential to be more specific than even the most highly selective enzyme-targeted inhibitors because essentially all proteases process multiple substrates. The challenge in developing substrate-targeted protease inhibitors centers on the development of high-affinity binding agents for short stretches of amino acids (linear epitopes). Recent experimental progress toward this goal and a number of other potential solutions are discussed.

Binding Sites↗
PubMed2002

Development of protein-detecting microarrays and related devices.

There is great interest in the development of devices capable of monitoring the levels and post-translational modification states of hundreds or thousands of proteins simultaneously. One way to do this would be to create protein-detecting microarrays roughly akin to the DNA microarrays that are used for genome-wide expression studies. Two major challenges must be addressed before practical devices of this type become available. One is the development of high-throughput methods for the isolation of protein-binding compounds that will act as capture molecules in the array. The second is the optimization of methods that register binding of target proteins to the immobilized ligands in a sensitive and quantitative fashion. Progress in these areas, and some of the challenges remaining, are reviewed in this article.

Antibodies↗
PubMedDate not supplied

Toward a general chemical method for rapidly mapping multi-protein complexes.

Ru(II)(bpy2)32+Cl2, ammonium persulfate, and visible light irradiation has been shown to rapidly and efficiently cross-link several interacting proteins. However, this methodology has not yet been used to map the architecture of large multi-protein complexes. In this study, this chemistry is applied to the crystallographically characterized yeast proteasome. The data obtained demonstrate both the method's increased generality and fidelity in comparison to traditional bifunctional cross-linking reagents, while also highlighting the future need for developing better analytical techniques to separate cross-linked products.

Cross-Linking Reagents↗