ABSTRACT
A series of transition-state analog inhibitors of the D-glutamic acid-adding enzyme (MurD) of bacterial peptidoglycan biosynthesis has been synthesized and evaluated for inhibition of the E. coli enzyme.
Subject(s)
Cell Wall/enzymology , Escherichia coli/enzymology , Peptide Synthases/antagonists & inhibitors , Molecular Structure , Organophosphorus Compounds/chemistry , Peptide Synthases/chemistryABSTRACT
By selective attachment of a DNA cleavage agent to specific residues in the yeast TATA box binding protein (yTBP), we demonstrate that, in solution, yTBP binds to the TATA boxes of both the adenovirus major late promoter and the yeast CYC1 promoter with only a modest preference in orientation and binds well to several overlapping binding sites. The general factors TFIIA and TFIIB each increase the rotational and translational selectivity of yTBP but are not sufficient, at least individually, to confer a unique polarity to the preinitiation complex. We conclude that TBP alone cannot define the productive orientation of general factor assembly on a promoter.
Subject(s)
DNA-Binding Proteins/metabolism , TATA Box , Transcription Factors/metabolism , Adenoviridae/genetics , Alkylation , Base Sequence , Binding Sites/genetics , DNA, Fungal/chemistry , DNA, Fungal/genetics , DNA, Fungal/metabolism , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/genetics , Models, Molecular , Molecular Sequence Data , Nucleic Acid Conformation , Promoter Regions, Genetic , Protein Binding , Protein Conformation , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , TATA-Box Binding Protein , Transcription Factors/chemistry , Transcription Factors/geneticsABSTRACT
At least three hundred million people worldwide are infected with the hepatitis B virus (HBV), and epidemiological studies show a clear correlation between chronic HBV infection and the development of hepatocellular carcinoma. HBV encodes a protein, pX, which abducts the cellular transcriptional machinery in several ways including direct interactions with bZIP transcription factors. These interactions increase the DNA affinities of target bZIP proteins in a DNA sequence-dependent manner. Here we use a series of bZIP peptide models to explore the mechanism by which pX interacts with bZIP proteins. Our results suggest that pX increases bZIP.DNA stability by increasing the stability of the bZIP dimer as well as the affinity of the dimer for DNA. Additional experiments provide evidence for a mechanism in which pX recognizes the composite structure of the peptide.DNA complex, not simply the primary peptide sequence. These experiments provide a framework for understanding how pX alters the patterns of transcription within the nucleus. The similarities between the mechanism proposed for pX and the mechanism previously proposed for the human T-cell leukemia virus protein Tax are discussed.
