ABSTRACT
Double- and triple-resonance heteronuclear NMR spectroscopy have been used to determine the high-resolution solution structure of the minimal B-Myb DNA-binding domain (B-MybR2R3) and to characterize the specific complex formed with a synthetic DNA fragment corresponding to the Myb target site on the Myb-regulated gene tom-1. B-MybR2R3 is shown to consist of two independent protein domains (R2 and R3) joined by a short linker, which have strikingly different tertiary structures despite significant sequence similarities. In addition, the C-terminal region of B-Myb R2 is confirmed to have a poorly defined structure, reflecting the existence of multiple conformations in slow to intermediate exchange. This contrasts with the tertiary structure reported for c-MybR2R3, in which both R2 and R3 have the same fold and the C-terminal region of R2 forms a stable, well-defined helix [Ogata, K., et al. (1995) Nat. Struct. Biol. 2, 309-320]. The NMR data suggest there are extensive contacts between B-MybR2R3 and its DNA target site in the complex and are consistent with a significant conformational change in the protein on binding to DNA, with one possibility being the formation of a stable helix in the C-terminal region of R2. In addition, conformational heterogeneity identified in R2 of B-MybR2R3 bound to the tom-1-A target site may play an important role in the control of gene expression by Myb proteins.
Subject(s)
Cell Cycle Proteins , DNA-Binding Proteins/chemistry , DNA/metabolism , Gene Expression Regulation , Protein Structure, Tertiary , Transcription Factors/chemistry , Animals , Binding Sites , Crystallography, X-Ray , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Macromolecular Substances , Models, Molecular , Nuclear Magnetic Resonance, Biomolecular , Oncogenes , Protein Binding , Protein Conformation , Proto-Oncogene Proteins/chemistry , Proto-Oncogene Proteins/metabolism , Proto-Oncogene Proteins c-myb , Sequence Homology, Amino Acid , Solutions , Trans-Activators/chemistry , Trans-Activators/metabolism , Transcription Factors/genetics , Transcription Factors/metabolismABSTRACT
A range of double and triple resonance heteronuclear NMR has been used to obtain nearly complete sequence-specific 15N, 13C and 1H resonance assignments for a 110-residue protein corresponding to the B-Myb DNA-binding domain (B-MybR2R3) and to determine its secondary structure in solution. The protein was found to contain two stable helices in repeat-2 (R2) and three in repeat-3 (R3), involving residues K12-K24 (R2-1), W30-H36 (R2-2), E64-V76 (R3-1), W81-L87 (R3-2) and D93-K105 (R3-3). In addition, the chemical shift and nuclear Overhauser effect data suggest that amino acids Q44-W49 near the C-terminus of R2 form an unstable or nascent helix, which could be stabilised on binding to a specific DNA target site. The two N-terminal helices in R2 and R3 occupy essentially identical positions in the two domains, consistent with the high level of sequence similarity between these regions. In contrast, the C-terminal region forming the third helix in R3 shows low sequence similarity with R2, accounting for the differences in secondary structure. In the case of B-MybR2R3, there is a clear chemical shift and line-broadening evidence for the existence of multiple conformations in the C-terminal region of R2, which is believed to form one half of the DNA-binding site. We propose that conformational instability of part of the DNA-binding motif is a way of increasing the specificity of Myb proteins for a relatively short (6-bp) DNA target site by reducing their affinity for non-specific DNA sequences compared to specific sites.
Subject(s)
Cell Cycle Proteins , DNA-Binding Proteins/chemistry , Transcription Factors/chemistry , Amino Acid Sequence , DNA/metabolism , DNA-Binding Proteins/metabolism , Magnetic Resonance Spectroscopy , Molecular Sequence Data , Protein Structure, Secondary , Proto-Oncogene Proteins/chemistry , Proto-Oncogene Proteins/metabolism , Proto-Oncogene Proteins c-myb , Sequence Homology, Amino Acid , Solutions , Trans-Activators/chemistry , Trans-Activators/metabolism , Transcription Factors/metabolismABSTRACT
The conformational analysis of three cyclic hexapeptides is presented. Cyclo-(-Gln6-Trp7-Phe8-Gly9-Leu10-D-Met11-) (1) and cyclo-(-Gln6-Trp7-Phe8-Gly9-Leu10-Met11-) (2) are NK-2 antagonists in the hamster trachea assay, whereas cyclo-(-Gln6-Trp7-Phe8-(R)-Gly9-[ANC-2]Leu10-Met11+ ++-) (3), where Gly9[ANC-2]Leu10 represents (2S)-2-((3R)-3-amino-2-oxo-1-pyrrolidinyl)-4-methylpentanoyl, is inactive as agonist and antagonist in this assay. In DMSO, the NMR results cannot be interpreted as being consistent with a single conformation. However, the combined interpretation of results from NMR spectroscopy, restrained molecular dynamics simulations with application of proton-proton distance information from ROESY spectra, and pharmacological results leads to a reduced number of conformational domains for each peptide, which can be compared with each other and may be classified as responsible for their biological activity. Trying to match the conformational domains approximately with regular beta- and gamma-turns, we find a gamma n-turn at the position of the methionine occurring in all peptides. For the active peptides 1 and 2 we arrive at an inverse gamma i-turn at Phe8, and beta I'- or beta II-turns with Gly9 and Leu10 at the corner positions, these beta-turns having a similar topology with respect to the linking peptide unit. Other conformational domains common to only 1 and 2 support their classification as responsible for the biological activity.
