TFIIA-TAF regulatory interplay: NMR evidence for overlapping binding sites on TBP.

TATA box binding protein (TBP)-promoter interaction nucleates assembly of the RNA polymerase II transcription initiation complex. Transcription factor IIA (TFIIA) stabilizes the TBP-promoter complex whereas the N-terminal domain of the largest TAF(II) inhibits TBP-promoter interaction. We have mapped the interaction sites on TBP of Drosophila TAF(II)230 and yeast TFIIA (comprising two subunits, TOA1 and TOA2), using nuclear magnetic resonance (NMR), and also report structural evidence that subdomain II of the TAF(II)230 N-terminal inhibitory domain and TFIIA have overlapping binding sites on the convex surface of TBP. Together with previous mutational and biochemical data, our NMR results indicate that subdomain II augments subdomain I-mediated inhibition of TBP function by blocking TBP-TFIIA interaction.

The influence of a scalar-coupled deuterium upon the relaxaton of a 15N Nucleus and its possible exploitation as a probe for side-chain interactions in proteins.

The magnitude of the quadrupole coupling constant (e2Qq/h) of a deuteron is a good probe for hydrogen bonding. In protein structures, hydrogen-bonding interactions between side chains, between side chaings and ligands, and between side chains and solvent are frequently found. An experiment that detects, via scalar coupling, the influence of a deuteron on the 15N nucleus of asparagine or glutamine side chains is presented. The experiment depends upon the resolution of the 1 delta 15 N(D) isotope shifts that allow the various isotopomers and isotopologues to be distinguished when 15N-labeled samples are dissolved in solvent mixtures of H2O/D2O. 15N lineshapes with theoretical simulations that provide estimates for the 2H quadrupole coupling constants are presented. The influence of 15N-2H dipolar-quadrupole cross correlation and the resulting small frequency shifts in the 15N multiplet are resolved in some of the spectra. The experimental data are provided using the free amino acids asparagine and glutamine for which the side chains were isotopically enriched in 15N and the recombinant pair of modules, fibronectin type 1 and epidermal growth factor, (F1-G) of tissue plasminogen activator, which were uniformly isotopically enriched in 15N.

Calexcitin B is a new member of the sarcoplasmic calcium-binding protein family.

Calexcitin (CE) is a calcium sensor protein that has been implicated in associative learning. The CE gene was previously cloned from the long-finned squid, Loligo pealei, and the gene product was shown to bind GTP and modulate K(+) channels and ryanodine receptors in a Ca(2+)-dependent manner. We cloned a new gene from L. pealei, which encodes a CE-like protein, here named calexcitin B (CE(B)). CE(B) has 95% amino acid identity to the original form. Our sequence analyses indicate that CEs are homologous to the sarcoplasmic calcium-binding protein subfamily of the EF-hand superfamily. Far and near UV circular dichroism and nuclear magnetic resonance studies demonstrate that CE(B) binds Ca(2+) and undergoes a conformational change. CE(B) is phosphorylated by protein kinase C, but not by casein kinase II. CE(B) does not bind GTP. Western blot experiments using polyclonal antibodies generated against CE(B) showed that CE(B) is expressed in the L. pealei optic lobe. Taken together, the neuronal protein CE represents the first example of a Ca(2+) sensor in the sarcoplasmic calcium-binding protein family.

Assignment of disulphide bonds in the X protein (HBx) of hepatitis B virus.

We have established the disulphide arrangement of cysteines in E. coli expressed HBx by chromatographic analysis of enzymatically cleaved protein and sequence analysis of cysteine containing fragments. Eight of the nine cysteines are disulphide linked in an interesting pattern. Each cysteine is linked to the fourth cysteine in a sequential manner and the last cysteine is free; the disulphide linkages are between Cys7 and Cys78, Cys17 and Cys115, Cys61 and Cys137, Cys69 and Cys143 while Cys148 is free.

Synthesis, and crystal and molecular structure of the 3(10)-helical alpha,beta-dehydro pentapeptide Boc-Leu-Phe-Ala-delta Phe-Leu-OMe.

alpha,beta-Dehydro amino acid residues are known to constrain the peptide backbone to the beta-bend conformation. A pentapeptide containing only one alpha,beta-dehydrophenylalanine (delta Phe) residue has been synthesized and crystallized, and its solid state conformation has been determined. The pentapeptide Boc-Leu-Phe-Ala-delta Phe-Leu-OMe (C39H55N5O8, Mw = 721.9) was crystallized from aqueous methanol. Monoclinic space group was P2(1), a = 10.290(2) degrees, b = 17.149(2) degrees, c = 12.179(2) A, beta = 96.64(1) degrees with two molecules in the unit cell. The x-ray (MoK alpha, lambda = 0.7107A) intensity data were collected using a CAD4 diffractometer. The crystal structure was determined by direct methods and refined using least-squares technique. R = 4.4% and Rw = 5.4% for 4403 reflections having magnitude of F0 > or = 3 sigma(magnitude of F0). All the peptide links are trans and the pentapeptide molecule assumes 3(10)-helical conformation. The mean phi,psi values, averaged over the first four residues, are -64.4 degrees, -22.4 degrees respectively. There are three 4-->1 intramolecular hydrogen bonds, characteristic of 3(10)-helix. In the crystal, the peptide helices interact through two head-to-tail, N-H-O intermolecular hydrogen bonds. The peptide molecules related by 2(1) screw symmetry form a skewed assembly of helices.

Quantitative evaluation of stigma polymorphism in a tristylous weed, Lythrum salicaria (Lythraceae).

Tristyly involves three different forms of flowers that differ reciprocally in the heights of stigmas and anthers within flowers. Apart from the style and stamen lengths, heterostylous species also demonstrate pollen and stigma polymorphisms. We quantified stigma polymorphism in tristylous Lythrum salicaria by measuring the stigma diameters, structure of papillae, and density and distribution of papillae on the stigma from flower samples of 201 individuals belonging to three morphs. The diameter of the stigma and the distribution of papillae were quantified using a scanning electron microscope, and the structure of papillae was determined using a light microscope. The stigma diameter in the long morph was significantly greater than in the mid and short morphs. While the density of stigmatic papillae was significantly greater in the mid and short morphs than in the long morph, the total number of papillae per stigma did not differ across morphs. The length and diameter of papillae at the apex, neck, and base were significantly greater in the long morph followed by the mid and short morphs. A discriminant function analysis separated the long morph from the mid and short morphs based on the canonical scores of measurements of papillae structure. The stigma polymorphism coupled with those of pollen may play a functional role in self-incompatibility mechanisms.

Some NMR experiments and a structure determination employing a [15N,2H] enriched protein.

We present the results of studies of an aqueous sample of a highly [15N,2H] enriched protein, the SH3 domain from Fyn. Measurements of 1H relaxation and interactions between H2O solvent and exchangeable protons are given, as well as a method for increasing the effective longitudinal relaxation of solvent exchangeable proton resonances. The long-range isotope shifts are measured, for 1H and 15N, which arise due to perdeuteration. Simulations, which employed a 7 or 8 spin relaxation matrix analysis, were compared to the experimental data from a time series of 2D NOESY datasets for some resonances. The agreement between experiment and simulation suggest that, with this 1H dilute sample, relatively long mixing times (up to 1.2 s) can be used to detect specific dipolar interactions between amide protons up to about 7A apart. A set of 155 inter-amide NOEs and 7 side chain NOEs were thus identified in a series of 3D HSQC-NOESY-HSQC experiments. These data, alone and in combination with previously collected restraints, were used to calculate sets of structures using X-PLOR. These results are compared to the available X-ray and NMR structures of the Fyn SH3 domain.

FRET-based in vivo Ca2+ imaging by a new calmodulin-GFP fusion molecule.

Intracellular Ca2+ acts as a second messenger that regulates numerous physiological cellular phenomena including development, differentiation and apoptosis. Cameleons, a class of fluorescent indicators for Ca2+ based on green fluorescent proteins (GFPs) and calmodulin (CaM), have proven to be a useful tool in measuring free Ca2+ concentrations in living cells. Traditional cameleons, however, have a small dynamic range of fluorescence resonance energy transfer (FRET), making subtle changes in Ca2+ concentrations difficult to detect and study in some cells and organelles. Using the NMR structure of CaM bound to the CaM binding peptide derived from CaM-dependent kinase kinase (CKKp), we have rationally designed a new cameleon that displays a two-fold increase in the FRET dynamic range within the physiologically significant range of cytoplasmic Ca2+ concentration of 0.05-1 microM.