Identification of the oriI-binding site of poliovirus 3C protein by nuclear magnetic resonance spectroscopy.

Replication of picornaviral genomes requires recognition of at least three cis-acting replication elements: oriL, oriI, and oriR. Although these elements lack an obvious consensus sequence or structure, they are all recognized by the virus-encoded 3C protein. We have studied the poliovirus 3C-oriI interaction in order to begin to decipher the code of RNA recognition by picornaviral 3C proteins. oriI is a stem-loop structure that serves as the template for uridylylation of the peptide primer VPg by the viral RNA-dependent RNA polymerase. In this report, we have used nuclear magnetic resonance (NMR) techniques to study 3C alone and in complex with two single-stranded RNA oligonucleotides derived from the oriI stem. The (1)H-(15)N spectra of 3C recorded in the presence of these RNAs revealed site-specific chemical shift perturbations. Residues that exhibit significant perturbations are primarily localized in the amino terminus and in a highly conserved loop between residues 81 and 89. In general, the RNA-binding site defined in this study is consistent with predictions based on biochemical and mutagenesis studies. Although some residues implicated in RNA binding by previous studies are perturbed in the 3C-RNA complex reported here, many are unique. These studies provide unique site-specific insight into residues of 3C that interact with RNA and set the stage for detailed structural investigation of the 3C-RNA complex by NMR. Interpretation of our results in the context of an intact oriI provides insight into the architecture of the picornavirus VPg uridylylation complex.

Humoral and cell-mediated immunity in mice with genetic deficiencies of prolactin, growth hormone, insulin-like growth factor-I, and thyroid hormone.

Prolactin (PRL), growth hormone (GH), insulin-like growth factor-I (IGF-I), and thyroid hormones have been proposed as critical immunoregulatory mediators, and their clinical use is being considered. The precise role played by each of these hormones in the generation of humoral and cell-mediated immune responses was assessed in a panel of mice with mutations that result in a selective reduction of PRL, GH, IGF-I, and/or thyroid hormone production. A surprising result, in view of previous studies indicating an immunoregulatory role for these hormones, was that all mice generated normal humoral and cell-mediated immune responses following challenge with T-independent and T-dependent antigens and with Listeria monocytogenes. A review of these findings in the context of previous data has resulted in the formulation of a working hypothesis proposing that these hormones act as anabolic and/or stress modulating mediators with effects on most cells, including those of the immune system. When considered in this context, it is possible to reconcile the contradictory data.

Proliferation of bone marrow pro-B cells is dependent on stimulation by the pituitary/thyroid axis.

The frequency and absolute number of pro-B, pre-B, and B cells in the bone marrow of the hypothyroid strain of mice are significantly reduced compared with those of their normal littermates. To investigate why this is the case, various B cell developmental processes were examined in the thyroid hormone-deficient mice. These studies revealed that the frequency of pro-B cells in the S-G2/M phase of the cell cycle was significantly reduced in hypothyroid mice. That thyroid hormone deficiency was responsible for this proliferation defect was established by demonstrating that treatment of hypothyroid mice with thyroxine resulted in a specific increase in the frequency and total number of cycling pro-B cells. The latter effect was paralleled by increases in the frequency and number of bone marrow B lineage cells. Additional in vitro experiments revealed that at least some thyroid hormone effects were directly mediated on the bone marrow. Taken together, these data demonstrate that thyroid hormones are required for normal B cell production in the bone marrow through regulation of pro-B cell proliferation and establish a role for the pituitary/thyroid axis in B cell development.

Chemical shift as a probe of molecular interfaces: NMR studies of DNA binding by the three amino-terminal zinc finger domains from transcription factor IIIA.

We report the NMR resonance assignments for a macromolecular protein/DNA complex containing the three amino-terminal zinc fingers (92 amino acid residues) of Xenopus laevis TFIIIA (termed zf1-3) bound to the physiological DNA target (15 base pairs), and for the free DNA. Comparisons are made of the chemical shifts of protein backbone 1HN, 15N, 13C alpha and 13C beta and DNA base and sugar protons of the free and bound species. Chemical shift changes are analyzed in the context of the structures of the zf1-3/DNA complex to assess the utility of chemical shift change as a probe of molecular interfaces. Chemical shift perturbations that occur upon binding in the zf1-3/DNA complex do not correspond directly to the structural interface, but rather arise from a number of direct and indirect structural and dynamic effects.

High-resolution solution structure of the retinoid X receptor DNA-binding domain.

The retinoid X receptor (RXR) is a member of the nuclear hormone receptor superfamily of transcriptional regulators and plays a central role in the retinoid and, through its ability to heterodimerize with other nuclear hormone receptors, non-steroid signaling pathways. The DNA-binding and recognition functions of RXR are located in a conserved 83 amino acid residue domain that recognizes the consensus sequence AGGTCA. In order to provide a detailed picture of its structure, we have calculated a high-resolution solution structure of the C195A RXRalpha DNA-binding domain. Structures were calculated using 1131 distance and dihedral angle constraints derived from 1H, 13C and 15N NMR spectra. The structures reveal a perpendicularly packed, "loop-helix" fold similar to other nuclear hormone receptor DNA-binding domains and confirm the existence of the C-terminal helix, which was first observed in the low-resolution NMR structure. The C-terminal helix is well formed and is stabilized by packing interactions with residues in the hydrophobic core. The solution structure of RXR is very similar to that determined by X-ray crystallographic studies of the RXR-TR heterodimer complex with DNA, except that in the latter case no electron density was observed for residues corresponding to the C-terminal helix. Other differences between the X-ray and NMR structures occur in the second zinc-binding loop, which is disordered in solution. Heteronuclear 15N NOE measurements suggest that this loop has enhanced flexibility in the free protein.

Three-dimensional solution structure of conotoxin psi-PIIIE, an acetylcholine gated ion channel antagonist.

The three-dimensional structure of conotoxin psi-PIIIE, a 24-amino acid peptide from Conus purpurascens, has been solved using two-dimensional (2D) 1H NMR spectroscopy. Conotoxin psi-PIIIE contains the same disulfide bonding pattern as the mu-conotoxins, which target skeletal muscle sodium channels, but has been shown to antagonize the acetylcholine gated cation channel through a noncompetitive mechanism. Structural information was obtained by the analysis of a series of 2D NOESY spectra as well as measurement of coupling constants from 1D 1H and PE-COSY NMR experiments. Molecular modeling calculations included the use of the distance geometry (DG) algorithm, simulated annealing techniques, and the restrained molecular dynamics method. The resulting structures are considerably similar to the previously published structures for the mu-conotoxins GIIIA and GIIIB, despite the lack of sequence conservation between conotoxin psi-PIIIE and the mu-conotoxins. The structure consists of a series of tight turns, each turn occurring in the position analogous to those of turns described in mu-GIIIA and mu-GIIIB. This suggests the disulfide bonding pattern is able to largely direct the structure of the peptides, creating a stable structural motif which allows extensive sequence substitution of non-cystine residues.

Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: determinants of affinity and sequence specificity.

The high resolution solution structure of a protein containing the three amino-terminal zinc fingers of Xenopus laevis transcription factor IIIA (TFIIIA) bound to its cognate DNA duplex was determined by nuclear magnetic resonance spectroscopy. The protein, which is designated zf1-3, binds with all three fingers in the DNA major groove, with a number of amino acids making base-specific contacts. The DNA structure is close to B-form. Although the mode of interaction of zf1-3 with DNA is similar to that of zif268 and other structurally characterized zinc finger complexes, the TFIIIA complex exhibits several novel features. Each zinc finger contacts four to five base-pairs and the repertoire of known base contact residues is extended to include a tryptophan at position +2 of the helix (finger 1) and arginine at position +10 (finger 3). Sequence-specific base contacts are made over virtually the entire length of the finger 3 helix. Lysine and histidine side-chains involved in base recognition are dynamically disordered in the solution structure; in the case of lysine, in particular, this could significantly decrease the entropic cost of DNA binding. The TGEKP(N) linker sequences, which are highly flexible in the unbound protein, adopt ordered conformations on DNA binding. The linkers appear to play an active structural role in stabilization of the protein-DNA complex. Substantial protein-protein contact surfaces are formed between adjacent fingers. As a consequence of these protein-protein interactions, the orientation of finger 1 in the major groove differs from that of the other fingers. Contributions to high affinity binding by zf1-3 come from both direct protein-DNA contacts and from indirect protein-protein interactions associated with structural organization of the linkers and formation of well-packed interfaces between adjacent zinc fingers in the DNA complex. The structures provide a molecular level explanation for the large body of footprinting and mutagenesis data available for the TFIIIA-DNA complex.

Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA.

The three N-terminal zinc fingers of transcription factor IIIA bind in the DNA major groove. Substantial packing interfaces are formed between adjacent fingers, the linkers lose their intrinsic flexibility upon DNA binding, and several lysine side chains implicated in DNA recognition are dynamically disordered.

Interaction of the RNA binding fingers of Xenopus transcription factor IIIA with specific regions of 5 S ribosomal RNA.

Zinc fingers 4 to 7 of Xenopus transcription factor IIIA (TFIIIA) represent the minimal polypeptide necessary for high-affinity binding to 5 S RNA. Mutations covering the entire 5 S RNA structure have been compared for their effects on the binding affinity of full-length TFIIIA and a polypeptide consisting of fingers 4 to 7 of TFIIIA (zf4-7). In addition, ribonuclease footprinting was used to compare the binding sites of TFIIIA and zf4-7 on 5 S RNA. The consistency between the data obtained from these two approaches provided a clear indication that zinc fingers 4 to 7 of TFIIIA bind to a central core region on the 5 S RNA molecule consisting of loop B/helix II/loop A/helix V/region E. This information was used to design a truncated 75-nucleotide-long RNA molecule that retains high affinity for zf4-7. Therefore, we conclude that the specific interaction of TFIIIA with 5 S RNA can be represented by a complex formed between a four zinc finger polypeptide and a truncated 5 S RNA molecule.

Bistramides A, B, C, D, and K: a new class of bioactive cyclic polyethers from Lissoclinum bistratum.

The isolation and characterization is described of four novel cyclic polyethers, bistramides B [2], C [3], D [4], and K [5], which are closely related to the previously reported bistramide A [1] from the New Caledonian urochordata Lissoclinum bistratum. The structures of these metabolites were defined by spectroscopic methods. The four compounds exhibited in vitro cytotoxicity toward six tumor cell lines, including the human non-small cell lung carcinoma (NSCLC-N6) line. Cytofluorimetric analysis with bistramide K showed a complete block of NSCLC-N6 cells in the G1 phase. Bistramide D and particularly bistramide K are less toxic than bistramides A, B, and C and are thereby effective in vivo against NSCLC-N6.

Applications of the improved computerized analysis of 2D INADEQUATE spectra.

This paper illustrates the use of the program CCBond to determine the carbon skeletons of bioorganic molecules in low concentration samples. Discussed is the structure elucidation of bistramide A, a compound extracted from a Fijian Lissoclinum sp. and cholesterol in 71- and 20-mumol samples, respectively. The detection limit of the automated bond extraction is shown to be dramatically improved compared to the manual interpretation of 2D INADEQUATE spectra.