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The structure of stem-loop V RNA is studied by nuclear magnetic resonance (NMR) spectroscopy and shown that it adopts a U-turn conformation, a common motif found in RNA. The analysis helps in understanding the role of U-turn motifs in RNA structure and function and provides details of the mechanism of substrate recognition in the Neurospora Varkud Satellite (VS) ribozyme.

The structure of the bacteriophage lambda N peptide/boxB RNA complex was investigated using heteronuclear magnetic resonance spectroscopy. Nuclear magnetic resonance spectroscopy was also employed to determine the structures of the complexes formed by the arginine-rich motifs of the immunodeficiency virus Tat and HIV-1 Rev proteins with their RNA ligands. Results show that the GAAGA boxB loop forms a GNRA fold which is a requirement in N binding. The structure of the complex suggests new modes of RNA folding and RNA-protein recognition.

The hammerhead ribozyme was analyzed using nuclear magnetic resonance experiments to determine the effect of different nucleotides at the cleavage site of the enzyme. Results indicate that guanine ribonucleotide has an inhibitory influence on the enzyme through the stabilization of the inactive conformation. Further, other nucleotides are able to generate alterations in the structure and dynamics of the active site by interacting with the amino acid residues at the binding site.

Intermolecular NOEs in a molecular complex comprising super15N, super13C labeled and unlabeled components were recorded, using new pulse schemes. Adiabatic super13C inversion pulses were used for filtering. Improved spectra was obtained relative to data from other purging schemes. Structural information was obtained for the amino-terminal domain of the N protein from bacteriophage lambda and boxB RNA, using the new scheme.

The structure and dynamics of leadzyme were investigated by heteronuclear NMR spectroscopy. The pKas for all the adenine bases in the lead-dependent ribozyme were found to range from

The hammerhead ribozyme undergo significant conformational changes in the conserved U-turn region, after cleavage of an RNA substrate. Heteronuclear multidimensional nuclear magnetic resonance (NMR) studies are conducted on hammerhead ribozyme complexed with cleaved and intact substrates. The three helices surrounding the catalytic core of the hammerhead ribozyme are formed with both cleaved and intact substrates. The sheared G-A base pairs are formed in the conserved region in absence of Mg2+. Two models are proposed to explain the activity of the ribozyme.

The additional distance produced for exchange-broadened amino protons in the nucleic acids substantially enhance the structural configuration of the GAAA tetraloop in the leadzyme. A 2D 15N-correlated NOESY experiment, performed on a 15N-labeled lead-dependent leadzyme, establishes the distance information for these amino protons. The procedure reveals 19 NOE for amino protons and negligible information for adenine and guanine amino protons.

The solution structure of bovine neutrophil beta-defensin-12 (BNBD-12) reveals an clearly formed triple-stranded, antiparallel beta-sheet as the main structural component of the peptide. The hydrophobic face is formed by the N-terminal beta-strand and three locally well-defined loops. The cationic face of BNBD-12 is formed by the beta-hairpin which contains numerous charged residues. It is also found that the absence of tertiary NOEs are responsible for N-terminal residues being disordered. Furthermore, the peptide fold of beta-defensins and the classical defensins are found to be similar.

The article explains the NMR structure of the complex that is formed by the carboxyl-terminal domain of human RAP74 and a phosphorylated peptide from the central domain of the FCP1 phosphatase. The molecular mechanism, as well as the properties of the complex is also discussed.

NMR spectroscopy, isothermal titration calorimetry (ITC) and site-directed mutagenesis studies are used for characterizing the interaction between the acidic transactivation domain Herpes Simplex Virion Protein 16 (VP16TAD) and Tfb1. Important differences between the p53TAD2/Tfb1 and the carboxyl-terminal subdomain of the VP16TAD (VP16C)/Tfb1 complexes have shown how selected activators such as p53 depend on phosphorylation events to selectively regulate transcription.

The high resolution NMR structure of stem-loop V (SL5) of Varkud satellite ribozyme in the presence of Mg ions is described. It is shown that [Mg.sup.2+] induces a conformational change in which the SL5 loop adopts a compact structure with most characteristics of canonical U-turn structures and Mg ions bound conformation of SL5 allows additional contacts with stem-loop I.

The nuclear magnetic resonance (NMR) structure of the amino-terminal domain from the Tfb1 (Tfb1(sub 1-115) subunit of yeast TFIIH is described. Tfb1(sub 1-115) contains a pleckstrin homology (PH) domain that is very similar to the PH domain of p62(sub 1-108).

The study demonstrated that the phosphorylation of S942-S944 occurs in a semiordered fashion with the initial phosphorylation occurring at either S492 or S944 followed by a second phosphorylation to yield the S942/S944 diphosphorylated species. The results provided new functional and structural information on the role of phosphorylation in the recognition of acidic-rich activation domains involved in transcriptional regulation, and bring insights into how CK2 and TFIIF regulate FCP1 function.

The study have characterized the interactions of Tat and RAP74 with the BRCT-containing central domain of FCP1(FCP1(sub 562-738)) and demonstrated that FCP1 is required for Tat-mediated transactivation in vitro and that amino acids 562-685 of FCP1 are necessary for Tat interaction in yeast two-hybrid studies. The result provides insights into the mechanisms by which activation by Tat.