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This paper describes a method for the rapid searching of 3d structural databases for molecules showing 3d shape similarity to a query structure. In the sperm program, molecular properties are projected onto the surface of a sphere and icosahedral symmetry is used to minimise storage requirements and accelerate comparison over all of 3d rotational space. The results of searches of a 30,000 compound database for molecules with a 3d shape resembling netropsin and daunomycin are described. In addition to molecules showing topological similarity to the query, hits are obtained showing considerable structural diversity. The results demonstrate that the method might be useful in the selection of new lead compounds as potential ligands for a given receptor.

Application d'une methode de RMN a 2 dimensions combinant les techniques COSY (Spectroscopie a 2 dimensions correlee) et NOESY (spectroscopie a 2 dimensions utilisant l'effet Overhauser nucleaire) a l'etude des conformations de macromolecules biologiques

The "colicin" fragments comprising the 49 3'-terminal nucleotides of 16 S ribosomal RNA have been isolated from wild-type Escherichia coli and from a kasugamycin-resistant mutant that lacks methylation of two geminal adenine residues. Proton nuclear magnetic resonance (n.m.r.) spectra (500 MHz) were recorded at various temperatures. The low-field resonances arising from the hydrogen-bonded iminoprotons of paired bases were assigned using the nuclear Overhauser effect (n.o.e.). Crucial to the interpretation of the spectra are the resonances that originate from the two hydrogen-bonded iminoprotons of a U X G basepair. Combined with temperature-jump relaxation kinetics experiments the n.o.e.s lead to the conclusion that a conserved A X U/U X G junction in the hairpin is a thermolabile dislocation in the helix. The n.m.r. spectra of the wild-type and mutant fragment are only different with respect to the iminoproton resonances of the two base-pairs adjoining the hairpin loop. The spectra recorded at various temperatures tend to indicate that dimethylation of the adenosines labilizes these base-pairs, but no definitive conclusions are drawn. The results confirm our previous views that dimethylation of the adenosine residues affects the conformation of the hairpin loop.

The application of 2D Ff NMR to the structural analysis of biological macromolecules has revolutionized the field. On the one hand networks of scalar coupled spins in complicated molecules such as proteins and nucleic acids can be analyzed by making use of coherent magnetization transfer in two-dimensional correlated spectroscopy (COSY) (l-4), on the other hand the proximity of specific nuclei in such molecules can be investigated by detecting incoherent magnetization transfer by means of nuclear Overhauser enhancement spectroscopy (NOESY) (5-7). During the last five years the number of techniques using coherent magnetization transfer has grown substantially: examples are relayed coherence spectroscopy and doublequantum spectroscopy (8-13). The latter techniques were shown to be a prerequisite in the unraveling of networks of scalar coupled spins which, due to ambiguities arising from extensive overlap, could not be resolved within COSY or SECSY (14-16). The process of incoherent transfer of magnetization, taking place via dipolar cross relaxation, is fundamentally different from coherent magnetization transfer which occurs via the J coupling between spins. In methods developed so far, the two phenomena have been employed strictly independently from one another; this is true even in the so-called COCONOSY experiment (I 7). However, there is no reason why a 2D FT NMR experiment should be based solely on either coherent or incoherent magnetization transfer (18). In this paper an experiment is described which couples coherent and incoherent transfer. It will be shown that such an experiment can be used as an aid in resolving ambiguities that may arise in NOESY spectra. To illustrate the basic principles of this new experiment, which we call doublequantum NOESY (DQ NOESY), we shall compare it with the conventional NOESY experiment (see Table 1). Both experiments can be divided in six periods and both experiments start by creating coherences which are frequency labeled during the evolution period I,. In a conventional NOESY experiment a 7r/2 pulse is used to create in-phase single-quantum coherence (i.e., transverse magnetization (5)). In DQ NOESY the preparation sequence of double-quantum spectroscopy (II, 19, 20), namely r/2-r-r-r--1r/2 is used, which gives rise to double-quantum coherences that are frequency labeled during the evolution period t, . After the evolution period

The RNA helix destabilizing properties of Escherichia coli initiation factor 3 protein (IF3), and its affinity for an evolutionarily conserved sequence at the 3' end of 16S rRNA, led us to examine the details of the protein-nucleic acid interactions upon IF3 binding to the 49-nucleotide 3'-terminal cloacin DF13 fragment of 16S rRNA by studying the circular dichroism (CD) and proton magnetic resonance spectra of the RNA, the protein, and their complex. In a physiological tris(hydroxymethyl)aminomethane buffer, where the interaction is primarily nonionic and sequence specific, addition of IF3 decreases the RNA 268-nm CD peak hyperbolically by 19% to an end point of about one IF3 per RNA strand. The titration curve is best fit by an association constant of (1.80 +/- 0.05) X 10(7) M-1, within the range estimated by a nuclease mapping study of the same system [Wickstrom, E. (1983) Nucleic Acids Res. 11, 2035-2052]. In a low-salt phosphate buffer without Mg2+, where the interaction is primarily ionic and nonspecific, titration with IF3 decreases the peak CD sigmoidally by 35% to an end point of two IF3 per strand. The titration curve is best fit by an intrinsic association constant of (1.7 +/- 0.7) X 10(6) M-1 for each IF3 and a cooperativity constant of 33 +/- 6. In a physiological phosphate buffer lacking Mg2+, the dispersion of aromatic proton magnetic resonance peaks and upfield-shifted methyl proton resonances indicates a high degree of secondary and tertiary structure in the protein. In an equimolar mixture of IF3 and RNA cloacin fragment, several changes in identifiable IF3 and RNA resonances are observed.(ABSTRACT TRUNCATED AT 250 WORDS)

30S ribosomes were isolated from a kasugamycin resistant mutant of E. coli that lacks methylgroups on two adjacent adenines in 16S ribosomal RNA. These ribosomes were methylated in vitro with a purified methylating enzyme and 5-S-adenosyl-(13C-methyl)-L-methionine chloride ((13C-methyl)-SAM) as methyldonor. After in situ cleavage of the 16S ribosomal RNA by the bacteriocin cloacin DF13, the 49 nucleotide fragment from the 3'-end of the RNA was isolated. The carbon-13 nuclear magnetic resonance spectra of the fragment at various temperatures were compared with those of 6-N-dimethyladenosine (m6(2)A) and 6-N-dimethyladenylyl-(3' leads to 5')-6-N-dimethyladenosine (m6(2)Am6(2)A). The data show that the two methylated adenines, which are part of a four membered hairpin loop, show a strong tendency to be stacked in analogy to the dinucleotide m6(2)Am6(2).

Resonances of the water exchangeable iminoprotons of the acceptor and D stem of yeast tRNAPhe have been assigned by means of Nuclear Overhauser Effects (NOE's). Assignments were made for spectra recorded from tRNA dialysed against a buffer with 110 mM sodium and 5 mM magnesium ions and against a buffer with 430 mM sodium and no magnesium ions. Remarkable is the assignment of a resonance at 13.6 - 13.7 ppm to the iminoproton of C11G24. This assignment as well as those of G1C72, G3C70, U7A66, U12A23 and C13G22 are different from those made previously on the basis of less direct evidence. NOE experiments performed at 45 degrees C support the view that the D stem together with the tertiary interaction U8A14 is one of the most stable parts of the molecule in the presence of magnesium ions. A comparison of the spectra recorded under the two different buffer conditions shows that an excess of 320 mM sodium ions is not capable to force the tRNA in the same conformation as 5 mM magnesium ions can do.