Distance measurement by energy transfer. Ribosomal proteins L6, L10 and L11 of Escherichia coli

Distances as degrees of freedom

Tertiary contact distance information of varying resolution for large biological molecules abounds in the literature. The results provided herein develop a framework by which information of this type can be used to reduce the allowable configuration space of a macromolecule. The approach combines graph theory and distance geometry. Large molecules are represented as simple, undirected graphs, with atoms, or groups, as vertices, and distances between them as edges. It is shown that determination of the exact structure of a molecule in three dimensions only requires the specification of all the distances in a single tetrahedron, and four distances to every other atom. This is 4N-10 distances which is a subset of the total N(N-1)/2 unique distances in a molecule consisting of N atoms. This requirement for only 4N-10 distances has serious implications for distance geometry implementations in which all N(N-1)/2 distances are specified by bounded random numbers. Such distance matrices represent overspecified systems which when solved lead to non-obvious distribution of any error caused by inherent contradictions in the input data. It is also shown that numerous valid subsets of 4N-10 distances can be constructed. It is thus possible to tailor a subset of distances using all known distances as degrees of freedom, and thereby reduce the configuration space of the molecule. Simple algebraic relationships are derived that relate sets of distances, and complicated rotations are avoided. These relationships are used to construct minimum, complete sets of distances necessary to specify the exact structure of the entire molecule in three dimensions from incomplete distance information, and to identify sets of inconsistent distances. The method is illustrated for the flexible structural types present in large ribosomal RNAs: 1.) A five-membered ring; 2.) a chemically bonded chain with its ends in contact (i.e., a hairpin loop); 3.) the spatial orientation of two separate molecules, and; 4.) an RNA helix that can have variation in individual base pairs, giving rise to global deviation from standardized helical forms.

Prediction of three-dimensional structure of Escherichia coli ribosomal RNA

A model for the tertiary structure of 23S, 16S and 5S ribosomal RNA molecules interacting with three tRNA molecules is presented using the secondary structure models common to E. coli, Z. mays chloroplast, and mammalian mitochondria. This ribosomal RNA model is represented by phosphorus atoms which are separated by 5.9 A in the standard A-form double helix conformation. The accumulated proximity data summarized in Table 1 were used to deduce the most reasonable assembly of helices separated from each other by at least 6.2 A. Straight-line approximation for single strands was adopted to describe the maximum allowed distance between helices. The model of a ribosome binding three tRNA molecules by Nierhaus (1984), the stereochemical model of codon-anticodon interaction by Sundaralingam et al. (1975) and the ribosomal transpeptidation model, forming an alpha-helical nascent polypeptide, by Lim & Spirin (1986), were incorporated in this model. The distribution of chemically modified nucleotides, cross-linked sites, invariant and missing regions in mammalian mitochondrial rRNAs are indicated on the model.

Localization of L11 on the Escherichia coli ribosome by singlet-singlet energy transfer

Isolated Escherichia coli ribosomal protein L11 was labeled with maleimidyl derivatives of coumarin or fluorescein at the thiol group of its single cysteine, then reconstituted singly or in pairs with other fluorescently labeled ribosomal components. The characteristics of fluorescence from the labeled protein were studied and its distance to other components was determined by non-radiative energy transfer. The distance between probes on L11 and cysteine residues on other proteins or the 3' end of the ribosomal RNAs were found to be: S1, 7.4-8.3 nm; S21, 7.6 nm; 23S RNA, 6.9 nm; 5S RNA, 7.6 nm; 16S RNA, greater than 8.5 nm. Considered together with previously published results these distances indicate that the location of L11 in the 50S subunit is below the lateral protuberance characterized by L7/L12.

Structure of protein-deficient 50 S ribosomal subunits. Particles without 5 S RNA-protein complex retain the L7/L12 stalk and associate with 30 S subunits

50 S ribosomal subunit derivatives without the 5 S RNA-protein complex obtained either by splitting with EDTA or by reconstitution from the 23 S RNA and proteins have been studied by electron microscopy. Removal of the 5 S RNA-protein complex is shown to affect neither the overall morphology of the larger ribosomal subunit nor the mode of its association with the small subunit.

Structure of protein-deficient 50 S ribosomal subunits. Nine core proteins induce the compact conformation of 23 S ribosomal RNA

The complex of 23 S ribosomal RNA with the nine core proteins L2, L3, L4, L13, L17, L20, L21, L22 and L23 obtained either by the disassembly procedure or by reconstitution has been studied by electron microscopy. This complex is found to be very similar to the intact 50 S subunit both in size and in shape.