Figure 4 . Stereoviews of three representative tRNA binding models on the ribosome showing spatial distributions of cross-linking nucleotides to r-proteins and rRNAs summarized in Table 1. Full drawings of the cross-linking nucleotides are shown, while the other nucleotides are only shown by P, C5' and C3' atoms. The locations of cross-linked r-protein names and abbreviated rRNA position names (small letters for 16S rRNA and capital letters for 23S rRNA, as listed in Table 1) are shown as close as possible to the corresponding nucleotides drawn with all atoms (except hydrogen). A-site tRNA, P-site tRNA and mRNA are indicated by the larger bold letters, A, P, and m, respectively. The chimeric largest variable loops are also shown. Chem3D program was used for drawing the atomic models. Labels showing the cross-linking positions have been added manually. ( a ) A-P tRNA pair model proposed in this work. mRNA is shown with all main chain atoms (viz. P-O5'-C5'-C4'-C3'-O3'-). ( b ) A-P tRNA pair is as in (a), but viewed from a slightly different direction. The E-site tRNA of the P-E tRNA pair along with its mRNA is superposed on the model of the A-P tRNA pair. The larger bold letter, E, denotes E-site tRNA. The smaller bold letters, D, [Psi] and V, denote the locations of D-, T[Psi]C- and largest variable loops of A-, P- and E-site tRNAs, respectively. (See Discussion for the reason why D1 is not shown.) ( c ) A- and P-site tRNA models connected with two codons representing the tRNA binding model used by Stark et al. (30). The angle between two L-shaped planes is 90^o. The other parts are as in (a). ( d ) A- and P-site tRNA models connected with two codons representing the tRNA binding model used by Agrawal et al. (31). The angle between two L-shaped planes is 160^o. mRNA is shown by P, C5' and C3' atoms. It is worth noting that this model is neither S-type nor R-type. The localizations of cross-linking nucleotides are only displayed for L2, L27 and S7, as well as for 23S rRNA positions. The other parts are as in (a).

Table 1 tRNA-ribosome cross-links summarized on the basis of three references (29,39,63) The small letters in the ribosomal site column indicate that the cross-linking data are not major but minor according to Rinke-Appel et al. (63).
cont...

Agrawal et al. ( 31 ) were able to localize A-, P- and E-site tRNAs in the E.coli ribosome from the difference map of two cryo-electron microscopy, one in the presence of three deacylated tRNAs and the other in the absence of tRNAs ( 32 ). The angle of the two planes representing the tRNAs bound to the A and P sites was found to be ~160^o, and quite different from the angles expected from either R- or S-type configurations. Moreover, the anticodon loop of the putative E-site tRNA was not bound to mRNA. This might mean that the E-site tRNA was noncognate. However, their results might not be the same as those that would have been obtained if they had used aminoacyl- and peptidyl-tRNAs, because two deacylated tRNA molecules do not have to contact with each other at their CCA ends, and also because aminoacyl-, peptidyl- and deacylated tRNAs do not bind to the ribosome at a time with sufficient stability. In contrast, the results of spin-contrast method of neutron diffraction presented a pair of tRNA molecules forming a very similar side-by-side shape with a pseudo-R-type angle of two tRNA planes between 50^o and 55^o on the E.coli ribosome both at the pre- and the post-translocational states ( 33 ; K.H.Nierhaus, personal communication). It should not be interpreted as R-type, because S-type is more favourable from the viewpoint of Nagano and Harel ( 5 ), Easterwood et al. ( 6 ) and Brimacombe ( 7 ), so far as the conformation of the anticodon loops bound to the neibouring codons is concerned. Therefore, it suggested that some conformational changes were involved during the pre- and the post-translocational states, as confirmed by the following. The better accessible nucleotide patterns of phosphorothioated tRNAs on the ribosome were quite different from those of isolated tRNAs and indicated conformational changes of tRNAs resulting in the formation of three types of binding sites called [alpha], [epsilon] and [delta] ( 33 ). The conventional A and E sites can be interpreted as the [alpha]-site of pre-translocational state and the [epsilon]-site of post-translocational state, respectively, while the conventional P-site should be distinguished into the [epsilon]-site of pre-translocational state and the [alpha]-site of post-translocational state. In other words, the two sites on the ribosome allowed for two tRNA molecules are [alpha] and [epsilon] sites for both pre- and post-translocational states. The binding site [delta] corresponds to the recognition mode of A-site only at the post-translocational state. These new findings can be explained by the S-type model of Nagano et al. ( 25 ) by introducing drastic conformational changes of D-loop in [alpha]-site tRNA, and also of T[psi]C-loop and acceptor stem in [epsilon]-site tRNA as well as by forming two G-C base pairs between the highly conserved guanines at positions 18 and 19 of the D-loop of [alpha]-site tRNA of A-P pair or P-E pair and cytosines at positions 56 and 61 of the T[psi]C-loop of [epsilon]-site tRNA of A-P pair or P-E pair. Such a pair of tRNA docking model was energetically refined. The A-P pair model is shown in Figure 1 a and b as coloured stereo pictures. The two G-C base pairs are magnified in Figure 1 b. The nucleotide sequence of the tRNA molecules shown in Figure 1 is that of yeast tRNA ^Phe .

By adding the largest variable loop of E.coli tRNA ₃ ^Ser , the model of the chimeric A-P tRNA pair was built. The stereo picture of the chimeric A-P tRNA pair with the largest variable loop is viewed from the anticodon loop and mRNA down the axis of rotation symmetry of the ribosomal three-tRNA binding model ( 25 ), as shown in Figure 2 , which is perpendicular to the view of Figure 1 . It can be seen from Figure 2 that various sizes of variable loops do not disturb the binding to mRNA at the anticodons in both A- and P-site tRNAs because variable loops are directing outwards from the axis of rotation symmetry, which is very close to the mRNA. Some of the 16S rRNA regions as well as mRNA surrounding the A-P pair are also shown in Figure 2 without any description about the logical bases of their localizations (K.Nagano and N.Nagano, unpublished results). It was important for the passage of mRNA to take into account the cross-linking data of Bogdanov et al. ( 34 ).

The P-E tRNA pair was obtained by rotating it by 50^o around the axis of rotation symmetry. The conformations of the anticodons of A-, P- and E-tRNAs bound to the mRNA codons of both A-P and P-E tRNA pairs are the same as those of three tRNAs of the Nagano et al. model ( 25 ), while the conformations of ACCA termini are different so that a helical form of nascent polypeptide is kept at the same positions before and after the translocation. Such a model around the ACCA termini of both P- and E-site tRNAs of the P-E tRNA pair as well as of nascent polypeptide is shown in Figure 3 . Thus, the A-P tRNA pair model, shown in Figure 1 a, has a transitionary tetrahedral C' atom of the nascent polypeptide directly connected with the amino nitrogen atom of the aminoacyl group of A-site tRNA, while the 3'-ends of both E- and P-site tRNAs of the P-E tRNA pair are separated by 38.5 Å (between two O3' atoms) with each other. The shifting distance of the centres of gravity between the A-P and P-E tRNA pairs was calculated to be 25.0 Å, which is about twice as large as the appoximated value, 13 Å, in the direction from the L7/L12 stalk to the L1 stalk of the ribosome, observed by Nierhaus and co-workers ( 33 ). It is important to note that the anticodon position of the P-site tRNA in the A-P tRNA pair model [viz. [epsilon] site of pre-translocational state ( 33 )] is kept at the same position as that of the P-site tRNA in the P-E tRNA pair model [viz. [alpha] site of post-translocational state ( 33 )]. This might not be true in the actual ribosome. The P-E tRNA pair could be better represented by rotating the A-P tRNA pair by 25^o around the symmetry axis instead of 50^o. It might be very confusing, however, because various biochemical and functional experiments such as cross- linking have been performed under a common name of P-site tRNA, if the P-site in the pre-translocational state (or in the A-P tRNA pair model) is different from that in the post- translocational state (or in the P-E tRNA pair model).

3D-REPRESENTATIONS OF CROSS-LINKING DATA ON THE THREE REPRESENTATIVE tRNA BINDING MODELS ON THE RIBOSOME

Footprinting experiments of Jørgensen et al. ( 36 ) revealed differences in the T[psi]C- and D-loops of tRNAs bound to the P and A sites. Bertram et al. ( 37 ) found a protection against kethoxal modification of G18 and G19 of tRNA ^Phe in the A-site. Furthermore, Abdurashidova et al. ( 38 ) found that a rather small protein, L27, was cross-linked from both G18 of A-site tRNA and C56 of P-site tRNA. The tRNA-ribosome cross-linking data from the papers of Zimmermann's group ( 8 , 9 ) and Brimacombe's group ( 39 ) are summarized in Table 1 . The most serious problem is to explain cross-linking data from position 20:1 of lupin Met-tRNA located at the A-site to the nucleotide somewhere from position 875 to 905 of 23S rRNA ( 39 ), suggesting a drastic conformational change in the A-site tRNA. The reason for this will be discussed later. Those cross-linking positions on the tRNA molecules of the ribosome are satisfied by our model with the chimeric largest variable loops, as shown by the Chem3D stereo picture in Figure 4 a and b. The A-P tRNA pair in Figure 4 b is the same as that in Figure 4 a except that the labels showing the cross-linking r-proteins and rRNAs and viewed from a slightly different direction from the corresponding model in Figure 4 a with some notations of D-loop (D), T[psi]C-loop ([psi]), and the largest variable loops (V). In Figure 4 b the E-site tRNA in the P-E tRNA pair model [viz. [epsilon] site of post-translocational state ( 33 )] along with its mRNA is also superimposed with some relevant cross-link labels. Figure 4 c shows the same cross-linking positions as those in Figure 4 a (except S19, L5 and L27 for U47 on the P-site tRNA because of no suitable space) on the 3D model of Brimacombe's group ( 30 ), which was built by rotating a crystallographically obtained tRNA conformation with the same largest variable loop as in Figure 4 a by 90^o and by connecting the two tRNA models with two adjacent codons. The distance between two O3' atoms of A76 of both A- and P-site tRNAs is 10 Å. It can be seen that the two points, C and D, appear on the opposite sides of its P-site tRNA, and that the line from A to B separates the A-site tRNA from the P-site tRNA. On the other hand, point B in Figure 4 a lies on the bottom of a cavity made by three triangular planes, ACB, CDB and DAB, and both A- and P-site tRNA molecules sit almost without serious invasions to those putative surfaces of 23S rRNAs. Figure 4 d shows the distributions of the cross-linking positions only for A, B, C and D as well as for the r-proteins, S7 and L27, on the 3D model of Frank's group ( 31 ), which was also built by the same method as that used in Figure 4 c by rotating one tRNA model by 160^o and by connecting the two tRNA models with two adjacent codons so as to avoid serious inter-atomic collisions, resulting in a sharp turn at the joint of two codons. The distance between two O3' atoms of A76 of both A- and P-site tRNAs in this model is 15 Å.

The largest distances between two cross-linking positions to r-proteins L27, L2 and S7 on the three models are calculated and listed in Table 2 . L27, L2 and S7 are composed of 84, 272 and 177 residues, respectively ( 52 ). Since both L2 and S7 are rather large, their largest distances on the models might be alright. However, L27 is a small protein, and its largest distances on both the Stark et al. ( 30 ) and Agrawal et al. models ( 31 ) seems too large when those values such as 85 Å * 60 Å and 100 Å * 60 Å, respectively, are compared with the approximate size of a crystal structure of a moderately sized protein of 124 residues, bovine pancreatic ribonuclease-S ( 53 ), 45 Å * 30 Å * 20 Å. It must be kept in mind that the possible conformation of L27, which seems to be more elongated and curved than that of ribonuclease-S, should not hinder the A-P tRNA pair model from translocating to the P-E tRNA pair model, and also the P-E tRNA pair model from accepting the next cognate aminoacyl-tRNA model at the right place of the recognition mode of A-site, viz. [delta] site in the post- translocational state of the ribosome ( 33 ).

Table 2 The approximate distances between two representative positions of cross-linking to r-proteins, L2, L27 and S7, as well as to positions, A, B, C and D of 23S rRNA listed in Table 1 for the three 3D models of two tRNA molecules on the ribosome shown in Figure 4a, c and d, respectively

In order to calculate the above approximate distances, N2 atoms of G bases, N6 atoms of A bases, O4 atoms of U bases, N4 atoms of C bases, and O6 atoms of Y bases were used. Although Stark et al. (30) and Agrawal et al. (31) did not indicate the positions of r-proteins such as S7, L2 and L27, distances between two cross-linking positions were calculated in this work for estimating the possible sizes of the representative three proteins under the assumption that both models of Stark et al. (30) and Agrawal et al. (31) are correct.

The distances of our model between the bases of the nucleotides at positions 37-37 (from A-site to P-site), 37-17 (from A-site to P-site), 17-37 (from A-site to P-site) and 17-17 (from A-site to P-site) are compared with the corresponding distance values estimated from the FRET measurements ( 54 , 55 ) and tabulated in Table 3 for the above three models with the chimeric largest variable loops along with the three models cited from Easterwood et al. ( 6 ). As far as the scores for two kinds of ranks in Table 3 are concerned, the McDonald and Rein model ( 56 ) is almost as good as our present model. It is also an S-type side-by-side model, but does not explain the base pairing possibility of G18 and G19 ( 37 ).

Another problem is the possibility of a conformational change at the anticodon loop of tRNAs. Nagano et al. ( 25 ) have obtained a three-tRNA binding model, in which an ideal A-form conformation of the anticodon is introduced and results in a fully exposed base of U33. It is known that the base of U33 is buried in the anticodon loop with a hydrogen bond between the N3 atom of U33 and the O5' atom of A36 (see Fig. 5c of ref. 12 ) of yeast tRNA ^Phe structure obtained by crystallography. We think that the conformational change in the anticodon loop could be essential for a codon to discriminate a cognate aminoacyl-tRNA from near-cognate and noncognate ones (K.Nagano and N.Nagano, unpublished results). The photoreactive cross-link from s ⁴ U33 to r-protein S7 ( 9 ), in Table 1 , seems to favour such an exposed U33 base conformation ( 25 ). As shown in Figure 4 a, the two cross- linking positions to S7, viz. U33 and Y37, appear very close to each other, while those of both Figure 4 c and d come on the opposite sides of the respective anticodon loops. If we seriously consider the possibility of modelling the regions of 16S rRNA, particularly around the decoding site C1400 as well as the 693-717, 936-966 and 1338-1378 of 16S rRNA, the spatial distribution of three S7 cross-linking points, U33 and Y37 of P-site tRNA and Y37 of A-site tRNA in Figure 4 c and d, would be almost the hardest obstacle to be overcome, although it might be just circumstantial evidence. We propose here a new tRNA binding model on the ribosome, as shown in Figures 1 , 2 , 3 and 4 a and b, before going further to make clear the mechanism of translation.

Table 3 Comparison of distances calculated from various two tRNA-binding models of S- and R-orientations compared with the experimentally estimated distances of FRET measurements
a, Taken from Paulsen et al. (55). b, Average of two models calculated by McDonald and Rein (56). c, Cited from Easterwood et al. (6). d, Summation of absolute distance values outside the the experimentally permissible ranges, viz. [Sigma][brvbar]r _i,model - r _{i,nearest premissible} [brvbar]. e, Summation of absolute distance values deviated from the experimentally expected mean value of distances, viz. [Sigma][brvbar]r _i,model - r _i,mean [brvbar]. f, Reference number. g, Distances for Nagano & Nagano model, Nagano et al. model (25), Stark et al. model (30) and Agrawal et al. model (31) were calculated using the coodinates of N1 atoms of pyrimidine bases and N9 atoms of purine bases. h, The increasing order of Score for Rank 1. i, The increasing order of Score for Rank 2.

DISCUSSION

Conservation of U33 in the anticodon loop of tRNA molecules

It has been known for years that the nucleotide one residue upstream on the 5' side of the anticodon is uracil with the exception of a few eukaryotic initiator tRNAs which have C33 ( 57 ) and elongator tRNAs of six Candida species which have G33 ( 58 , 59 ). In so far as a single base pairing is concerned, an A-G pairing could have a similar geometry to the ordinary A-U pairing ( 60 , 61 ). Another advantage of U33 could be the smaller size of the pyrimidine base rather than the purine base, particularly when a drastic conformational change occurs on the pyrimidine-rich 5' side of the anticodon loop.

Woo et al. ( 62 ) have found that U33 of yeast initiator tRNA ^fMet has a half exposed U33, and have proposed a uridine swivel hypothesis. If we consider that the initiator tRNA occupies directly the P-site, it does not contradict our present models at all.

Why aminoacyl-, peptidyl- and deacylated tRNA do not bind to the ribosome at a time as a stable complex

It is known that aminoacyl-, peptidyl- and deacylated tRNAs do not bind to the ribosome at a time with sufficient stability. In the model of Nagano et al. ( 25 ), three equivalent tRNA molecules are arranged with symmetry of rotation, suggesting considerable binding stability. One of the important points of the A-P and P-E tRNA pair models presented in this work is that the binding capacity between the two tRNA molecules cannot be extended to three adjacent tRNA molecules. That is to say, when another tRNA molecule comes to join the tRNA complex, one must leave the complex simultaneously, as well known experimentally. This is because the D-stem of A-site tRNA in the A-P tRNA pair (or P-site tRNA in the P-E tRNA pair) is too close to the axis of rotation symmetry to harmonize with the geometry of the anticodon loops and mRNA. Accordingly, if three tRNAs must bind to the ribosome at a time, at least one of them should take a different conformation, as is the case for aminoacyl-tRNA in the recognition mode of A-site.

Why a cross-link from position 20:1 of lupin tRNA ^Met located at the A-site to position 875-905 of 23S rRNA is serious without a drastic conformational change

It has not been known that helix 38 (868-909) of 23S rRNA is highly conserved and bind to either a r-protein or a specific region of tRNA before position 20:1 of lupin tRNA ^Met is found to be cross-linked to it ( 63 ). This is why Mitchell et al. ( 64 ) had located it at the solvent side of the 50S subunit, far away from the ribosomal A-site. On the other hand, the A-site-bound tRNA is surrounded by highly conserved rRNA regions and r-protein L2. Considering that the P-site bound tRNA is situated between the L1 stalk and the central protuberance of the ribosome, as can be seen from the distributions of the cross-linking positions on the models shown in Figure 4 a-d, and that the 3' end regions of both A- and P-site tRNAs are surrounded by the 23S rRNA region of peptidyl transferase centre, where L2 functions covering the range from 1757 to 2010 of 23S rRNA ( 65 ), there would be almost no space for the position 20:1 of crystallographically observed L-shaped tRNA structure to be bound to the loop end of helix 38 of 23S rRNA without shutting down the entrance of the next A-site tRNA. It would be much clearer if we think that position 8 of A-site tRNA, which is located on the opposite side of the crystal structure of tRNA, also cross-links to the same loop end, as shown by A2 in Table 1 and Figure 4 b, and that position 47 of A-site tRNA cross-links to the head of helix 89 of 23S rRNA (G in Table 1 and Fig. 4 b), which is known to be located near the L7/L12 stalk of the ribosome ( 63 , 66 ). On the contrary, the point D1 in Table 1 is not shown in Figure 4 b, because the cross-linking position to 2309 of 23S rRNA, which is too close to those of D and D2 in Figure 4 b, could not be satisfied with the present model of A-site tRNA in the A-P pair of the pre-translocational state. We think that this state of cross-linking could be realized in the recognition mode of A-site, which holds a low affinity aminoacyl- tRNA binding ([delta] site; 33 ). We have built such a model, in which position 47 of P-site tRNA is very close to position 20 of the tRNA at the site (K.Nagano and N.Nagano, unpublished data). The points H and H1 in Figure 4 b could also be better explained by such a mechanism. The distribution of the cross-linking positions from the aminoacyl-end (N) in Table 1 ( 48 , 67 , 68 ) could be the result of dynamic character at the highly conserved rRNA region at the peptidyl transferase centre. This kind of flexibility in the rRNA structure must be taken into account for explaining the distribution of rRNA cross-linking positions shown in Figure 4 b.

CONCLUSIONS

The experimental data accumulated so far with respect to tRNA molecules on the ribosome and their environmental r-proteins and rRNAs can be understood by a new ribosomal three-tRNA binding model better than by the other conventional models. It is an S-type side-by-side model, in which two adjacent tRNA molecules are bound together via two highly conserved D-loop and T[psi]C-loop regions in addition to the adjacent codon-anticodon base pairings. We hope we could extend the present method towards a reasonable tertiary structure prediction for r-proteins such as L27 and L2.

ACKNOWLEDGEMENTS

We are grateful to Drs K. H. Nierhaus and R. Brimacombe of Max-Planck-Institut für Molekulare Genetik, Berlin-Dahlem, Germany, for various suggestions and useful discussions. We also thank Dr N. Tomioka of Faculty of Pharmaceutical Sciences, University of Tokyo, for helping us to use the AMBER program.

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