Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome reveals its chaperone action

Abstract

Trigger factor (TF), the first chaperone in eubacteria to encounter the emerging nascent chain, binds to the large ribosomal subunit in the vicinity of the protein exit tunnel opening and forms a sheltered folding space. Here, we present the 3.5-Å crystal structure of the physiological complex of the large ribosomal subunit from the eubacterium Deinococcus radiodurans with the N-terminal domain of TF (TFa) from the same organism. For anchoring, TFa exploits a small ribosomal surface area in the vicinity of proteins L23 and L29, by using its ''signature motif'' as well as additional structural elements. The molecular details of TFa interactions reveal that L23 is essential for the association of TF with the ribosome and may serve as a channel of communication with the nascent chain progressing in the tunnel. L29 appears to induce a conformational change in TFa, which results in the exposure of TFa hydrophobic patches to the opening of the ribosomal exit tunnel, thus increasing its affinity for hydrophobic segments of the emerging nascent polypeptide. This observation implies that, in addition to creating a protected folding space for the emerging nascent chain, TF association with the ribosome prevents aggregation by providing a competing hydrophobic environment and may be critical for attaining the functional conformation necessary for chaperone activity.protein folding ͉ nascent chain ͉ ribosomal exit tunnel ͉ ribosomal crystallography ͉ Deinococcus radiodurans

Trigger Factor Forms a Protective Shield for Nascent Polypeptides at the Ribosome

“…However, our finding that TF was able to transiently shield nascent polypeptides exposing up to 37 or 41 kDa outside the ribosome raises the question of how such large proteins can be accommodated underneath TF. It is possible that the cavity formed between the ribosomal surface and the N-terminal tail and C-terminal arms of TF can adopt a significantly larger volume (Ͼ14 kDa) than originally anticipated based on the structural models (5)(6)(7)15). Another explanation is that large nascent polypeptides are incorporated underneath the entire TF molecule additionally involving the C-terminal region beyond the C-terminal arms and perhaps the PPIase domain.…”

“…On the other hand, the models predict different volumes for the space formed by the ribosomal surface and the N-terminal tail and C-terminal arms of TF. While two models propose that this space resembles a cavity which is large enough to accommodate protein domains or small proteins of ϳ14 kDa or even larger (5,6), the third model suggests a rather narrow crevice more suitable to bind an unfolded polypeptide (7). These contradictory models of the conformation of TF on the ribosome make it difficult to define a mechanism of action for TF and do not further clarify what effects TF exerts on nascent polypeptides.…”

Versatility of Trigger Factor Interactions with Ribosome-Nascent Chain Complexes

“…Interestingly, the hydrophobic character of the nascent chain only moderately affected the residence time of TF on the ribosome, as measured with TF-B, but rather increased the on-rate for TF binding to the ribosome, presumably by providing additional interaction surfaces. Thus, whereas TF binding to the L23/L29 docking site on the ribosome is a prerequisite for nascent chain interaction, resulting in a conformational change in TF that facilitates nascent chain association (16,19), the presence of hydrophobic elements in the nascent chain emerging from the ribosome appears to increase the avidity of TF for ribosome docking.…”

“…The second contact involves ribosomal protein L29, which is not essential for TF-ribosome interaction (6). In the Deinococcus radiodurans co-crystal structure, the TF N-domain undergoes a conformational change in the ribosomebound form (19). As a result, the N-domain exposes hydrophobic surfaces toward the opening of the ribosomal exit tunnel, presumably providing a binding surface for the emerging nascent chain that would be absent in the non-ribosome bound form.…”

Interplay between trigger factor and other protein biogenesis factors on the ribosome

“…SRP and TF together can bind to the ribosome, although both contact protein L23 at the peptide exit ( Fig. 1) 3,[14][15][16][17][18] ; changes in crosslinking patterns indicate that conformational changes accompany the accommodation of the two ligands on one ribosome 19,20 .…”