The structure of Escherichia coli signal recognition particle revealed by scanning transmission electron microscopy

Annular dark field transmission electron microscopy for protein structure determination

Recently annular dark field (ADF) transmission electron microscopy (TEM) has been advocated as a means of recording images of biological specimens with better signal to noise ratio (SNR) than regular bright field images. I investigate whether and how such images could be used to determine the three-dimensional structure of proteins given that an ADF aperture with a suitable pass-band can be manufactured and used in practice. I develop an approximate theory of ADF-TEM image formation for weak amplitude and phase objects and test this theory using computer simulations. I also test whether these simulated images can be used to calculate a three-dimensional model of the protein using standard software and discuss problems and possible ways to overcome these.

Fidelity of cotranslational protein targeting by the signal recognition particle

Accurate folding, assembly, localization, and maturation of newly synthesized proteins are essential to all cells and require high fidelity in the protein biogenesis machineries that mediate these processes. Here, we review our current understanding of how high fidelity is achieved in one of these processes, the cotranslational targeting of nascent membrane and secretory proteins by the signal recognition particle (SRP). Recent biochemical, biophysical, and structural studies have elucidated how the correct substrates drive a series of elaborate conformational rearrangements in the SRP and SRP receptor GTPases; these rearrangements provide effective fidelity checkpoints to reject incorrect substrates and enhance the fidelity of this essential cellular pathway. The mechanisms used by SRP to ensure fidelity share important conceptual analogies with those used by cellular machineries involved in DNA replication, transcription, and translation, and these mechanisms likely represent general principles for other complex cellular pathways.

Signal recognition particle: an essential protein-targeting machine

The signal recognition particle (SRP) and its receptor compose a universally conserved and essential cellular machinery that couples the synthesis of nascent proteins to their proper membrane localization. The past decade has witnessed an explosion in in-depth mechanistic investigations of this targeting machine at increasingly higher resolutions. In this review, we summarize recent work that elucidates how the SRP and SRP receptor interact with the cargo protein and the target membrane, respectively, and how these interactions are coupled to a novel GTPase cycle in the SRP·SRP receptor complex to provide the driving force and enhance the fidelity of this fundamental cellular pathway. We also discuss emerging frontiers in which important questions remain to be addressed.

Exploring the interactions between signal sequences and E. coli SRP by two distinct and complementary crosslinking methods

Photoaffinity crosslinking comprises a group of invaluable techniques used to investigate in detail a binding interaction between two polypeptides. As the diverse photo crosslinking techniques available display inherent differences, the method of choice will provide specific information about a particular system under study. We used two complementary crosslinking approaches: photo-induced crosslinking of unmodified proteins (PICUP) and benzophenone-mediated (BPM) crosslinking to extensively examine the interaction between the signal recognition particle (SRP) and signal sequences. Signal peptide binding by SRP presents a central puzzle in the protein targeting process because signal sequences must be recognized with fidelity but lack strict primary structural homology. The concurrent use of PICUP and BPM crosslinking to link signal peptides to E. coli SRP allowed us to explore the crosslinking pattern resulting from using different crosslinking chemistries, varying the position of the photoprobe in the hydrophobic core of the signal sequence, and shifting the crosslinking reactive group away from the signal peptide backbone. By PICUP, signal peptides crosslinked exclusively to the NG domain of the SRP protein Ffh, regardless of the position of the reactive residue. Benzophenone-modified amino acids preferentially crosslinked the signal peptide to the C-terminal (M) domain of Ffh. We conclude that signal peptide binding is largely mediated by the M domain. Importantly, our data also indicate intimate, at least transient, contacts between the hydrophobic core of the signal peptide and the NG domain. These results reopen the possibility of a direct involvement of the NG domain in signal sequence recognition.

The signal recognition particle (SRP) RNA links conformational changes in the SRP to protein targeting

The RNA component of the signal recognition particle (SRP) is universally required for cotranslational protein targeting. Biochemical studies have shown that SRP RNA participates in the central step of protein targeting by catalyzing the interaction of the SRP with the SRP receptor (SR). SRP RNA also accelerates GTP hydrolysis in the SRP.SR complex once formed. Using a reverse-genetic and biochemical analysis, we identified mutations in the E. coli SRP protein, Ffh, that abrogate the activity of the SRP RNA and cause corresponding targeting defects in vivo. The mutations in Ffh that disrupt SRP RNA activity map to regions that undergo dramatic conformational changes during the targeting reaction, suggesting that the activity of the SRP RNA is linked to the major conformational changes in the signal sequence-binding subunit of the SRP. In this way, the SRP RNA may coordinate the interaction of the SRP and the SR with ribosome recruitment and transfer to the translocon, explaining why the SRP RNA is an indispensable component of the protein targeting machinery.