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Elongation factor G (EF-G) catalyzes tRNA translocation on the ribosome. Here a cryo-EM reconstruction of the 70S*EF-G ribosomal complex at 7.3 A resolution and the crystal structure of EF-G-2*GTP, an EF-G homolog, at 2.2 A resolution are presented. EF-G-2*GTP is structurally distinct from previous EF-G structures, and in the context of the cryo-EM structure, the conformational changes are associated with ribosome binding and activation of the GTP binding pocket. The P loop and switch II approach A2660-A2662 in helix 95 of the 23S rRNA, indicating an important role for these conserved bases. Furthermore, the ordering of the functionally important switch I and II regions, which interact with the bound GTP, is dependent on interactions with the ribosome in the ratcheted conformation. Therefore, a network of interaction with the ribosome establishes the active GTP conformation of EF-G and thus facilitates GTP hydrolysis and tRNA translocation.

The 3C-like protease (3CL pro ) of severe acute respiratory syndrome coronavirus (SARS-CoV) cleaves 11 sites in the polyproteins, including its own N-and C-terminal autoprocessing sites, by recognizing P4-P1 and P1′. In this study, we determined the crystal structure of 3CL pro with the C-terminal prosequence and the catalytic-site C145A mutation, in which the enzyme binds the C-terminal prosequence of another molecule. Surprisingly, Phe at the P3′ position [Phe(P3′)] is snugly accommodated in the S3′ pocket. Mutations of Phe(P3′) impaired the C-terminal autoprocessing, but did not affect N-terminal autoprocessing. This difference was ascribed to the P2 residue, Phe(P2) and Leu(P2), in the C-and N-terminal sites, as follows. The S3′ subsite is formed by Phe(P2)-induced conformational changes of 3CL pro and the direct involvement of Phe(P2) itself. In contrast, the N-terminal prosequence with Leu(P2) does not cause such conformational changes for the S3′ subsite formation. In fact, the mutation of Phe(P2) to Leu in the C-terminal autoprocessing site abolishes the dependence on Phe(P3′). These mechanisms explain why Phe is required at the P3' position when the P2 position is occupied by Phe rather than Leu, which reveals a type of subsite cooperativity. Moreover, the peptide consisting of P4-P1 with Leu(P2) inhibits protease activity, whereas that with Phe (P2) exhibits a much smaller inhibitory effect, because Phe(P3′) is missing. Thus, this subsite cooperativity likely exists to avoid the autoinhibition of the enzyme by its mature C-terminal sequence, and to retain the efficient C-terminal autoprocessing by the use of Phe(P2).SARS | 3CL protease | specificity | subsite cooperativity | crystal structure

A spectroscopic method, based on the interface selectivity of second-harmonic generation, is used to obtain the polarity of liquid interfaces. In this paper the second-harmonic measurement of the spectrum of the polarity indicator molecule N, N′-diethyl-p-nitroaniline (DEPNA) at the air/water interface demonstrates the method. Two different approaches are used to measure the intramolecular charge transfer (CT) absorption band position of DEPNA at the air/water interface. The DEPNA CT band blue-shifts from 429 nm in bulk water (polar solvent) to 359 nm in bulk hexane (nonpolar solvent) and 329 nm in the gas phase (no solvent). At the air/water interface, the charge transfer peak band maximum occurs at 373 nm, which indicates that the polarity of the air/water interface is similar to those of the bulk solvents carbon tetrachloride and butyl ether. The DEPNA results together with the results from another solvatochromic polarity indicator molecule, ET-(30), which will be reported elsewhere, show that the polarity results of the air/water interface are general.