Crystal structure of the intact archaeal translation initiation factor 2 demonstrates very high conformational flexibility in the alpha- and beta-subunits

In Eukarya and Archaea, translation initiation factor 2 (eIF2/aIF2), which contains three subunits (α, β, and γ), is pivotal for binding of charged initiator tRNA to the small ribosomal subunit. The crystal structure of the full-sized heterotrimeric aIF2 from Sulfolobus solfataricus in the nucleotide-free form has been determined at 2.8-Å resolution. Superposition of four molecules in the asymmetric unit of the crystal and the comparison of the obtained structures with the known structures of the aIF2αγ and aIF2βγ heterodimers revealed high conformational flexibility in the α- and β-subunits. In fact, the full-sized aIF2 consists of a rigid central part, formed by the γ-subunit, domain 3 of the α-subunit, and the N-terminal α-helix of the β-subunit, and two mobile “wings,” formed by domains 1 and 2 of the α-subunit, the central part, and the zinc-binding domain of the β-subunit. High structural flexibility of the wings is probably required for interaction of aIF2 with the small ribosomal subunit. Comparative analysis of all known structures of the γ-subunit alone and within the heterodimers and heterotrimers in nucleotide-bound and nucleotide-free states shows that the conformations of switch 1 and switch 2 do not correlate with the assembly or nucleotide states of the protein.     

Role of helix 0 of the N-BAR domain in membrane curvature generation

A group of proteins with cell membrane remodeling properties is also able to change dramatically the morphology of liposomes in vitro, frequently inducing tubulation. For a number of these proteins, the mechanism by which this effect is exerted has been proposed to be the embedding of amphipathic helices into the lipid bilayer. For proteins presenting BAR domains, removal of an N-terminal amphipathic α-helix (H0-NBAR) results in much lower membrane tubulation efficiency, pointing to a fundamental role of this protein segment. Here, we studied the interaction of a peptide corresponding to H0-NBAR with model lipid membranes. H0-NBAR bound avidly to anionic liposomes but partitioned weakly to zwitterionic bilayers, suggesting an essentially electrostatic interaction with the lipid bilayer. Interestingly, it is shown that after membrane incorporation, the peptide oligomerizes as an antiparallel dimer, suggesting a potential role of H0-NBAR in the mediation of BAR domain oligomerization. Through monitoring the effect of H0-NBAR on liposome shape by cryoelectron microscopy, it is clear that membrane morphology is not radically changed. We conclude that H0-NBAR alone is not able to induce vesicle curvature, and its function must be related to the promotion of the scaffold effect provided by the concave surface of the BAR domain.     

The Thermus thermophilus5S rRNA–Protein Complex: Identification of Specific Binding Sites for Proteins L5 and L18 in the 5S rRNA

Three 5S rRNA-binding ribosomal proteins (L5, L18, TL5) of extremely thermophilic bacterium Thermus thermophilushave earlier been isolated. Structural analysis of their complexes with rRNA requires identification of their binding sites in the 5S rRNA. Previously, a TL5-binding site has been identified, a TL5–RNA complex crystallized, and its structure determined to 2.3 Å. The sites for L5 and L18 were characterized, and two corresponding 5S rRNA fragments constructed. Of these, a 34-nt fragment specifically interacted with L5, and a 55-nt fragment interacted with L5, L18, and with both proteins. The 34-nt fragment–L5 complex was crystallized; the crystals are suitable for high-resolution X-ray analysis.     

Emission of alfvén waves from a nonuniform MHD waveguide

The efficiency of the wave energy loss from a nonuniform MHD waveguide due to the conversion of the trapped magnetosonic waveguide modes into runaway Alfvén waves is estimated theoretically. It is shown that, if the waveguide parameters experience a jumplike change along the waveguide axis, the interaction between the waveguide modes and Alfvén waves occurs precisely at this “jump.” This effect is incorporated into the boundary conditions. A set of coupled integral equations with a singular kernel is derived in order to determine the transmission and reflection coefficients for the waveguide modes. The poles in the kernels of the integral operators correspond to the surface waves. When the jump in the waveguide parameters is small, analytic expressions for the frequency dependence of the transformation coefficients are obtained by using a model profile of the Alfvén velocity along the magnetic field. For the jump characterized by the small parameter value ε=0.3, the wave-amplitude transformation coefficient can amount to 5–10%. Under the phase synchronization condition (when the phase velocities of the waveguide modes on both sides of the jump are the same), the wave-energy transformation coefficient is much higher: it increases from a fraction of one percent to tens of percent. The transformation of fast magnetosonic waves into Alfvén waves is resonant in character, which ensures the frequency and wavelength filteringof the emitted Alfvén perturbations.