Dynamics and electrostatics define an allosteric druggable site within the receptor-binding domain of SARS-CoV-2 spike protein

The pathogenesis of the SARS-CoV-2 virus initiates through recognition of the angiotensin-converting enzyme 2 (ACE2) receptor of the host cells by the receptor-binding domain (RBD) located at the spikes of the virus. Here, using molecular dynamics simulations, we have demonstrated the allosteric crosstalk within the RBD in the apo- and the ACE2 receptor-bound states, revealing the contribution of the dynamics-based correlated motions and the electrostatic energy perturbations to this crosstalk. While allostery, based on correlated motions, dominates inherent distal communication in the apoRBD, the electrostatic energy perturbations determine favorable pairwise crosstalk within the RBD residues upon binding to ACE2. Interestingly, the allosteric path is composed of residues which are evolutionarily conserved within closely related coronaviruses, pointing toward the biological relevance of the communication and its potential as a target for drug development

Locking and Unlocking of Ribosomal Motions

AbstractDuring the ribosomal translocation, the binding of elongation factor G (EF-G) to the pretranslocational ribosome leads to a ratchet-like rotation of the 30S subunit relative to the 50S subunit in the direction of the mRNA movement. By means of cryo-electron microscopy we observe that this rotation is accompanied by a 20 Å movement of the L1 stalk of the 50S subunit, implying that this region is involved in the translocation of deacylated tRNAs from the P to the E site. These ribosomal motions can occur only when the P-site tRNA is deacylated. Prior to peptidyl-transfer to the A-site tRNA or peptide removal, the presence of the charged P-site tRNA locks the ribosome and prohibits both of these motions

Characterization of the nuclear export adaptor protein Nmd3 in association with the 60S ribosomal subunit

3D reconstruction by cryo-EM provides the first structural description of a ribosomal biogenesis factor (Nmd3) in complex with the 60S ribosomal subunit

Structural Diversity in Bacterial Ribosomes: Mycobacterial 70S Ribosome Structure Reveals Novel Features

Here we present analysis of a 3D cryo-EM map of the 70S ribosome from Mycobacterium smegmatis, a saprophytic cousin of the etiological agent of tuberculosis in humans, Mycobacterium tuberculosis. In comparison with the 3D structures of other prokaryotic ribosomes, the density map of the M. smegmatis 70S ribosome reveals unique structural features and their relative orientations in the ribosome. Dramatic changes in the periphery due to additional rRNA segments and extra domains of some of the peripheral ribosomal proteins like S3, S5, S16, L17, L25, are evident. One of the most notable features appears in the large subunit near L1 stalk as a long helical structure next to helix 54 of the 23S rRNA. The sharp upper end of this structure is located in the vicinity of the mRNA exit channel. Although the M. smegmatis 70S ribosome possesses conserved core structure of bacterial ribosome, the new structural features, unveiled in this study, demonstrates diversity in the 3D architecture of bacterial ribosomes. We postulate that the prominent helical structure related to the 23S rRNA actively participates in the mechanisms of translation in mycobacteria

Mechanistic Insight into the Reactivation of BCAII Enzyme from Denatured and Molten Globule States by Eukaryotic Ribosomes and Domain V rRNAs

In all life forms, decoding of messenger-RNA into polypeptide chain is accomplished by the ribosome. Several protein chaperones are known to bind at the exit of ribosomal tunnel to ensure proper folding of the nascent chain by inhibiting their premature folding in the densely crowded environment of the cell. However, accumulating evidence suggests that ribosome may play a chaperone role in protein folding events in vitro. Ribosome-mediated folding of denatured proteins by prokaryotic ribosomes has been studied extensively. The RNA-assisted chaperone activity of the prokaryotic ribosome has been attributed to the domain V, a span of 23S rRNA at the intersubunit side of the large subunit encompassing the Peptidyl Transferase Centre. Evidently, this functional property of ribosome is unrelated to the nascent chain protein folding at the exit of the ribosomal tunnel. Here, we seek to scrutinize whether this unique function is conserved in a primitive kinetoplastid group of eukaryotic species Leishmania donovani where the ribosome structure possesses distinct additional features and appears markedly different compared to other higher eukaryotic ribosomes. Bovine Carbonic Anhydrase II (BCAII) enzyme was considered as the model protein. Our results manifest that domain V of the large subunit rRNA of Leishmania ribosomes preserves chaperone activity suggesting that ribosome-mediated protein folding is, indeed, a conserved phenomenon. Further, we aimed to investigate the mechanism underpinning the ribosome-assisted protein reactivation process. Interestingly, the surface plasmon resonance binding analyses exhibit that rRNA guides productive folding by directly interacting with molten globule-like states of the protein. In contrast, native protein shows no notable affinity to the rRNA. Thus, our study not only confirms conserved, RNA-mediated chaperoning role of ribosome but also provides crucial insight into the mechanism of the process

Intrinsic Molecular Properties of the Protein–Protein Bridge Facilitate Ratchet-Like Motion of the Ribosome

The ribosomal intersubunit bridges maintain the overall architecture of the ribosome and thereby play a pivotal role in the dynamics of translation. The only protein–protein bridge, b1b, is formed by the two proteins, S13 and L5 of the small and large ribosomal subunits, respectively. B1b absorbs the largest movement during ratchet-like motion, and its two proteins reorganize in different constellations during this motion of the ribosome. Our results in this study of b1b in the Escherichia coli 70S ribosome suggest that the intrinsic molecular features of the bridging proteins allow the bridge to modulate the ratchet-like motion in a controlled manner. Additionally, another large subunit protein, L31, seems to participate with S13 and L5 in the formation, dynamics, and stabilization of this bridge

Structural analysis of the <i>Msm</i>50S.

<p>(A) Secondary structure diagram of the <i>M. laprae</i> 23S rRNA (left: 5′ end; right: 3′ end). Locations of extra rRNA helices in mycobacterium are highlighted (orange) and marked in the 5′ 23S rRNA structure (domains I, II, III). (B) Stereo view of the solvent side of <i>Msm</i>50S (blue wire mesh) with the coordinates <i>of E. coli</i> 50S subunit (23S rRNA pale cyan, 5S rRNA deep blue, proteins grey) docked inside. The atomic structure is adopted from the crystal structure of <i>E. coli</i> 70S ribosome (Protein Data Bank ID code 2I2V). Major additional density clusters are highlighted in different colors; steeple, deep pink; H15/H16a, orange; H31a, purple; additional density of L25, yellow; additional densities of proteins around the tunnel exit, green. Landmarks are as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031742#pone-0031742-g001" target="_blank">Figure 1</a>.</p

Structural analysis of the <i>Msm</i>30S.

<p>(A) Secondary structure diagram of the <i>M. tuberculocis</i> 16S rRNA. The helices which are different in mycobacterial 16S rRNA as compared to the <i>E. coli</i> 16S rRNA are marked (shorter, red; longer, cyan). (B) Stereo view of the solvent side of <i>Msm</i>30S (yellow wire mesh) with the docked crystal structure of <i>E. coli</i> 30S subunit (16S rRNA in olive, proteins in grey colour) (pdb code: 2I2U). Major extra density clusters (solid yellow) are shown. Proteins with additional segments are coloured and designated with their names. Density cluster marked with asterisk (*) represents the density corresponding to extra components of h9 and proteins S16, S17. Landmarks are as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031742#pone-0031742-g001" target="_blank">Figure 1</a>.</p

List of <i>M. smegmatis</i> ribosomal proteins that are bigger than their <i>E. coli</i> counter parts (proteins more than 12 amino acids (aa) longer are mentioned here).

<p>List of <i>M. smegmatis</i> ribosomal proteins that are bigger than their <i>E. coli</i> counter parts (proteins more than 12 amino acids (aa) longer are mentioned here).</p