The ribosome and its role in protein folding: looking through a magnifying glass

Javed, Abid; Christodoulou, John; Cabrita, Lisa D.; Orlova, Elena V.

doi:10.1107/s2059798317007446

Cited by 36 publications

(33 citation statements)

References 139 publications

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“…Ribosomes are nano-machines that translate information coded in a messenger RNA into proteins in all living organisms. Recently, it has been found that ribosomes can also play a significant role in the process of co-translational folding by modulating the folding of a nascent chain (NC) during translation (Kaiser et al, 2011;Cabrita et al, 2016;Javed et al, 2017;Samulson et al, 2018;Liu et al, 2019). Nascent chains (NC) can begin to acquire secondary structural elements in a cotranslational manner during emergence via the ribosome exit tunnel within the large subunit of the ribosome (Netzer W. et al, 1997;Thommen et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Visualising nascent chain dynamics at the ribosome exit tunnel by cryo-electron microscopy

Javed

Cabrita

Cassaignau

et al. 2019

Preprint

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One of the important questions in protein synthesis on the ribosome is how the nascent polypeptide chains fold during translation. Addressing this question has strong implications to health and disease. Ribosomes play an essential role in maintaining a healthy cellular proteome by modulating co-translational folding. And folding of the nascent chain (NC) is likely to be initiated within the ribosomal exit tunnel. Here, we report high-resolution cryo-EM structures of stalled ribosome nascent-chain complexes (RNCs) at two biosynthetic translation time-points that examine the role of the ribosome during co-translational folding. Structures of the RNCs reveal that NC is highly dynamic and adopts a range of trajectories within the vestibule of the exit tunnel, affecting positions of the folded immunoglobulin domain outside the ribosome. Local rearrangements of several ribosomal components suggest key sensor checkpoints that monitor co-translational protein folding. ribosome | nascent chain | co-translational folding | cryo-EM

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Section: Introductionmentioning

confidence: 99%

Visualising nascent chain dynamics at the ribosome exit tunnel by cryo-electron microscopy

Javed

Cabrita

Cassaignau

et al. 2019

Preprint

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“…In the context of a diffusing particle inside the tunnel, we previously found [9] that this radial increase creates a strong entropic barrier, which can be compensated by the electrostatic potential if the particle is positively charged. More generally, it was also experimentally shown that electrostatics in the ribosomal tunnel modulate chain elongation rates [9,17] and can even induce ribosome stalling [46]. At the proteome-wide level, averaging the charged amino acid frequency over all translated genes in S. cerevisiae revealed an elevated (respectively, decreased) amount of positively (respectively, negatively) charged amino acids in the first ∼ 20 codons [9].…”

Section: Impact On the Nascent Polypeptide Chain Transitmentioning

confidence: 95%

Differences in the path to exit the ribosome across the three domains of life

Duc

Batra

Bhattacharya

et al. 2018

Preprint

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Recent advances in biological imaging have led to a surge of fine-resolution structures of the ribosome from diverse organisms. Comparing these structures, especially the exit tunnel, to characterize the key similarities and differences across species is essential for various important applications, such as designing antibiotic drugs and understanding the intricate details of translation dynamics. Here, we compile and compare 20 fine-resolution cryo-EM and X-ray crystallography structures of the ribosome recently obtained from all three domains of life (bacteria, archaea and eukarya). We first show that a hierarchical clustering of tunnel shapes closely reflects the species phylogeny. Then, by analyzing the ribosomal RNAs and proteins localized near the tunnel, we explain the observed geometric variations and show direct association between the conservations of the geometry, structure, and sequence. We find that the tunnel is more conserved in its upper part, from the polypeptide transferase center to the constriction site. In the lower part, tunnels are significantly narrower in eukaryotes than in bacteria, and we provide evidence for the existence of a second constriction site in eukaryotic tunnels. We also show that ribosomal RNA and protein sequences are more likely to be conserved closer to the tunnel, as is the presence of positively charged amino acids. Overall, our comparative analysis shows how the geometric and biophysical properties of the exit tunnel play an important role in ensuring proper transit of the nascent polypeptide chain, and may explain the differences observed in several co-translational processes across species.

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“…In addition to offering a mechanism to explain long-distance communication in fully translated proteins, our helix stabilization model might be relevant to co-translational folding. The ribosomal exit tunnel can accommodate [34][35][36][37] and stabilize helices 38 , but the potential role of these transient helices remains unclear. We posit that the stabilizing effect of the tunnel on these transient helices might be transmitted to the exposed nascent polypeptide chain, thereby stabilizing folding of the emerging N-terminus.…”

Section: Implications For Co-translational Foldingmentioning

confidence: 99%

Modulating long-range energetics via helix stabilization: a case study using T4 lysozyme

Rosemond

Hamadani

Cate

et al. 2018

Preprint

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Cooperative protein folding requires distant regions of a protein to interact and provide mutual stabilization. The mechanism of this long-distance coupling remains poorly understood. Here, we use T4 lysozyme (T4L*) as a model to investigate long-range communications across a globular protein. T4L* is composed of two structurally distinct subdomains, although it behaves in a two-state manner at equilibrium. The subdomains of T4L* are connected via two topological connections: the N-terminal helix that is structurally part of the C-terminal subdomain (the A-helix) and a long helix that spans both subdomains (the C-helix). To understand the role that the C-helix plays in cooperative folding, we analyzed a circularly permuted version of T4L* (CP13*), whose subdomains are connected only by the C-helix. We demonstrate that when isolated as individual fragments, both subdomains of CP13* can fold autonomously into marginally stable conformations. The energetics of the N-terminal subdomain depend on the formation of a salt bridge known to be important for stability in the full-length protein. We show that the energetic contribution of the salt bridge to the stability of the N-terminal fragment increases when the C-helix is stabilized, such as occurs upon folding of the Cterminal subdomain. These results suggest a model where long-range energetic coupling is mediated by helix stabilization.Keywords: protein folding, effective concentration, cooperativity, helix stabilization, T4 lysozyme, In this work, we investigate how a helix spanning the two subdomains of T4 lysozyme* couples distant regions of the protein. We find evidence for a model of long-distance coupling that relies on the cooperative nature of helix formation to stabilize a long-range tertiary salt bridge interaction at one end of the helix and thereby couple the folding of T4 lysozyme's subdomains. This mechanistic model may have implications for co-translational folding. IntroductionCooperativity is a hallmark of globular proteins. At equilibrium, many small (<200 residues) globular proteins fold in an apparent two-state manner (U⇌N), populating either a completely folded or unfolded conformation 1,2 . The stability of the folded protein (ΔG UN = G N -G U ) is the sum of many interactions, both local and long-range. While the chemical nature and mechanism of the short-range, local interactions can be easy to identify and investigate, it is difficult to probe the long-range interactions that cause the structure and energetics in one region to be coupled to those in another region and thus lead to two-state behavior. For repeat proteins, such as ankrin domains, this coupling has been attributed to a large interfacial energy that, in some cases, overshadows the lack of intrinsic stability of the individual repeats 3,4 .Here, we explore coupling between distant regions of a protein using the protein T4 lysozyme*, T4L* (* denotes the cysteine-free pseudo-wild type variant 5 ). T4L* is a well-studied globular protein; the stabilities and structures of hundreds of...

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The ribosome and its role in protein folding: looking through a magnifying glass

Cited by 36 publications

References 139 publications

Visualising nascent chain dynamics at the ribosome exit tunnel by cryo-electron microscopy

Visualising nascent chain dynamics at the ribosome exit tunnel by cryo-electron microscopy

Differences in the path to exit the ribosome across the three domains of life

Modulating long-range energetics via helix stabilization: a case study using T4 lysozyme

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