Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites

Ratje, Andreas Heinrich; Loerke, Justus; Mikolajka, Aleksandra; Brünner, Matthias; Hildebrand, Peter W.; Starosta, Agata L.; Dönhöfer, Alexandra; Connell, Sean R.; Fucini, Paola; Mielke, Thorsten; Whitford, Paul C.; Onuchic, José N.; Yu, Yanan; Sanbonmatsu, Karissa Y.; Hartmann, Roland K.; Penczek, Pawel A.; Wilson, Daniel N.; Spahn, C.M.T.

doi:10.1038/nature09547

Cited by 349 publications

(533 citation statements)

References 41 publications

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“…3A, solvent and top views) (29); (iii) small subunit head swivel, a rotation of the subunit head about its long axis (Fig. 3A, top view) (30); and (iv) small subunit head closure, a "nodding" motion of the head (Fig. 3A, side and solvent views) (31).…”

Section: Resultsmentioning

confidence: 99%

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Trajectories of the ribosome as a Brownian nanomachine

Dashti

Schwander

Langlois

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

229

222

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A Brownian machine, a tiny device buffeted by the random motions of molecules in the environment, is capable of exploiting these thermal motions for many of the conformational changes in its work cycle. Such machines are now thought to be ubiquitous, with the ribosome, a molecular machine responsible for protein synthesis, increasingly regarded as prototypical. Here we present a new analytical approach capable of determining the free-energy landscape and the continuous trajectories of molecular machines from a large number of snapshots obtained by cryogenic electron microscopy. We demonstrate this approach in the context of experimental cryogenic electron microscope images of a large ensemble of nontranslating ribosomes purified from yeast cells. The freeenergy landscape is seen to contain a closed path of low energy, along which the ribosome exhibits conformational changes known to be associated with the elongation cycle. Our approach allows model-free quantitative analysis of the degrees of freedom and the energy landscape underlying continuous conformational changes in nanomachines, including those important for biological function.cryo-electron microscopy | elongation cycle | manifold embedding | nanomachines | translation

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Section: Resultsmentioning

confidence: 99%

“…3A, side and solvent views) (31). The first three motions are correlated and known to be associated with the process of mRNAtRNA translocation (30,32), whereas the fourth is known to accompany the selection of cognate aminoacyl tRNA during the process of decoding (31).…”

Section: Resultsmentioning

confidence: 99%

Trajectories of the ribosome as a Brownian nanomachine

Dashti

Schwander

Langlois

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

229

222

View full text Add to dashboard Cite

show abstract

“…The letters separated by the ‘/’ indicate the tRNA binding sites in the 30S and 50S ribosomes, respectively. The two letters (ap) for the 30S binding site indicate the intra-30S hybrid state due to the 30S head swivel [16]. Conversely, in Int1, the tRNAs are in the ap/ap (the two letters for the 50S binding site indicate the intermediate location of the tRNA between the classic A- and P-sites [17,18]) and pe/E configurations.…”

Section: Resultsmentioning

confidence: 99%

Dual DNA rulers reveal an ‘mRNA looping’ intermediate state during ribosome translocation

Yin

Wang

2018

RNA Biology

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The precise 3-nucleotide movement of mRNA is critical for translation fidelity. One mRNA translocation error propagates to all of the following codons, which is detrimental to the cell. However, none of the current methods can reveal the mRNA dynamics near the ribosome entry site, which limits the understanding of this important issue. We have developed an assay of dual DNA rulers that provides such capability. By uniquely probing both the 3ʹ- and 5ʹ-ends of mRNA, we observed an antibiotic-trapped intermediate state that is consistent with a ribosomal conformation containing mRNA asymmetric partial displacements at its entry and exit sites. Based on the available ribosome structures and computational simulations, we proposed a ‘looped’ mRNA conformation, which suggested a stepwise ‘inchworm’ mechanism for ribosomal translocation. The same ‘looped’ intermediate state identified with the dual rulers persists with a ‘-1’ frameshifting motif, indicating that the branching point of normal and frameshifting translocations occurs at a later stage of translocation.

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“…These simulations enabled us to determine whether L1,2 deletion affects the ISC-binding pocket as part of a global change in the dynamics, or through a specific communication route. Because structure-based simulations (38,45), which are grounded in energy landscape theory (46), accurately describe the native-ensemble structural fluctuations of biomolecular systems (10,38,(47)(48)(49)(50)(51), we utilized an all-atom structure-based model (38) to explore the mechanism of L1,2-ISC-pocket communication. This model does not explicitly include long-or short-range electrostatic interactions, but it allows for the dissection of the geometric features that may impact function and folding.…”

Section: Resultsmentioning

confidence: 99%

Allostery in the ferredoxin protein motif does not involve a conformational switch

Nechushtai

Lammert²,

Michaeli³

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

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Regulation of protein function via cracking, or local unfolding and refolding of substructures, is becoming a widely recognized mechanism of functional control. Oftentimes, cracking events are localized to secondary and tertiary structure interactions between domains that control the optimal position for catalysis and/or the formation of protein complexes. Small changes in free energy associated with ligand binding, phosphorylation, etc., can tip the balance and provide a regulatory functional switch. However, understanding the factors controlling function in single-domain proteins is still a significant challenge to structural biologists. We investigated the functional landscape of a single-domain planttype ferredoxin protein and the effect of a distal loop on the electron-transfer center. We find the global stability and structure are minimally perturbed with mutation, whereas the functional properties are altered. Specifically, truncating the L1,2 loop does not lead to large-scale changes in the structure, determined via X-ray crystallography. Further, the overall thermal stability of the protein is only marginally perturbed by the mutation. However, even though the mutation is distal to the iron-sulfur cluster (∼20 Å), it leads to a significant change in the redox potential of the ironsulfur cluster (57 mV). Structure-based all-atom simulations indicate correlated dynamical changes between the surface-exposed loop and the iron-sulfur cluster-binding region. Our results suggest intrinsic communication channels within the ferredoxin fold, composed of many short-range interactions, lead to the propagation of long-range signals. Accordingly, protein interface interactions that involve L1,2 could potentially signal functional changes in distal regions, similar to what is observed in other allosteric systems.electron transfer | functional energy landscape | iron-sulfur proteins | protein folding O ver the last several decades, our understanding of protein function has evolved from a rather static perspective, where signaling and function have been understood through surface complementarity arguments, such as the "lock and key" paradigm (1, 2), to a more dynamic view where protein conformational fluctuations are inextricably linked to function (3). As our understanding of protein dynamics expands, we are revealing many mechanisms by which proteins exploit conformational fluctuations to perform cellular function. In multidomain proteins, relative repositioning of domains is often linked to their levels of activity. For example, large-scale domain rearrangements in the four-domain Src kinase (4) and C-terminal Src kinase (5, 6) lead to these proteins being in so-called "on" or "off" states, and functional regulation may be obtained by adjusting the balance between these conformations (7). In proteins such as adenylate kinase, domain rearrangements can be rate limiting during each round of catalysis (8), where the enzyme cycles between ligandcompetent and ligand-release conformations. Because the kinetics of these tra...

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Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites

Cited by 349 publications

References 41 publications

Trajectories of the ribosome as a Brownian nanomachine

Trajectories of the ribosome as a Brownian nanomachine

Dual DNA rulers reveal an ‘mRNA looping’ intermediate state during ribosome translocation

Allostery in the ferredoxin protein motif does not involve a conformational switch

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