Disorder guides domain rearrangement in elongation factor Tu

Exploring Protein Conformational Changes Using a Large-Scale Biophysical Sampling Augmented Deep Learning Strategy

Inspired by the success of deep learning in predicting static protein structures, researchers are now actively exploring other deep learning algorithms aimed at predicting the conformational changes of proteins. Currently, a major challenge in the development of such models lies in the limited training data characterizing different conformational transitions. To address this issue, molecular dynamics simulations is combined with enhanced sampling methods to create a large-scale database. To this end, the study simulates the conformational changes of 2635 proteins featuring two known stable states, and collects the structural information along each transition pathway. Utilizing this database, a general deep learning model capable of predicting the transition pathway for a given protein is developed. The model exhibits general robustness across proteins with varying sequence lengths (ranging from 44 to 704 amino acids) and accommodates different types of conformational changes. Great agreement is shown between predictions and experimental data in several systems and successfully apply this model to identify a novel allosteric regulation in an important biological system, the human β-cardiac myosin. These results demonstrate the effectiveness of the model in revealing the nature of protein conformational changes.

Allosteric pathways of SARS and SARS-CoV-2 spike protein identified by neural relational inference

The receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein must undergo a crucial conformational transition to invade human cells. It is intriguing that this transition is accompanied by a synchronized movement of the entire spike protein. Therefore, it is possible to design allosteric regulators targeting non-RBD but hindering the conformational transition of RBD. To understand the allosteric mechanism in detail, we establish a computational framework by integrating coarse-grained molecular dynamic simulations and a state-of-the-art neural network model called neural relational inference. Leveraging this framework, we have elucidated the allosteric pathway of the SARS-CoV-2 spike protein at the residue level and identified the molecular mechanisms involved in the transmission of allosteric signals. The movement of D614 is coupled with that of Q321. This interaction subsequently influences the movement of K528/K529, ultimately coupling with the movement of RBD during conformational changes. Mutations that weaken the interactions within this pathway naturally block the allosteric signal transmission, thereby modulating the conformational transitions. This observation also offers a rationale for the distinct allosteric patterns observed in the SARS-CoV spike protein. Our result provides a useful method for analyzing the dynamics of potential viral variants in the future.

Conformational changes of ribosomes during translation elongation resolved by molecular dynamics simulations

Molecular dynamics simulations have emerged as a powerful set of tools to unravel the intricate dynamics of ribosomes during protein synthesis. Recent advancements in this field have enabled simulations to delve deep into the conformational rearrangements of ribosomes and associated factors, providing invaluable insights into the intricacies of translation. Emphasis on simulations has recently been on translation elongation, such as tRNA selection, translocation, and ribosomal head-swivel motions. These studies have offered crucial structural interpretations of how genetic information is faithfully translated into proteins. This review outlines recent discoveries concerning ribosome conformational changes occurring during translation elongation, as elucidated through molecular dynamics simulations.

Phosphorylated Adapter RNA Export Protein Is Methylated at Lys 381 by an Methyltransferase-like 21C (METTL21C)

Methyltransferase-like 21C (METTL21C) is a member of the non-histone methyltransferase superfamily, which mainly mediates the methylation of lysine (Lys) residues. The main types of modification are Lys dimethylation and trimethylation. However, at present, most of the studies on METTL21C are focused on humans and mice, and there are few reports on poultry. Therefore, chicken embryo fibroblasts (DF-1) were selected as the object of study. To explore the function of chicken METTL21C (chMETTL21C) in the proliferation of DF-1 cells, flow cytometry and qPCR were used to detect the function of chicken METTL21C in the proliferation of DF-1 cells. The results showed that overexpression of METTL21C blocked the cell cycle in the G1max S phase, thus inhibiting cell proliferation. In addition, based on proteomic analysis, stable overexpression of METTL21C may inhibit the proliferation of DF-1 cells by mediating lysine trimethylation of proliferation-related proteins phosphorylated adapter RNA export protein (PHAX), nucleoside diphosphate kinases (NDPKs), eukaryotic transcription extension factor (eukaryotic translation elongation factor 1A,e EF1A), and inversin (Invs). Through immunoprecipitation (co-IP) and liquid chromatography-mass spectrometry (LC-MS/MS) analysis, METTL21C-mediated PHAX Lys-381 methylation was confirmed to be involved in the regulation of DF-1 cell proliferation. The results of this study provide a reference for analyzing the methylation function of METTL21C and the mechanism of regulating the growth and development of chicken cells.

Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding

Accurate protein synthesis is determined by the two-subunit ribosome's capacity to selectively incorporate cognate aminoacyl-tRNA for each mRNA codon. The molecular basis of tRNA selection accuracy, and how fidelity can be affected by antibiotics, remains incompletely understood. Using molecular simulations, we find that cognate and near-cognate tRNAs delivered to the ribosome by Elongation Factor Tu (EF-Tu) can follow divergent pathways of motion into the ribosome during both initial selection and proofreading. Consequently, cognate aa-tRNAs follow pathways aligned with the catalytic GTPase and peptidyltransferase centers of the large subunit, while near-cognate aa-tRNAs follow pathways that are misaligned. These findings suggest that differences in mRNA codon-tRNA anticodon interactions within the small subunit decoding center, where codon-anticodon interactions occur, are geometrically amplified over distance, as a result of this site's physical separation from the large ribosomal subunit catalytic centers. These insights posit that the physical size of both tRNA and ribosome are key determinants of the tRNA selection fidelity mechanism.

Precise Steric Features Control Aminoacyl-tRNA Accommodation on the Ribosome

Protein synthesis involves a complex series of large-scale conformational changes in the ribosome. While long-lived intermediate states of these processes can be characterized by experiments, computational methods can be used to identify the interactions that contribute to the rate-limiting free-energy barriers. To this end, we use a simplified energetic model to perform molecular dynamics (MD) simulations of aminoacyl-tRNA (aa-tRNA) accommodation on the ribosome. While numerous studies have probed the energetics of the early stages of accommodation, we focus on the final stage of accommodation, where the 3'-CCA tail of aa-tRNA enters the peptidyl transferase center (PTC). These simulations show how a distinct intermediate is induced by steric confinement of the tail, immediately before it completes accommodation. Multiple pathways for 3'-CCA tail accommodation can be quantitatively distinguished, where the tail enters the PTC by moving past a pocket enclosed by Helix 89, 90, and 92, or through an alternate route formed by Helix 93 and the P-site tRNA. C2573, located within Helix 90, is shown to provide the largest contribution to this late-accommodation steric barrier, such that sub-Å perturbations to this residue can alter the time scale of tail accommodation by nearly an order of magnitude. In terms of biological function, these calculations suggest how this late-stage sterically induced barrier may contribute to tRNA proofreading by the ribosome.

Diffuse Ions Coordinate Dynamics in a Ribonucleoprotein Assembly

Proper ionic concentrations are required for the functional dynamics of RNA and ribonucleoprotein (RNP) assemblies. While experimental and computational techniques have provided many insights into the properties of chelated ions, less is known about the energetic contributions of diffuse ions to large-scale conformational rearrangements. To address this, we present a model that is designed to quantify the influence of diffuse monovalent and divalent ions on the dynamics of biomolecular assemblies. This model employs all-atom (non-H) resolution and explicit ions, where effective potentials account for hydration effects. We first show that the model accurately predicts the number of excess Mg²⁺ ions for prototypical RNA systems, at a level comparable to modern coarse-grained models. We then apply the model to a complete ribosome and show how the balance between diffuse Mg²⁺ and K⁺ ions can control the dynamics of tRNA molecules during translation. The model predicts differential effects of diffuse ions on the free-energy barrier associated with tRNA entry and the energy of tRNA binding to the ribosome. Together, this analysis reveals the direct impact of diffuse ions on the dynamics of an RNP assembly.

Peculiarities in Activation of Hydrolytic Activity of Elongation Factors

Translational GTPases (trGTPases) belong to the family of G proteins and play key roles at all stages of protein biosynthesis on the ribosome. Unidirectional and cyclic functioning of G proteins is ensured by their ability to switch between the active and inactive states due to GTP hydrolysis accelerated by the auxiliary GTPase-activating proteins. Although trGTPases interact with the ribosomes in different conformational states, they bind to the same conserved region, which, unlike in classical GTPase-activating proteins, is represented by ribosomal RNA. The resulting catalytic sites have almost identical structure in all elongation factors suggesting a common mechanism of GTP hydrolysis. However, fine details of the activated state formation and significantly different rates of GTP hydrolysis indicate the existence of distinctive features upon GTP hydrolysis catalyzed by the different factors. Here, we present a contemporary view on the mechanism of GTPase activation and GTP hydrolysis by the elongation factors EF-Tu, EF-G, and SelB based on the analysis of structural, biochemical, and bioinformatics data.

Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading

Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA delivered by elongation factor EF-Tu¹. Understanding the molecular mechanism of proofreading requires visualizing GTP-catalyzed elongation, which has remained a challenge^2–4. Here, time-resolved cryo-EM revealed 33 states following aminoacyl-tRNA delivery by EF-Tu•GTP. Instead of locking cognate tRNA upon initial recognition, the ribosomal decoding center (DC) dynamically monitors codon-anticodon interactions before and after GTP hydrolysis. GTP hydrolysis allows EF-Tu’s GTPase domain to extend away, releasing EF-Tu from tRNA. Then, the 30S subunit locks cognate tRNA in the DC, and rotates, enabling the tRNA to bypass 50S protrusions during accommodation into the peptidyl transferase center. By contrast, the DC fails to lock near-cognate tRNA, allowing dissociation of near-cognate tRNA during both initial selection (before GTP hydrolysis) and proofreading (after GTP hydrolysis). These findings reveal structural similarity between initial selection^5,6 and the previously unseen proofreading, which together govern efficient rejection of incorrect tRNA.

Elongation Factor Tu Switch I Element is a Gate for Aminoacyl-tRNA Selection

Selection of correct aminoacyl (aa)-tRNA at the ribosomal A site is fundamental to maintaining translational fidelity. Aa-tRNA selection is a multistep process facilitated by the guanosine triphosphatase elongation factor (EF)-Tu. EF-Tu delivers aa-tRNA to the ribosomal A site and participates in tRNA selection. The structural mechanism of how EF-Tu is involved in proofreading remains to be fully resolved. Here, we provide evidence that switch I of EF-Tu facilitates EF-Tu's involvement during aa-tRNA selection. Using structure-based and explicit solvent molecular dynamics simulations based on recent cryo-electron microscopy reconstructions, we studied the conformational change of EF-Tu from the guanosine triphosphate to guanine diphosphate conformation during aa-tRNA accommodation. Switch I of EF-Tu rapidly converts from an α-helix into a β-hairpin and moves to interact with the acceptor stem of the aa-tRNA. In doing so, switch I gates the movement of the aa-tRNA during accommodation through steric interactions with the acceptor stem. Pharmacological inhibition of the aa-tRNA accommodation pathway prevents the proper positioning of switch I with the aa-tRNA acceptor stem, suggesting that the observed interactions are specific for cognate aa-tRNA substrates, and thus capable of contributing to the fidelity mechanism.

Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection

Elongation factor Tu (EF-Tu) facilitates rapid and accurate selection of aminoacyl-tRNA (aa-tRNA) by the bacterial ribosome during protein synthesis. We show that EF-Tu dissociates from the ribosome as aa-tRNA navigates the accommodation corridor en route to peptide bond formation. We find that EF-Tu’s release from the ribosome during aa-tRNA selection can be reversible. We also demonstrate that new ternary complex formation, accompanied by futile cycles of GTP hydrolysis, can occur on aa-tRNA bound within the ribosome. These findings inform on the decoding mechanism, the contributions of EF-Tu to the fidelity of translation, and the potential consequences of reduced rates of peptide bond formation on cellular physiology.

The substrate for ribosomes actively engaged in protein synthesis is a ternary complex of elongation factor Tu (EF-Tu), aminoacyl-tRNA (aa-tRNA), and GTP. EF-Tu plays a critical role in mRNA decoding by increasing the rate and fidelity of aa-tRNA selection at each mRNA codon. Here, using three-color single-molecule fluorescence resonance energy transfer imaging and molecular dynamics simulations, we examine the timing and role of conformational events that mediate the release of aa-tRNA from EF-Tu and EF-Tu from the ribosome after GTP hydrolysis. Our investigations reveal that conformational changes in EF-Tu coordinate the rate-limiting passage of aa-tRNA through the accommodation corridor en route to the peptidyl transferase center of the large ribosomal subunit. Experiments using distinct inhibitors of the accommodation process further show that aa-tRNA must at least partially transit the accommodation corridor for EF-Tu⋅GDP to release. aa-tRNAs failing to undergo peptide bond formation at the end of accommodation corridor passage after EF-Tu release can be reengaged by EF-Tu⋅GTP from solution, coupled to GTP hydrolysis. These observations suggest that additional rounds of ternary complex formation can occur on the ribosome during proofreading, particularly when peptide bond formation is slow, which may serve to increase both the rate and fidelity of protein synthesis at the expense of GTP hydrolysis.

tRNA Dissociation from EF-Tu after GTP Hydrolysis: Primary Steps and Antibiotic Inhibition

In each round of ribosomal translation, the translational GTPase elongation factor Tu (EF-Tu) delivers a transfer RNA (tRNA) to the ribosome. After successful decoding, EF-Tu hydrolyzes GTP, which triggers a conformational change that ultimately results in the release of the tRNA from EF-Tu. To identify the primary steps of these conformational changes and how they are prevented by the antibiotic kirromycin, we employed all-atom explicit-solvent molecular dynamics simulations of the full ribosome-EF-Tu complex. Our results suggest that after GTP hydrolysis and Pi release, the loss of interactions between the nucleotide and the switch 1 loop of EF-Tu allows domain D1 of EF-Tu to rotate relative to domains D2 and D3 and leads to an increased flexibility of the switch 1 loop. This rotation induces a closing of the D1-D3 interface and an opening of the D1-D2 interface. We propose that the opening of the D1-D2 interface, which binds the CCA tail of the tRNA, weakens the crucial EF-Tu-tRNA interactions, which lowers tRNA binding affinity, representing the first step of tRNA release. Kirromycin binds within the D1-D3 interface, sterically blocking its closure, but does not prevent hydrolysis. The resulting increased flexibility of switch 1 explains why it is not resolved in kirromycin-bound structures.

Ribosome Structure, Function, and Early Evolution

Ribosomes are among the largest and most dynamic molecular motors. The structure and dynamics of translation initiation and elongation are reviewed. Three ribosome motions have been identified for initiation and translocation. A swivel motion between the head/beak and the body of the 30S subunit was observed. A tilting dynamic of the head/beak versus the body of the 30S subunit was detected using simulations. A reversible ratcheting motion was seen between the 30S and the 50S subunits that slide relative to one another. The 30S⁻50S intersubunit contacts regulate translocation. IF2, EF-Tu, and EF-G are homologous G-protein GTPases that cycle on and off the same site on the ribosome. The ribosome, aminoacyl-tRNA synthetase (aaRS) enzymes, transfer ribonucleic acid (tRNA), and messenger ribonucleic acid (mRNA) form the core of information processing in cells and are coevolved. Surprisingly, class I and class II aaRS enzymes, with distinct and incompatible folds, are homologs. Divergence of class I and class II aaRS enzymes and coevolution of the genetic code are described by analysis of ancient archaeal species.