scholarly journals Crystal structure of eukaryotic ribosome and its complexes with inhibitors

2017 ◽  
Vol 372 (1716) ◽  
pp. 20160184 ◽  
Author(s):  
Gulnara Yusupova ◽  
Marat Yusupov
Keyword(s):  
Crystal Structure ◽  
Ribosomal Rna ◽  
Protein Biosynthesis ◽  
Protein Translation ◽  
Peptide Bond ◽  
Binding Mode ◽  
High Eukaryote ◽  
Peptide Bond Formation ◽  
80S Ribosome ◽  
Eukaryotic Ribosome

A high-resolution structure of the eukaryotic ribosome has been determined and has led to increased interest in studying protein biosynthesis and regulation of biosynthesis in cells. The functional complexes of the ribosome crystals obtained from bacteria and yeast have permitted researchers to identify the precise residue positions in different states of ribosome function. This knowledge, together with electron microscopy studies, enhances our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transport of the nascent peptide, are regulated. In this review, we discuss the crystal structure of the entire 80S ribosome from yeast, which reveals its eukaryotic-specific features, and application of X-ray crystallography of the 80S ribosome for investigation of the binding mode for distinct compounds known to inhibit or modulate the protein-translation function of the ribosome. We also refer to a challenging aspect of the structural study of ribosomes, from higher eukaryotes, where the structures of major distinctive features of higher eukaryote ribosome—the high-eukaryote–specific long ribosomal RNA segments (about 1MDa)—remain unresolved. Presently, the structures of the major part of these high-eukaryotic expansion ribosomal RNA segments still remain unresolved. This article is part of the themed issue ‘Perspectives on the ribosome’.

Biochemistry instructors’ use of intentions for student learning to evaluate and select external representations of protein translation

2019 ◽  
Vol 20 (4) ◽  
pp. 787-803
Author(s):  
Thomas J. Bussey ◽  
MaryKay Orgill
Keyword(s):  
Student Learning ◽  
Visual Cues ◽  
Bond Formation ◽  
Protein Translation ◽  
Peptide Bond ◽  
External Representation ◽  
External Representations ◽  
Peptide Bond Formation ◽  
Scientific Phenomena ◽  
Selection Of

Instructors draw on their intentions for student learning in the enactment of curriculum, particularly in the selection and presentation of external representation of scientific phenomena. These representations both create opportunities for students to experience non-experiential biochemical phenomena, such as protein translation, and constrain the possibilities for student learning based on the limited number of features depicted and the visual cues used to draw viewers attention to those features. In this study, we explore biochemistry instructors’ intentions for student learning about protein translation and how those intentions influence their selection of external representations for instruction. A series of instructor interviews were used to identify information that students need to know in order to develop a biochemically accurate understanding of protein translation. We refer to this information as the “critical features” of protein translation. Two dominant themes of critical features were identified: (1) components/structures of protein translation and (2) interactions/chemistry of protein translation. Three general components (the ribosome, the mRNA, and the tRNA) and two primary interactions (base pairing and peptide bond formation) were described by all instructors. Instructors tended to favor simpler, stylized representations that closely aligned with their stated critical features of translation for instructional purposes.

Purification of factor EF-P, a protein that stimulates peptide-bond synthesis with certain aminoacyl-tRNA analogues

1979 ◽  
Vol 57 (6) ◽  
pp. 749-757 ◽  
Author(s):  
Bernard R. Glick ◽  
Robert M. Green ◽  
M. Clelia Ganoza
Keyword(s):  
Escherichia Coli ◽  
Molecular Weight ◽  
Protein Biosynthesis ◽  
Bond Formation ◽  
Frictional Coefficient ◽  
Peptide Bond ◽  
Asymmetric Structure ◽  
Peptide Bond Formation ◽  
Apparent Homogeneity ◽  
Stokes Radius

Factor EF-P is a nonribosomal (soluble) protein of Escherichia coli that stimulates peptide bond synthesis when certain aminoacyl-tRNA analogues are used. The purification of this protein to apparent homogeneity is described here. EF-P has a molecular weight of about 21 000, a Stokes radius of 27 Å (1 Å = 0.1 nm), and a frictional coefficient of 1.48, suggesting an asymmetric structure. By this and a number of other criteria, EF-P is a new factor that controls peptide bond formation during protein biosynthesis.

scholarly journals The parable of the caveman and the Ferrari: protein synthesis and the RNA world

2017 ◽  
Vol 372 (1716) ◽  
pp. 20160187 ◽  
Author(s):  
Harry F. Noller
Keyword(s):  
Protein Synthesis ◽  
Ribosomal Rna ◽  
Rna World ◽  
Bond Formation ◽  
Peptide Bond ◽  
Peptide Bond Formation ◽  
Ribonucleoprotein Particle ◽  
Supportive Role

The basic steps of protein synthesis are carried out by the ribosome, a very large and complex ribonucleoprotein particle. In keeping with its proposed emergence from an RNA world, all three of its core mechanisms—aminoacyl-tRNA selection, catalysis of peptide bond formation and coupled translocation of mRNA and tRNA—are embodied in the properties of ribosomal RNA, while its proteins play a supportive role. This article is part of the themed issue ‘Perspectives on the ribosome’.

Oligonucleotide promoted peptide bond formation using a tRNA mimicking approach

2017 ◽  
Vol 53 (36) ◽  
pp. 5013-5016
Author(s):  
H.-P. Mattelaer ◽  
C.-A. Mattelaer ◽  
N. Papastavrou ◽  
W. Dehaen ◽  
P. Herdewijn
Keyword(s):  
Nucleic Acids ◽  
Bond Formation ◽  
Protein Translation ◽  
Peptide Bond ◽  
Simplified Model ◽  
Peptide Bond Formation ◽  
Hybrid Species ◽  
Leaving Group

TransferRNA's role in protein translation is the prime example of an Informational Leaving Group (ILG). A simplified model produced oligophenylalanine with a modified uracil as an ILG in the presence of specific oligonucleotides. Our preliminary studies contribute to the importance of hybrid species in bridging the gap between peptides and nucleic acids.

scholarly journals Abstract P-29: Cryoem Study of the Inhibition of Bacterial Ribosomes by Madumycin II

2021 ◽  
Vol 11 (Suppl_1) ◽  
pp. S24-S25
Author(s):  
Alena Yakusheva ◽  
Olga Shulenina ◽  
Evgeny Pichkur ◽  
Alena Paleskava ◽  
Alexander Myasnikov ◽  
...  
Keyword(s):  
Amino Acid ◽  
High Resolution ◽  
Bond Formation ◽  
Protein Translation ◽  
Peptide Bond ◽  
Peptide Bond Formation ◽  
Peptidyl Transferase ◽  
Peptidyl Transferase Center ◽  
70S Ribosome ◽  
Madumycin Ii

Background: The efficiency of widely used antibiotics is limited by continuous improvement of resistance mechanisms. Thus, the research of poorly studied drugs that have not received practical use until now becomes relevant again. Protein translation is one of the major targets for antibiotics. Madumycin II (MADU) is an antibiotic of the streptogramin A class that binds to the peptidyl transferase center of the initiated bacterial 70S ribosome inhibiting the first cycle of peptide bond formation (I.A. Osterman et al. Nucleic Acids Res., 2017). The ability of MADU to interfere with translating ribosome is an open question that we address by investigation of high-resolution cryo-EM structures of MADU bound 70S ribosome complexes from Escherichia coli. Methods: Purified initiated and translating ribosome complexes preincubated with MADU were applied onto freshly glow discharged carbon-coated grids (Quantifoil R 1.2/1.3) and flash-frozen in the liquid ethane pre-cooled by liquid nitrogen in the Vitrobot Mark IV. Frozen grids were transferred into an in-house Titan Krios microscope. Data were collected using EPU software. Movie stacks were preprocessed in Warp software. For image processing, we have used several software packages: Relion 3.1, CryoSPARC, and CisTEM. The model was built in Coot. Results: We have obtained high-resolution cryo-EM structures of two ribosomal complexes with MADU before and after the first cycle of peptide bond formation with an average resolution of 2.3 Å. Preliminary analysis of the structures shows no major differences in the MADU binding mode to the ribosomal complexes under study suggesting that the quantity of amino acid residues attached to the P-site tRNA does not impact MADU bonding. Moreover, in both cases, we observed similar destabilization of the CCA-ends of A- and P-site tRNAs underlining the comparable influence of MADU on the ribosomal complexes. Conclusion: Our results suggest that although MADU binding site is located in the peptidyl transferase center, the presence of the second amino acid residue on the P-site tRNA does not preclude antibiotic binding. We assume that further elongation of the polypeptide chain would not have any impact either. High conformational lability of the CCA-ends of tRNA at the A and P sites upon binding of MADU obviously plays an important role in the inhibition mechanism of the bacterial ribosome. The further structural and biochemical analysis will be necessary to shed more light on the detailed mechanism of MADU action.

scholarly journals Functional implications of ribosomal protein L2 in protein biosynthesis as shown by in vivo replacement studies

1998 ◽  
Vol 331 (2) ◽  
pp. 423-430 ◽  
Author(s):  
Monika ÜHLEIN ◽  
Wolfgang WEGLÖHNER ◽  
Henning URLAUB ◽  
Brigitte WITTMANN-LIEBOLD
Keyword(s):  
Ribosomal Proteins ◽  
Protein Biosynthesis ◽  
Complex Structure ◽  
Peptide Bond ◽  
Histidine Residue ◽  
Peptide Bond Formation ◽  
Homologous Proteins ◽  
Translational Activity ◽  
Translational Apparatus

The translational apparatus is a highly complex structure containing three to four RNA molecules and more than 50 different proteins. In recent years considerable evidence has accumulated to indicate that the RNA participates intensively in the catalysis of peptide-bond formation, whereas a direct involvement of the ribosomal proteins has yet to be demonstrated. Here we report the functional and structural conservation of a peptidyltransferase centre protein in all three phylogenetic domains. In vivo replacement studies show that the Escherichia coli L2 protein can be replaced by its homologous proteins from human and archaebacterial ribosomes. These hybrid ribosomes are active in protein biosynthesis, as proven by polysome analysis and poly(U)-dependent polyphenylalanine synthesis. Furthermore, we demonstrate that a specific, highly conserved, histidine residue in the C-terminal region of L2 is essential for the function of the translational apparatus. Replacement of this histidine residue in the human and archaebacterial proteins by glycine, arginine or alanine had no effect on ribosome assembly, but strongly reduced the translational activity of ribosomes containing these mutants.

scholarly journals Structural and functional studies revealed key mechanisms underlying elongation step of protein translation

2020 ◽  
Vol 52 (7) ◽  
pp. 749-756 ◽  
Author(s):  
Ling Zhang ◽  
Yinghui Wang ◽  
Hong Dai ◽  
Jie Zhou
Keyword(s):  
Protein Translation ◽  
Peptide Bond ◽  
Peptide Bond Formation ◽  
Codon Recognition ◽  
Functional Studies ◽  
Elongation Cycle ◽  
Sequential Addition ◽  
Elongation Step ◽  
Made In ◽  
Key Questions

Abstract The ribosome is an ancient and universally conserved macromolecular machine that synthesizes proteins in all organisms. Since the discovery of the ribosome by electron microscopy in the mid-1950s, rapid progress has been made in research on it, regarding its architecture and functions. As a machine that synthesizes polypeptides, the sequential addition of amino acids to a growing polypeptide chain occurs during a phase called the elongation cycle. This is the core step of protein translation and is highly conserved between bacteria and eukarya. The elongation cycle involves codon recognition by aminoacyl tRNAs, catalysis of peptide bond formation, and the most complex operation of translation—translocation. In this review, we discuss the fundamental results from structural and functional studies over the past decades that have led to understanding of the three key questions underlying translation.

Ribosome structural dynamics in translocation: yet another functional role for ribosomal RNA

2017 ◽  
Vol 50 ◽  
Author(s):  
Harry F. Noller ◽  
Laura Lancaster ◽  
Srividya Mohan ◽  
Jie Zhou
Keyword(s):  
Protein Synthesis ◽  
Structural Dynamics ◽  
Ribosomal Rna ◽  
Messenger Rna ◽  
Peptide Bond ◽  
Peptide Bond Formation ◽  
Detailed Structural Analysis ◽  
Ribonucleoprotein Complexes ◽  
Elongation Phase ◽  
Polypeptide Chains

AbstractRibosomes are remarkable ribonucleoprotein complexes that are responsible for protein synthesis in all forms of life. They polymerize polypeptide chains programmed by nucleotide sequences in messenger RNA in a mechanism mediated by transfer RNA. One of the most challenging problems in the ribosome field is to understand the mechanism of coupled translocation of mRNA and tRNA during the elongation phase of protein synthesis. In recent years, the results of structural, biophysical and biochemical studies have provided extensive evidence that translocation is based on the structural dynamics of the ribosome itself. Detailed structural analysis has shown that ribosome dynamics, like aminoacyl-tRNA selection and catalysis of peptide bond formation, is made possible by the properties of ribosomal RNA.

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