Single-Molecule Analysis of Ribosome and Initiation Factor Dynamics During the Late Stages of Translation Initiation PDF Download
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Author: Daniel David MacDougall
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Languages : en
Pages :
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Book Description
The data strongly suggest the occurrence of simultaneous occupancy of the ribosome by IF2 and ternary complex, implying that the ribosome is structurally capable of recruiting ternary complex prior to IF2 release from the 70S IC. The observation that the ribosome can accommodate more than one translation factor at a time may have important implications for understanding how it efficiently coordinates factor binding and release throughout protein synthesis, and opens the door to mechanistic studies of the ribosomal L7/L12 stalk, presumed to play a prominent role in these processes.
Author: Daniel David MacDougall
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
The data strongly suggest the occurrence of simultaneous occupancy of the ribosome by IF2 and ternary complex, implying that the ribosome is structurally capable of recruiting ternary complex prior to IF2 release from the 70S IC. The observation that the ribosome can accommodate more than one translation factor at a time may have important implications for understanding how it efficiently coordinates factor binding and release throughout protein synthesis, and opens the door to mechanistic studies of the ribosomal L7/L12 stalk, presumed to play a prominent role in these processes.
Author:
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Languages : en
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Book Description
Like most biological polymerization reactions, ribosome-catalyzed protein synthesis, or translation, can be divided into initiation, elongation, and termination stages. Initiation is the rate-limiting stage of translation and a critical site for translational control of gene expression. Throughout all stages of protein synthesis, the ribosome is aided by essential protein co-factors known as translation factors. I have studied the role that two translation initiation factors, IF1 and IF3, play in the mechanism and regulation of translation initiation in Escherichia coli. Specifically, I have used single-molecule fluorescence resonance energy transfer (smFRET) as a primary tool for investigating how the dynamics of IF1 and IF3 regulate the accuracy with which the translational machinery selects an initiator transfer RNA (tRNA) and the correct messenger RNA (mRNA) start codon during the initiation stage of protein synthesis.
Author: Marina V. Rodnina
Publisher: Springer Science & Business Media
ISBN: 3709102154
Category : Medical
Languages : en
Pages : 428
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Book Description
The ribosome is a macromolecular machine that synthesizes proteins with a high degree of speed and accuracy. Our present understanding of its structure, function and dynamics is the result of six decades of research. This book collects over 40 articles based on the talks presented at the 2010 Ribosome Meeting, held in Orvieto, Italy, covering all facets of the structure and function of the ribosome. New high-resolution crystal structures of functional ribosome complexes and cryo-EM structures of translating ribosomes are presented, while partial reactions of translation are examined in structural and mechanistic detail, featuring translocation as a most dynamic process. Mechanisms of initiation, both in bacterial and eukaryotic systems, translation termination, and novel details of the functions of the respective factors are described. Structure and interactions of the nascent peptide within, and emerging from, the ribosomal peptide exit tunnel are addressed in several articles. Structural and single-molecule studies reveal a picture of the ribosome exhibiting the energy landscape of a processive Brownian machine. The collection provides up-to-date reviews which will serve as a source of essential information for years to come.
Author: Albert Tsai
Publisher:
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Category :
Languages : en
Pages :
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Book Description
Translation is the final step that converts genetic information into proteins composed of amino acids using the ribosome-- a complex molecular machine that coordinates the kinetics, chemistry, and mechanics necessary to synthesize a polypeptide. Translation is highly dynamic with processes taking place on the microseconds to minutes timescales. Among the different techniques employed to probe the dynamics of translation, single-molecule fluorescence occupies a unique position, being able to track heterogeneous compositional and conformational changes occurring within tens of milliseconds to minutes. Leveraging several fluorescent signals, we probed the dynamics of translation initiation. Instead of a linear pathway, we observed several different pathways all leading to the formation of an elongation competent ribosome complex, with the flux through each modulated by initiation factors, tRNAs, and mRNA sequence. Next, we tracked how the aminoglycoside family of antibiotics inhibits ribosome and tRNA dynamics during peptide synthesis (elongation), concluding that their potency as bactericides stems from kinetically inhibiting elongation. Finally, we transitioned from model systems into observing elongation dynamics on a biologically functional protein stall sequence, SecM. Our results suggest that stalling the ribosome requires several precisely-timed peptide-ribosome interactions and that ribosomes stall in a distribution of locations on the SecM sequence. These results demonstrate the power of single-molecule fluorescence to monitor global translation dynamics, as well as highlighting the importance of the temporal dimension in forming a coherent and global mechanism for translation.
Author: Michael B. Mathews
Publisher:
ISBN: 9781621821861
Category : Genetic translation
Languages : en
Pages : 499
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Book Description
A subject collection from Cold Spring Harbor Perspectives in Biology.
Author: Heinz Bielka
Publisher: Walter de Gruyter GmbH & Co KG
ISBN: 3112729757
Category : Science
Languages : en
Pages : 340
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Book Description
No detailed description available for "The Eukaryotic Ribosome".
Author: Knud H. Nierhaus
Publisher: John Wiley & Sons
ISBN: 9783527306381
Category : Science
Languages : en
Pages : 608
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Book Description
Knud Nierhaus, who has studied the ribosome for more than 30 years, has assembled here the combined efforts of several scientific disciplines into a uniform picture of the largest enzyme complex found in living cells, finally resolving many decades-old questions in molecular biology. In so doing he considers virtually all aspects of ribosome structure and function -- from the molecular mechanism of different ribosomal ribozyme activities to their selective inhibition by antibiotics, from assembly of the core particle to the regulation of ribosome component synthesis. The result is a premier resource for anyone with an interest in ribosomal protein synthesis, whether in the context of molecular biology, biotechnology, pharmacology or molecular medicine.
Author: Colin EcheverrÃa Aitken
Publisher:
ISBN:
Category :
Languages : en
Pages : 216
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Book Description
Author: Peiwu Qin
Publisher:
ISBN:
Category : Electronic dissertations
Languages : en
Pages : 189
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Book Description
The Ribosome is the protein factory with multiple coordinated components working together to translate the genetic code in the mRNA into protein sequence. Since it was discovered in 1955, the research around the ribosome has been pushed forward by hundreds of labs worldwide. In 2000, the breakthrough was marked by the publication of the ribosome structures at atomic resolution. Structures help people design and explain the biochemical data deeper and better. However, the ribosome is not static. It is a dynamic and highly regulated machine. The function of the ribosome can be understood further only if we can follow the dynamics of individual components in different functional states. Solution NMR is a powerful technique for studying protein dynamics. However, the gigantic nature of the ribosome makes this task daunting. Thanks to the development of single molecule techniques, the first real time ribosome dynamics was done in 2004 by Scott Blanchard when he was a post-doctorate with Steven Chu and Joseph Puglisi. After that, more than 300 research papers and reviews have been published about singe molecule ribosome studies. Both single molecule FRET and optical tweezers have been successfully used to address the dynamic process of protein translation. In 2008 and 2009, Dr. Peter Cornish and Dr. Dmitri Ermolenko followed the ribosome intersubunit rotation and L1 stalk dynamics in real time during the process of translocation, which was the first direct evidence of ribosome dynamics itself since the previous study inferred the ribosome dynamics from tRNA motion. The previous study could not exclude the possibility that the observed dynamics resulted purely from tRNA. Cornish and Ermolenko concluded that ribosome dynamics is a spontaneous process that is driven by thermodynamic Brownian motion. This pioneering study opened a window to address many unresolved problems such as the perturbation of the dynamic effects by structured RNA, mRNA unwinding, and ribosomal frameshifting. We found that the presence of RNA structure induces the ribosome into a new FRET state that we named super rotated state. The population distribution of the super rotated state is correlated with the thermostability and the distance of RNA structure to the ribosome. We can reduce the population of the super rotated state and reverse this change. Using other RNA structures like DNA:RNA hybrid and a pseudoknot, the ribosome can also be induced into the super rotated state. The different global conformations of ribosome when linear or structured RNA are present are shown by small angle X-ray scattering. The changes in the pair distance distribution function indicate the rotational change of ribosome theoretically. Structured RNA inhibits the regular intersubunit rotation and drives the ribosome into the super rotated state. However, the structured RNA cannot stop the open-to-close transition of the L1 stalk, which still can fluctuate between three different functional states. These results propose that ribosome dynamics is composed of several independent units with their own identity. Since the super rotated state also can be induced by DNA:RNA hybrid, we can investigate how far the RNA structure is away from the ribosome when the ribosome can sense the presence of these RNA structures.
Author: Alexander Spirin
Publisher: Springer Science & Business Media
ISBN: 1461578175
Category : Science
Languages : en
Pages : 417
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Book Description
This book is based on an advanced course of lectures on ribosome structure and protein biosynthesis that I offer at the Moscow State University. These lectures have been part of a general course on molecular biology for almost three decades, and they have undergone considerable evolution as knowledge has been pro gressing in this field. The progress continues, and readers should be prepared that some facts, statements, and ideas included in the book may be incomplete or out of-date. In any case, this is primarily a textbook, but not a comprehensive review. It provides a background of knowledge and current ideas in the field and gives ex amples of observations and their interpretations. I understand that some interpre tations and generalizations may be tentative or disputable, but I hope that this will stimulate thinking and discussing better than if I left white spots. The book has a prototype: it is my monograph "Ribosome Structure and Pro tein Biosynthesis" published by the Benjamin/Cummings Publishing Company, Menlo Park, California, in 1986. Here I have basically kept the former order of pre sentation ofthe topics and the subdivision into chapters. The contents ofthe chap ters, however, have been significantly revised and supplemented. The newly writ ten chapters on translational control in prokaryotes (Chapter 16) and eukaryotes (Chapter 17) are added.
