Download or read book Solution Structure and Dynamics of the Ribosome written by Thuylinh Nguyenle and published by . This book was released on 2004 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Ribosomes Structure Function and Dynamics written by Marina V. Rodnina and published by Springer Science & Business Media. This book was released on 2011-12-10 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Protein Synthesis and Ribosome Structure written by Knud H. Nierhaus and published by John Wiley & Sons. This book was released on 2009-07-10 with total page 597 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Ribosomes written by Alexander Spirin and published by Springer Science & Business Media. This book was released on 2013-03-09 with total page 417 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Structure and Dynamics of Solutions written by H. Ohtaki and published by Elsevier. This book was released on 2013-10-22 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent advances in the study of structural and dynamic properties of solutions have provided a molecular picture of solute-solvent interactions. Although the study of thermodynamic as well as electronic properties of solutions have played a role in the development of research on the rate and mechanism of chemical reactions, such macroscopic and microscopic properties are insufficient for a deeper understanding of fast chemical and biological reactions. In order to fill the gap between the two extremes, it is necessary to know how molecules are arranged in solution and how they change their positions in both the short and long range. This book has been designed to meet these criteria. It is possible to develop a sound microscopic picture for reaction dynamics in solution without molecular-level knowledge of how reacting ionic or neutral species are solvated and how rapidly the molecular environment is changing with time. A variety of actual examples is given as to how and when modern molecular approaches can be used to solve specific solution problems. The following tools are discussed: x-ray and neutron diffraction, EXAFS, and XANES, molecular dynamics and Monte Carlo computer simulations, Raman, infrared, NMR, fluorescence, and photoelectron emission spectroscopic methods, conductance and viscosity measurements, high pressure techniques, and statistical mechanics methods. Static and dynamic properties of ionic solvation, molecular solvation, ion-pair formation, ligand exchange reactions, and typical organic solvents are useful for bridging the gap between classical thermodynamic studies and modern single-molecule studies in the gas phase. The book will be of interest to solution, physical, inorganic, analytical and structural chemists as well as to chemical kineticists.
Download or read book The Ribosome written by Walter Ensign Hill and published by ASM Press. This book was released on 1990 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is recommended as a 'hitchhiker's guide to the ribosome' for everyone with an interest in translation, RNA-protein structures, and macromolecular structure-function relationships Science >.
Download or read book Probing the Assembly of the Ribosome Insights from Computational Studies on Ribosomal Proteins written by Brittany Burton Lott and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Ribosomes are complex cellular machines that synthesize new proteins in the cell. The accurate and efficient assembly of ribosomal proteins (r-proteins) and ribosomal RNA (rRNA) to form a functional ribosome is important for cell growth, metabolic reactions, and other cellular processes. Ribosomal assembly has been an active research topic for many years because understanding the assembly mechansims can provide insight into protein/RNA recognitions that are important in many other cellular processes, as well as help optimize the development of antibacterial therapeutics. Experimental and computational sutdies thus far have greatly improved our understanding of assembly, yet many questions remain unanswered regarding the complex behaviors of r-proteins and rRNA during the process. To further understand ribosome assembly, we have computationally studied the sequences, structures, and dynamic properties of r-proteins from the 30S subunit and their relationships to RNA binding. We discuss the statistically greater amount of positively charged residues in r-proteins compared to other housekeeping proteins and observe a high level of charged interactions between r-proteins and rRNA in the assembled structure. We also detect a significant correlation between the overall flexibility of a protein and the number of contact points it makes with its rRNA binding site. Protein residues contacting with rRNA are observed to be more mobile in solution when compared to the non-contacting residues. We also describe common modes of structural dynamics, revealing likely conformational changes the proteins make prior to binding, how they relate to possible binding mechanisms used during the assembly and to the location of the protein in the fully assembled ribosome.
Download or read book The Ribosome written by Aleksandr S. Spirin and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 173 pages. Available in PDF, EPUB and Kindle. Book excerpt: This monograph is neither a historical outline of the development of the concepts of protein biosynthesis and the structure and functions of the ribosomes, nor an exhaustive survey of the literature on these questions. The monograph is based upon an analysis of the modern trends in this field. The purpose of the monograph was to formulate more or less generalized representations of the structure and" function of the ribosome, as we envision it at the present day. It may be that this attempt is premature for a number of reasons, and the concepts outlined here will very soon be revised. Nonetheless, despite this risk, we believe it to be advisable to undertake this attempt for the following reasons: firstly, the undertaken analysis could aid in the comprehension of the substantial mass of extremely scattered experimental data on the ribosomes presently available; secondly, in any event, even if most of the concepts outlined rapidly become obselete, they can still serve as a stimulus for a whole series of experiments; and thirdly, we hope that some of the concepts outlined will still remain essentially correct and relatively stable. In view of the aforementioned, we should make the following reservations. First of all, we made no attempt to cite all the literature on the problems discussed, but considered it sufficient to illustrate the various premises with one or several sample references.
Download or read book Structure Expression From proteins to ribosomes written by Mukti H. Sarma and published by Adenine Press, Incorporated. This book was released on 1988 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Ribosome written by Margaret S. Vanloock and published by . This book was released on 2000 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Structure and Dynamics of RNA written by P. H. van Knippenberg and published by Springer Science & Business Media. This book was released on 2013-03-08 with total page 335 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains contributions from the speakers at the NATO Advanced Research Workshop on "3D 5tructure and Dynamics of RNA", which was held in Renesse, The Netherlands, 21 - 24 August, 1985. Two major developments have determined the progress of nucleic acid research during the last decade. First, manipulation of genetic material by recombinant DNA methodology has enabled detailed studies of the function of nucleic acids in vivo. 5econd, the use of powerful physical methods, such as X-ray diffraction and nuclear magnetic resonance spectroscopy, in the study of biomacromolecules has provided information regarding the structure and the dynamics of nucleic acids. Both developments were enabled by the advance of synthetic methods that allow preparation of nucleic acid molecules of required sequence and length. The basic understanding of nucleic acid function will ultimately depend on a close collaboration between molecular biologists and biophy sicists. In the case of RNA, the ground rules for the formation of secondary structure have been derived from physical studies of oligoribonucleotides. Powerfull spectroscopic techniques have revealed more details of ~~A structure including novel conformations (e.g. left-handed Z-RNA). A wealth of information has been obtained by studying the relatively small transfer RNA molecules. A few of these RNAs have been crystallized, enabling determination of their three-dimensional structure. It has become apparent that "non-classical" basepairing between distal nucleotides gives rise to tertiary interactions, determining the overall shape of the molecule.
Download or read book Single Molecule Studies of RNA Unwinding and Ribosome Conformational Changes written by Dongmei Yu and published by . This book was released on 2014 with total page 237 pages. Available in PDF, EPUB and Kindle. Book excerpt: High-resolution structures of the ribosome have captured the endpoints of large-scale rearrangements of the ribosome. Direct observation of ribosome dynamics has been hindered by ensemble averaging in bulk solutions. Single-molecule methods, which eliminate these averaging effects, have emerged as powerful tools to probe many once-inaccessible biological processes. Here using single-molecule FRET, we observe the dynamic perturbation of the ribosome by structured mRNA, which renders the L1 stalk in an open state and induces a super-rotated conformation of the small subunit. We also found that when RNA structures are two nucleotide away from the mRNA entrance tunnel, the DNA:RNA structure still can induce the hyper rotated state and fluctuate among three different rotational state. The ability of inducing the hyper rotates state is correlated with RNA thermal stability and has nothing to do with the type of RNA structure. Ribosome can unwind RNA structure without the assistance of any other factors, which confirms the helicase function of ribosome. The advantage of single molecule is to follow the dynamics of single molecule in vitro. Single molecule techniques only can follow specific part or residues of large complex and it cannot give the information of all the atoms simultaneously. Solution NMR is not a single molecule technique and is a bulk dynamics basically. However, solution NMR can probe the dynamics of every atom and give you much more information even if they are averaged information. In the future, the complementary study of protein dynamics with both single molecule and NMR will provide more detail dynamics from protein in vitro.
Download or read book Ribosomes Structure Function and Genetics written by Glenn Chambliss and published by . This book was released on 1980 with total page 1020 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Ribosome Structure and Protein Biosynthesis written by Aleksandr Sergeevich Spirin and published by Benjamin-Cummings Publishing Company. This book was released on 1986 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Subcellular Fractionation written by John M. Graham and published by Oxford University Press. This book was released on 1997 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the fast changing world of cell biology it is often required that particular membranes or subcellular organisms be isolated from the structure for investigative purposes. This book shows how to do this in a practical, hands-on way.
Download or read book Single Molecule Studies of Ribosome Dynamics written by Peiwu Qin and published by . This book was released on 2013 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
