Download or read book The Importance of Rna Sequence and Structure in the Assembly and Function of Signal Recognition Particle written by David Alan Selinger and published by . This book was released on 1993 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book RNA Sequence Structure and Function written by Jan Gorodkin and published by . This book was released on 2014 with total page 533 pages. Available in PDF, EPUB and Kindle. Book excerpt: The existence of genes for RNA molecules not coding for proteins (ncRNAs) has been recognized since the 1950's, but until recently, aside from the critically important ribosomal and transfer RNA genes, most focus has been on protein coding genes. However, a long series of striking discoveries, from RNA's ability to carry out catalytic function, to discovery of riboswitches, microRNAs and other ribo-regulators performing critical tasks in essentially all living organisms, has created a burgeoning interest in this primordial component of the biosphere. However, the structural characteristics and evolutionary constraints on RNA molecules are very different from those of proteins, necessitating development of a completely new suite of informatic tools to address these challenges. In RNA Sequence, Structure, Function: Computational and Bioinformatic Methods, expert researchers in the field describe a substantial and relevant fraction of these methodologies from both practical and computational/algorithmic perspectives. Focusing on both of these directions addresses both the biologist interested in knowing more about RNA bioinformatics as well as the bioinformaticist interested in more detailed aspects of the algorithms. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results. Thorough and intuitive, RNA Sequence, Structure, Function: Computational and Bioinformatic Methods aids scientists in continuing to study key methods and principles of RNA bioinformatics.
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book RNA 3D Structure Analysis and Prediction written by Neocles Leontis and published by Springer Science & Business Media. This book was released on 2012-06-05 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has proven crucial for understanding in atomic detail how they carry out their biological functions. Because of the huge number of potentially important RNA molecules in biology, many more than can be studied experimentally, we need theoretical approaches for predicting 3D structures on the basis of sequences alone. This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.
Download or read book Structure function Relationships in RNA Molecules written by Chris Baugh and published by . This book was released on 2000 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Enzymes written by Ross Dalbey and published by Elsevier. This book was released on 2007-08-28 with total page 651 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume of The Enzymes features high-caliber thematic articles on the topic of molecular machines involved in protein transport across cellular membranes. The book consists of five parts which span the range of membranes including bacterial, endoplasmic reticulum, mitochondrial, chloroplast, and peroxismal.
Download or read book The Enzymes written by and published by Elsevier. This book was released on 2023-11-07 with total page 318 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Enzymes, Volume 54 highlights new advances in enzymes, with new chapters on a variety of topics, including the History of The Enzymes, Impact of The Enzymes in chronicling biochemical processes and pathways, Metabolism and Catalysis, Mitochondrial ATP synthase, The respiratory chain, A century of mitochondrial research, Five decades of metalloenzymology, Mechanisms of catalysis, Mitochondrial fatty acid synthesis and associated processes, Signaling, MAPK cascades: Origins, mechanisms and current status, Sphingolipids: From structural components to signaling hubs, Protein Homeostasis and Hydrolysis, Mitochondrial AAA+ proteases, Hsp70 and JDP proteins: structure-function perspective on molecular chaperone activity. Other sections cover DNA Replication and Repair, Structure-function studies of DNA replication proteins, and Helicases required for nucleotide excision repair. Provides the authority and expertise of leading contributors from an international board of authors Updated release includes the latest information on enzymes
Download or read book Deciphering of Packing Signal Hypothesis in Bacterophage RNA Recognition by the MS2 Capsid Protein in Virus Assembly written by Lokendra Poudel and published by . This book was released on 2018 with total page 131 pages. Available in PDF, EPUB and Kindle. Book excerpt: MS2 is a classical example of a single-stranded RNA virus for which the genomic RNA plays pivotal roles in the virus assembly process. Multiple dispersed RNA sequence/structure motifs, packaging signals (PSs) varying around a central recognition motif, interact with capsid protein in a process referred to as packaging signal mediated assembly. While the discovery and identification of these PSs was based on bioinformatics and geometric approaches, in tandem with sophisticated experimental protocols, we approach this problem by an altogether different philosophy, using a large-scale quantitative ab initio methodology centered on critical aspects of the consensus PS recognition motif. DFT calculations are carried out on four nucleopro tein complexes (PDB IDs: 1ZDI, 1ZDH, 5MSF and 6MSF) that are representative of the phage MS2 PSs. We have calculated atomic partial charge in the models using ab initio DFT based OLCAO method. The calculated partial charge distribution of individual protein and RNA residues indicates that the gross features is the same in CP because they have identical sequences, but there are some important minor differences due to the different RNAs to which they bind. It shows that CP is lost and ssRNA is gained charge in all models. The loss of charge by CP in order of 6MSF>5MSF>1ZDI>1ZDH in CP-RNA complex. We have also calculated strength of the interfacial hydrogen bonding (HB) configurations between protein and RNA. The interfacial HBs enable us to locate the exact binding sites of both nucleoprotein, corresponding to the sites exhibiting the strongest interfacial HBs, here identified to be (TYR85-U−5) in 1ZDI and LYS43 A−4 in 1ZDH, 5MSF and 6MSF. The formation of stronger HBs can be traced to the change in the sequence of the mutated RNA, and three-base loop motif leading to more pronounced HB fit between the amino acids and nucleobases. We have quantify HB with a physical quantum quantity of bond order (BO) and summed up all BO values of interfacial HBs as a total bond order (TBO). This is very important quantum quantity for strength of binding between CP and ssRNA. We found that he interfacial TBO are in order of 6MSF>1ZDI>5MSF>1ZDH. The binding between CP with RNA is higher in three-base loop motif than tetra-base loop motif and the mutate form of RNA has higher binding than wild type RNA. Moreover, simulation provided quantitative information on the strength of CP-RNA interactions with respect to RNA sequences. Finally, our study exemplifying the role that modern computational techniques can play in further advancing the field of physical virology.
Download or read book Macromolecular Crystallography written by Maria Armenia Carrondo and published by Springer. This book was released on 2011-12-01 with total page 213 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a collection of the contributions presented at the 42nd Erice Crystallographic Course whose main objective was to train the younger generation on advanced methods and techniques for examining structural and dynamic aspects of biological macromolecules. The papers review the techniques used to study protein assemblies and their dynamics, including X-ray diffraction and scattering, electron cryo-electron microscopy, electro nanospray mass spectrometry, NMR, protein docking and molecular dynamics. A key theme throughout the book is the dependence of modern structural science on multiple experimental and computational techniques, and it is the development of these techniques and their integration that will take us forward in the future.
Download or read book Macromolecular Crystallography written by Maria Armenia Carrondo and published by Springer Science & Business Media. This book was released on 2011-12-01 with total page 213 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a collection of the contributions presented at the 42nd Erice Crystallographic Course whose main objective was to train the younger generation on advanced methods and techniques for examining structural and dynamic aspects of biological macromolecules. The papers review the techniques used to study protein assemblies and their dynamics, including X-ray diffraction and scattering, electron cryo-electron microscopy, electro nanospray mass spectrometry, NMR, protein docking and molecular dynamics. A key theme throughout the book is the dependence of modern structural science on multiple experimental and computational techniques, and it is the development of these techniques and their integration that will take us forward in the future.
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 RNA Structure and Function in the Assembly and Replication of Turnip Crinkle Virus written by Ning Wei and published by . This book was released on 1990 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Effects of Local RNA Sequence and Structural Contexts on Ribonuclease P Processing Specificity written by Jing Zhao and published by . This book was released on 2019 with total page 165 pages. Available in PDF, EPUB and Kindle. Book excerpt: The affinity and kinetics of RNA and protein association depends on the stability of the RNA-protein complex as well as the structure and stability of the free RNA and protein. While much is known about how proteins and enzymes bind their specific sites in RNA, less is understood about the effects of RNA sequence and structure contexts surrounding these specific binding sites on binding. Ribonuclease P (RNase P) is a ribonucleoprotein enzyme involved in tRNA processing that relies on the protein subunit that forms essential contacts to a linear sequence of 3-8 nucleotides in the 5′ leader of precursor tRNA (ptRNA). Therefore, binding is likely to be influenced by the presence of competing secondary structure in the free RNA leader sequence. To address this issue, we pursued two primary lines of investigation. First, we compared the kinetics of RNA cleavage in monocistronic and polycistronic ptRNAs, which offers the opportunity to investigate the role of local RNA contexts on recognition. Kinetic analysis by using single turnover kinetics in vitro, cleavage site mapping and uniform substrate labelling on polycistronic ptRNAval VW reproduces the 3′ to 5′ ordered processing observed in vivo suggesting this is the most predominant pathway by RNase P. In-line probing further reveals the effects of both ptRNAs order and leader structure on directional processing. Kinetic analysis on valV and valW individually suggests that valV is an intrinsically slow and valW is an intrinsically fast substrate due to the leader structure on valV. Therefore, ordered processing can arise from the ability of genomically encoded sequences to form inhibitory secondary structure proximal to the RNase P cleavage site that inhibits processing. In a parallel experiment, we designed three different ptRNA substrate pools with randomized leader sequences proximal to the RNase P cleavage site, but with different RNA sequences appended upstream. Using a high throughput approach the rate constants for all the individual RNA substrates in the population were determined, and the resulting data was analyzed to test the effect of variation in both sequence and secondary structure on processing specificity globally. The effects of two upstream extensions (21A and 21B) containing transversion mutations were compared. Also, a third population (21C) was designed to form a stable stem loop that should insulate the randomized protein binding site from the effects of inhibitory interactions with additional leader sequences. Using a high-throughput sequencing kinetics (HiTS-KIN) method, we determined the rate constants for all sequence variants at N (-1) to N(-6) in the 21A, B and C backgrounds. Comparison of the three HiTS-KIN data clearly demonstrates that formation of inhibitory secondary structures influences the association kinetics of a subset of substrates. Together, the comparative HiTS-KIN analyses in vitro and mechanistic basis of ordered genomic encoded polycistronic ptRNAs processing demonstrate the contribution of structure and sequence variations to RNase P processing specificity. Surprisingly, the results from both studies reveal several substrates that are processed rapidly despite the presence of structure in the 5′ leader sequence. Altogether, these results provide a better understanding of intrinsic molecular recognition properties of similar multiple substrate RNA processing enzymes, reveal in detail the effects of sequence and structure contexts on RNA molecular recognition, and suggest new questions for future study of this important area of research.
Download or read book EJB Reviews written by P. Christen and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the mid-1980s the European Journal of Biochemistry set out to publish review articles. The enterprise proved successful, resulting in high-level reviews written by well-known scientists appearing in the Journal. The reviews represent emerging and rapidly growing fields of research in fundamental as well as applied areas of biochemistry, such as medicine, biotechnology, agriculture and nutrition. Novel methodological and technological approaches which stimulate biochemical research are also included. The authors of the reviews are explicitly asked to be critical, selective, evaluative and interdisciplinary oriented. The reviews should encourage young scientists to think independently and creatively, and inform active investigators about the state of the art in a given field.
Download or read book Physiology of the Gastrointestinal Tract written by Kim E. Barrett and published by Elsevier. This book was released on 2006-05-10 with total page 2098 pages. Available in PDF, EPUB and Kindle. Book excerpt: FROM THE PREFACE: The original purpose of the First Edition of Physiology of the Gastrointestinal Tract to collect in one set of volumes the most current and comprehensive knowledge in our field was also the driving force for the Fourth Edition. The explosion of information at the cellular level, made possible in part by the continued emergence of powerful molecular and cellular techniques, has resulted in a greater degree of revision than that of any other edition. The first section, now titled "Basic Cell Physiology and Growth of the Gl Tract" contains numerous new chapters on topics such as transcriptional regulation, signaling networks in development, apoptosis, and mechanisms in malignancies. Most of the chapters in this section were edited by Juanita L. Merchant. Section II has been renamed "Neural Gastroenterology and Motility" and has been expanded from seven chapters with rather classic titles to more than twenty chapters encompassing not only the movement of the various parts of the digestive tract but also cell physiology, neural regulation, stress, and the regulation of food intake. Almost all of the chapters were recruited and edited by Jackie D. Wood. The third section is entirely new and contains chapters on "Immunology and Inflammation" which were edited by Kim E. Barrett. The fourth section on the "Physiology of Secretion" consists of chapters with familiar titles, but with completely updated information to reflect the advances in our understanding of the cellular processes involved in secretion. The last section on "Digestion and Absorption" contains new chapters on the intestinal barrier, protein sorting and ion channels along with those focusing on the uptake of specific nutrients. These chapters were recruited and edited by Hamid M. Said and Fayez K. Ghishan. · Collected in one set - the most current and comprehensive coverage of gastrointestinal physiology · Information presented in a style that is both readable and understandable · Valuable to the specialized researcher, the clinical gastroenterologist, the teacher, and the student · Features an entirely new section on Immunology and Inflammation · Each section edited by the preeminent scientist in the field
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2005 with total page 780 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book RNA protein Interactions written by Kiyoshi Nagai and published by Oxford University Press, USA. This book was released on 1994 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of RNA-protein interactions is crucial to understanding the mechanisms and control of gene expression and protein synthesis. The realization that RNAs are often far more biologically active than was previously appreciated has stimulated a great deal of new research in this field. Uniquely, in this book, the world's leading researchers have collaborated to produce a comprehensive and current review of RNA-protein interactions for all scientists working in this area. Timely, comprehensive, and authoritative, this new Frontiers title will be invaluable for all researchers in molecular biology, biochemistry and structural biology.
