Rna Structural Characterization Of Rna Binding Protein Binding Sites PDF Download
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Author | : Yash Patel |
Publisher | : |
Total Pages | : |
Release | : 2021 |
Genre | : |
ISBN | : |
Download RNA Structural Characterization of RNA-binding Protein Binding Sites Book in PDF, ePub and Kindle
"The interaction between RNA and RNA-binding proteins (RBPs) facilitates key processes, such as gene expression regulation, mRNA transport, and splicing, within the lifetime of the RNA. Studies of these interactions have demonstrated the importance of not only RNA sequence-level motifs but also of the RNA structural context surrounding the RBP binding site. Whereas sequence-focused studies have identified well-characterized sequence elements serving as RBP binding sites, the structural considerations remain limited to a small set of RNA secondary structural elements. We present a study identifying local 3D RNA modules associated with the binding of specific RBPs. Using datasets composed of 3D RNA modules extracted from experimentally-determined structures, we annotate eukaryotic mRNA sequences and relate the presence of these local structures with RBP binding. We report several specific RNA modules, each associated with the binding of specific RBPs, along with a link between certain modules and mRNA subcellular localization"--
Author | : National Research Council |
Publisher | : National Academies Press |
Total Pages | : 186 |
Release | : 1987-02-01 |
Genre | : Computers |
ISBN | : 0309062284 |
Download Computer Assisted Modeling Book in PDF, ePub and Kindle
In much of biology, the search for understanding the relation between structure and function is now taking place at the macromolecular level. Proteins, nucleic acids, and polysaccharides are macromolecule--polymers formed from families of simpler subunits. Because of their size and complexity, the polymers are capable of both inter- and intramolecular interactions. These interactions confer upon the polymers distinctive three-dimensional shapes. These tertiary configurations, in turn, determine the function of the macromolecule. Computers have become so inextricably involved in empirical studies of three-dimensional macromolecular structure that mathematical modeling, or theory, and experimental approaches are interrelated aspects of a single enterprise.
Author | : Kiyoshi Nagai |
Publisher | : Oxford University Press, USA |
Total Pages | : 302 |
Release | : 1994 |
Genre | : Medical |
ISBN | : |
Download RNA-protein Interactions Book in PDF, ePub and Kindle
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.
Author | : Elan A. Shatoff |
Publisher | : |
Total Pages | : 0 |
Release | : 2021 |
Genre | : Molecular structure |
ISBN | : |
Download Computational Analysis of the Interplay Between RNA Structure and Function Book in PDF, ePub and Kindle
RNA is ubiquitous in the cellular environment, and it can function in innumerable ways with a variety of interaction partners. A RNA molecule's structure, in particular the set of base pairing interactions between the nucleotides of the molecule known as secondary structure, can help determine its function. Since most proteins can only bind to either single stranded or double stranded RNA, RNA secondary structure can also help determine where and how RNA-protein binding interactions occur. In this work I investigate computational models for RNA-protein interactions in a variety of different contexts. In Chapter 2 I probe the effect of single nucleotide variations on RNA-protein binding as mediated by RNA secondary structure. Single nucleotide variations are single nucleotide changes in an organism's genome that can often cause disease, and may do so through a number of different mechanisms. In this work we propose that sequence changes can affect accessibility to protein binding sites through changes in secondary structure, even when these sequence changes occur tens of nucleotides outside of protein binding sites. We find that single nucleotide variations can have a many fold effect on the binding affinity of proteins for RNA, and characterize the genome-wide effect of single nucleotide variations on HuR binding. HuR is a single-stranded RNA binding protein that binds to AU-rich sequences, and has links to diseases such as cancer. We also find an asymmetry in this effect for HuR, indicating that this effect may be under selection. Following the previous work, which utilizes a model incorporating single stranded RNA binding proteins into RNA secondary structure folding, I introduce a model for incorporating double stranded RNA binding proteins (dsRBPs) into RNA secondary structure partition function calculations in Chapter 3. The dsRBPs are an important but understudied class of proteins that have uses in a wide range of processes. We implement our model in the ViennaRNA package, and validate it by calculating a number of experimental observables for transactivation response element RNA-binding protein. We find that RNA secondary structure can have a many fold effect on the effective binding affinity of dsRBPs, and show that calculated affinities for pre-miRNA-like constructs correlate with experimentally measured processing rates. Our model provides a novel method for interrogating the interplay between dsRBPs and RNA secondary structure. In Chapter 4 I study RNA-protein interactions in a different context, and investigate the role of Shine-Dalgarno (SD) sequences in translation in the Bacteroidetes. The Bacteroidetes are a phylum of bacteria known to rarely use SD sequences, but after performing a survey of SD usage in the phylum we find that certain ribosomal protein genes utilize them, particularly rpsU. A cryo-electron microscopy structure of the ribosome from Flavobacterium johnsoniae, a member of the Bacteroidetes, also shows that S21, which is encoded by the ribosomal open reading frame rpsU, sequesters the anti-Shine-Dalgarno (ASD) sequence. In our survey of SD sequences we also find covariation between the SD sequence of rpsU and the ASD sequence. These observations suggest an autoregulatory model for S21 in the Bacteroidetes.
Author | : Frank J. Schmidt |
Publisher | : Humana Press |
Total Pages | : 0 |
Release | : 2014-10-29 |
Genre | : Medical |
ISBN | : 9781493918959 |
Download RNA-RNA Interactions Book in PDF, ePub and Kindle
In this volume expert researchers in the field detail many of the methods which are now commonly used to study RNA. These methods are presented as a guidebook to scientists who are experienced with RNA research and want to brush up on a new technique. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Thorough and intuitive, RNA-RNA Interactions: Methods and Protocols guides scientists investigating biological systems and studying RNA.
Author | : |
Publisher | : |
Total Pages | : 20 |
Release | : 1955 |
Genre | : Brightlingsea (England) |
ISBN | : |
Download Brightlingsea, Essex. The Official Guide. With Map and ... Illustrations Book in PDF, ePub and Kindle
Author | : Zdravko Lorkovic |
Publisher | : CRC Press |
Total Pages | : 174 |
Release | : 2012-08-10 |
Genre | : Science |
ISBN | : 149871336X |
Download RNA Binding Proteins Book in PDF, ePub and Kindle
Gene expression in eukaryotes is regulated at different levels, which need to be coordinated to implement the information in the genome. Now it is clear that post-transcriptional regulation of gene expression such as pre-mRNA splicing, mRNA transport, editing, turnover and translation are as important as the control of transcription. In all aspects
Author | : |
Publisher | : Academic Press |
Total Pages | : 675 |
Release | : 2015-06-06 |
Genre | : Science |
ISBN | : 0128019360 |
Download Structures of Large RNA Molecules and Their Complexes Book in PDF, ePub and Kindle
This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in RNA folding and dynamics, RNA-protein interactions and large RNPs. Continues the legacy of this premier serial with quality chapters on structures of large RNA molecules and their complexes
Author | : Roland K. Hartmann |
Publisher | : John Wiley & Sons |
Total Pages | : 1370 |
Release | : 2015-06-22 |
Genre | : Science |
ISBN | : 3527327762 |
Download Handbook of RNA Biochemistry Book in PDF, ePub and Kindle
The second edition of a highly acclaimed handbook and ready reference. Unmatched in its breadth and quality, around 100 specialists from all over the world share their up-to-date expertise and experiences, including hundreds of protocols, complete with explanations, and hitherto unpublished troubleshooting hints. They cover all modern techniques for the handling, analysis and modification of RNAs and their complexes with proteins. Throughout, they bear the practising bench scientist in mind, providing quick and reliable access to a plethora of solutions for practical questions of RNA research, ranging from simple to highly complex. This broad scope allows the treatment of specialized methods side by side with basic biochemical techniques, making the book a real treasure trove for every researcher experimenting with RNA.
Author | : Rick Russell |
Publisher | : Springer Science & Business Media |
Total Pages | : 238 |
Release | : 2012-12-09 |
Genre | : Science |
ISBN | : 1461449545 |
Download Biophysics of RNA Folding Book in PDF, ePub and Kindle
This volume, written by experts in the field, discusses the current understanding of the biophysical principles that govern RNA folding, with featured RNAs including the ribosomal RNAs, viral RNAs, and self-splicing introns. In addition to the fundamental features of RNA folding, the central experimental and computational approaches in the field are presented with an emphasis on their individual strengths and limitations, and how they can be combined to be more powerful than any method alone; these approaches include NMR, single molecule fluorescence, site-directed spin labeling, structure mapping, comparative sequence analysis, graph theory, course-grained 3D modeling, and more. This volume will be of interest to professional researchers and advanced students entering the field of RNA folding.