Author: Sang Won Lee Publisher: ISBN: Category : Ligand binding (Biochemistry) Languages : en Pages : 206
Book Description
Nucleic acids are highly dynamic and are not present as a single rigid structure. For RNA molecules, the structure, energetics and dynamics are closely connected to their cellular functions, therefore it is very important to characterize these interactions. Conventional biophysical methods such as X-ray crystallography and NMR are highly powerful tools in deriving the structures of RNA molecules at the atomic level. However, structural conformational dynamics are difficult to probe due to rapid structural inter-conversion. Using the theophylline-binding RNA aptamer and transcription antiterminator N protein/ boxB RNA complex as two different model systems, here we employed femtosecond time-resolved spectroscopy as a main tool, using 2-aminopurine as a probe to capture the dynamic base stacking interactions. In the theophylline-binding RNA aptamer, we found that some regions of the aptamers are conformationally heterogeneous in the free state, while other regions are pre-organized in their bound-state conformation. In the boxB RNA, we proposed a revised model for the boxB RNA/N peptide interface which consists of three different patterns of states with stacking/unstacking interaction. We also achieved an increase in the stacking population by using new RNA binding ligands. In conclusion, we observed RNA as an ensemble of structures in different structural contexts rather than a single rigid static structure. We proposed a detailed model for free RNA and RNA/ligand complexes using the femtosecond time-resolved spectroscopy that is complementary to these from conventional biophysical methods such as NMR and X-ray crystallography.
Author: Alberto Jorge Vazquez Anderson Publisher: ISBN: Category : Languages : en Pages : 532
Book Description
RNA, previously recognized merely as a messenger of genetic information, has been recently rediscovered as a versatile molecule with a central role in cellular regulation. These regulatory functions are enabled by its specific chemical makeup that allows it to fold into intricate and flexible structures. In stark contrast with DNA, RNA forms a variety of structural motifs that serve as efficient points of contact in molecular recognition. It is therefore clear, that dynamic RNA structures dictate the binding availability of interfaces that play important roles in molecular regulation inside living cells. As such, the need for tools that can accurately capture and predict RNA structure in vivo continues to be essential to understand RNA function. To this end, my dissertation focuses on the development of molecular tools to predict and characterize accessible RNA interfaces in their native environment. First, I established the usefulness of a fluorescence-based in vivo oligonucleotide hybridization approach to identify accessible interfaces by characterizing numerous RNA regions in several biologically relevant molecules in E. coli. I then described these RNA interactions using a biophysical model based on thermodynamic principles and incorporating large sets of data collected using this fluorescence-based system. This approach displayed improved prediction capabilities of RNA accessibility compared to un-optimized versions without incorporation of in vivo data. Finally, I detailed the development and application of a high throughput tool for the large-scale characterization of accessible interfaces within native RNAs in a single experiment. In this approach, in vivo oligonucleotide hybridization was coupled to transcriptional elongation control to allow analysis via next generation sequencing. This tool was used to obtain complete landscapes of functional structure for 72 regulatory molecules in a single experiment (>1000 regions). Altogether the results of this high throughput approach revealed a pattern indicating that RNA-RNA interaction sites are either highly accessible or highly protected, suggesting their binding status (e.g. actively bound or unbound). In addition, within bacterial small RNAs, our approached revealed the role of the global regulator Hfq as universal structural relaxer. The compendium of these tools provides a unique and fundamental perspective in the study of functional RNA structure, namely, the identification of dynamic structures. Furthermore, the information provided by these approaches significantly aids in the design of synthetic RNAs for a variety of purposes, including gene expression control.
Author: Publisher: Academic Press ISBN: 0128168323 Category : Science Languages : en Pages : 468
Book Description
RNA Recognition, Volume 623, the latest volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This updated volume covers a variety of topics, including The Preparation of cooperative RNA recognition complexes for crystallographic structural studies, Methods for thermal denaturation studies of fluorogenic aptamers, Dynamic combinatorial chemistry as a rapid, fragment-based approach to RNA-targeted compound discovery, Using a click chemistry assay to identify natural product ligands for pre-microRNAs, Lessons from exploration of chemical and structural small molecule:RNA space, Using ligand-observed NMR to study RNA-small molecule interactions, and much more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology series Includes the latest information on RNA Recognition
Author: National Research Council Publisher: National Academies Press ISBN: 0309062284 Category : Computers Languages : en Pages : 186
Book Description
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: P. Therese Lang Publisher: ISBN: Category : Languages : en Pages : 538
Book Description
The aim of this thesis was to improve computational methods for structure based drug design, particularly for RNA targets. For the first portion, we present a critical evaluation of various computational drug design algorithms for their ability to predict experimental binding poses and rank libraries of small molecules against protein targets. In particular, we characterize the strengths and weaknesses of the ligand sampling method for the DOCK suite of programs. In the second portion of the thesis, we apply the lessons learned from protein targets to the disruption of protein-RNA interactions critical to the life cycle of the HIV virus. As a class, RNA historically has presented a difficult computational challenge both due to its highly localized charge and flexibility. Therefore, we have extended protocols and added new protocols in existing software packages such as DOCK and AMBER to predict experimental binding poses, once again validating our results using experimental data. Finally, we apply these protocols both to develop libraries of small molecules against druggable RNA targets and to establish a fragment-based library designed to find new scaffolds for RNA.
Author: Jienyu Ding Publisher: Springer Nature ISBN: 1071626876 Category : Science Languages : en Pages : 256
Book Description
This volume provides a wide spectrum of multidisciplinary approaches for studying RNA structure and dynamics, including detailed accounts of experimental and computational procedures. Chapters guide readers through cryo-electron microscopy, crystallography, isothermal titration calorimetry, small angle X-ray scattering, single-molecule Förster Energy transfer, X-ray free electron laser, atomic force microscopy, computational simulation, and prediction. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, RNA Structure and Dynamics aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.
Author: Publisher: Academic Press ISBN: 0128019360 Category : Science Languages : en Pages : 675
Book Description
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: Neocles Leontis Publisher: Springer Science & Business Media ISBN: 3642257402 Category : Science Languages : en Pages : 402
Book Description
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.
Author: Sang Won Lee
Author: Alberto Jorge Vazquez Anderson
Author: 
Author: National Research Council
Author: P. Therese Lang
Author: Jienyu Ding
Author: 
Author: Neocles Leontis
Author: Peter C. Anderson
Author: Tamara Šmidlehner