Author: JASON A. MCEVOYPublisher: Lulu.com
ISBN: 0359602312
Category : Chemistry
Languages : en
Pages : 322
Book Description
Molecular Recognition of RNA
Author: Daniel James BattleMOLECULAR RECOGNITION: BIOTECHNOLOGY, CHEMICAL ENGINEERING AND MATERIALS APPLICATIONS
Author: JASON A. MCEVOYPublisher: Lulu.com
ISBN: 0359602312
Category : Chemistry
Languages : en
Pages : 322
Book Description
Computational Methods as Applied to Molecular Recognition in RNA.
Author: P. Therese LangPublisher:
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.
The Molecular Recognition of RNA by Amincyclitol Libraries
Author: Claire NunnsMolecular Recognition of Dynamic RNA Structures
Author: Sang Won LeePublisher:
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.
Basics of Molecular Recognition
Author: Dipankar ChatterjiPublisher: CRC Press
ISBN: 1482219697
Category : Medical
Languages : en
Pages : 139
Book Description
Basics of Molecular Recognition explores fundamental recognition principles between monomers or macromolecules that lead to diverse biological functions. Based on the author's longtime courses, the book helps readers understand the structural aspects of macromolecular recognition and stimulates further research on whether molecules similar to DNA o
Recent Trends in Molecular Recognition
Author: F. DiederichPublisher: Springer Science & Business Media
ISBN: 366203574X
Category : Science
Languages : en
Pages : 274
Book Description
Reasoning in terms of molecular recognition may be traced back to Emil Fischer, who practiced the art of chemistry at Humboldt University in Prussian Berlin a century ago. Today, it is clearly recognized that molecular recognition impacts and determines all life processes. It has become a key research field in both chemistry and biology and the emerging interface of what now is being called "chemical biology". The technological advances derived from this knowledge are particularly important, diverse, and directly evident in the pharmaceutical industry. Under the auspices of the Ernst Schering Research Foundation, a workshop held in Berlin in February 1998 addressed novel basic developments of potential relevance to drug research efforts. A balance of timely research topics in molecular recognition is presented in the lectures delivered by a multidisciplinary international panel of renowned scholars and documented in this volume.
Multifunctional Molecular Recognition of DNA/RNA Secondary Structure by Molecular Senzors
Author: Tamara ŠmidlehnerRNA Recognition
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: Peter C. Anderson