Simulation Studies Of The Glycosylation Code
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Simulation Studies Of The Glycosylation Code
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Author : Christopher Ellis
language : en
Publisher:
Release Date : 2014
Simulation Studies Of The Glycosylation Code written by Christopher Ellis and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with categories.
This thesis reports computational studies that investigate the impact of protein-carbohydrate and protein-protein interactions upon protein structure and folding. Thecore of this thesis, which is found in Chapters 2 and 3, examines the biophysical consequences of glycosylation.In Chapter 2, replica-exchange molecular dynamics (REMD) simulations investigatethe underlying mechanism for an experimentally observed conformational switch that is induced by the glycosylation of a short peptide. In order to distinguish between the effects of specific and nonspecific interactions with the carbohydrate, these simulations considered model peptides that were N-linked to a disaccharide and also to a steric crowder of the same shape. The simulations suggest that nonspecific steric crowding by the N-linked disaccharide did not significantly alter the peptide free energy surface. However, the combination of steric crowding with specific interactions, e.g. hydrogen bonding and aromatic-glycan stacking, dramatically impacts the peptide ensemble and stabilizes the conformational switch. Motivated by these results, Chapter 3 investigates sequence specific effects of N-linked glycosylation by performing a series of REMD simulations for peptides that correspond to point mutations from the sequence considered in Chapter 2. The simulations suggest that sequences with glycine adjacent to the glycosylation site readily form compact beta-turns upon glycosylation, while sequences with alanine in this location appear to be much less influenced by the glycan. Somewhat surprisingly, the simulations suggest that aromatic-glycan interactions are less significant for this conformational switch. In order to corroborate the REMD simulations, we also performed bioinformatic analysis of a dataset of glycoprotein structures. This analysis indicated that the simulations of short glycopeptides are quite predictive of the conformations adopted by glycosylated sequences in the context of full length glycoproteins.Chapters 4 and 5 address considerably different systems. Chapter 4 investigates the molecular interactions governing ubiquitin-ubiquilin binding via structure alignment and a series of conventional MD simulations. These simulations demonstrate that subtle differences between the hydrophobic binding pockets of ubiquitin and the ubiquitin-like domain dramatically alter their conformational ensemble and also their binding.
Annual Reports In Computational Chemistry
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Author : Ralph A. Wheeler
language : en
Publisher: Elsevier
Release Date : 2010-09-06
Annual Reports In Computational Chemistry written by Ralph A. Wheeler and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-09-06 with Science categories.
Annual Reports in Computational Chemistry is a new periodical providing timely and critical reviews of important topics in computational chemistry as applied to all chemical disciplines. Topics covered include quantum chemistry, molecular mechanics, force fields, chemical education, and applications in academic and industrial settings. Each volume is organized into (thematic) sections with contributions written by experts. Focusing on the most recent literature and advances in the field, each article covers a specific topic of importance to computational chemists. Annual Reports in Computational Chemistry is a "must" for researchers and students wishing to stay up-to-date on current developments in computational chemistry. Broad coverage of computational chemistry and up-to-date information Topics covered include bioinformatics, drug discovery, protein NMR, simulation methodologies, and applications in academic and industrial settings Each chapter reviews the most recent literature on a specific topic of interest to computational chemists
Small Molecules And Peptide Based Candidates As Therapeutics And Vaccines For Covid 19 Pandemic
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Author : Da’san Mahmoud Mousa Jaradat
language : en
Publisher: Frontiers Media SA
Release Date : 2021-11-16
Small Molecules And Peptide Based Candidates As Therapeutics And Vaccines For Covid 19 Pandemic written by Da’san Mahmoud Mousa Jaradat and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-11-16 with Science categories.
Topic Editor Dr. Balakumar Chandrasekaran holds patents relating to N-substituted isatin hydrazones as antimycobacterial and antimicrobial agents, and Pharmaceutical Compounds. Topic Editor Dr. Munir Al-Zeer holds a patent relating to Method for the Preparation of an Influenza Virus. All other Topic Editors declare no competing interests.
Biomedical Index To Phs Supported Research Project Number Listing Investigator Listing
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Author :
language : en
Publisher:
Release Date : 1989
Biomedical Index To Phs Supported Research Project Number Listing Investigator Listing written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1989 with Medicine categories.
Ribosome Inactivating Toxins
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Author : Julien Barbier
language : en
Publisher: MDPI
Release Date : 2019-01-17
Ribosome Inactivating Toxins written by Julien Barbier and has been published by MDPI this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-01-17 with Medicine (General) categories.
This book is a printed edition of the Special Issue "Ribosome Inactivating Toxins" that was published in Toxins
Biomedical Index To Phs Supported Research
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Author :
language : en
Publisher:
Release Date : 1992
Biomedical Index To Phs Supported Research written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1992 with Medicine categories.
Research Grants
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Author :
language : en
Publisher:
Release Date : 1988
Research Grants written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1988 with Medicine categories.
Free Energy Calculations
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Author : Christophe Chipot
language : en
Publisher: Springer
Release Date : 2007-08-09
Free Energy Calculations written by Christophe Chipot and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-08-09 with Science categories.
This volume offers a coherent account of the concepts that underlie different approaches devised for the determination of free energies. It provides insight into the theoretical and computational foundations of the subject and presents relevant applications from molecular-level modeling and simulations of chemical and biological systems. The book is aimed at a broad readership of graduate students and researchers.
National Institutes Of Health Research Grants
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Author :
language : en
Publisher:
Release Date : 1989
National Institutes Of Health Research Grants written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1989 with Medicine categories.
Functional And Structural Proteomics Of Glycoproteins
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Author : Raymond J. Owens
language : en
Publisher: Springer
Release Date : 2014-11-23
Functional And Structural Proteomics Of Glycoproteins written by Raymond J. Owens and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-11-23 with Science categories.
It has been predicted that nearly half of all human proteins are glycosylated indicating the significance of glycoproteins in human health and disease. For example, the glycans attached to proteins have emerged as important biomarkers in the diagnosis of diseases such as cancers and play a significant role in how pathogenic viruses gain entry into human cells. The study of glycoproteins has now become a truly proteomic science. In the last few years, technology developments including in silico methods, high throughput separation and detection techniques have accelerated the characterization of glycoproteins in cells and tissues. Glyco-engineering coupled to rapid recombinant protein production has facilitated the determination of glycoprotein structures key to exploring and exploiting their functional roles. Each chapter in this volume is written by experts in the field and together provide a review of the state of the art in the emerging field of glycoproteomics.