Computational Studies Of Carbohydrate Protein Interactions
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Computational Studies Of Carbohydrate Protein Interactions
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Author : Alessandra Lacetera
language : en
Publisher:
Release Date : 2017
Computational Studies Of Carbohydrate Protein Interactions written by Alessandra Lacetera and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with categories.
Molecular modelling techniques have been extensively applied to the elucidation of glycan-protein interactions at the atomic level of several systems with biological and therapeutic interests, and have provided new insights for the understanding of the molecular recognition events underlying the biological functions of these systems. In this Thesis, the general objective is to elucidate the carbohydrate-protein interactions at the atomic level through computational techniques. In particular, the following systems have been studied: human galectins -1, -3, and -7, Pisum sativum lectin, Maackia amurensis seed lectin, and glycosyltransferase GalNAc-T2. The final aim is to provide new insights for the understanding of the molecular recognition events underlying the biological functions of these proteins...
Protein Interactions Computational Methods Analysis And Applications
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Author : M Michael Gromiha
language : en
Publisher: World Scientific
Release Date : 2020-03-05
Protein Interactions Computational Methods Analysis And Applications written by M Michael Gromiha and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-03-05 with Science categories.
This book is indexed in Chemical Abstracts ServiceThe interactions of proteins with other molecules are important in many cellular activities. Investigations have been carried out to understand the recognition mechanism, identify the binding sites, analyze the the binding affinity of complexes, and study the influence of mutations on diseases. Protein interactions are also crucial in structure-based drug design.This book covers computational analysis of protein-protein, protein-nucleic acid and protein-ligand interactions and their applications. It provides up-to-date information and the latest developments from experts in the field, using illustrations to explain the key concepts and applications. This volume can serve as a single source on comparative studies of proteins interacting with proteins/DNAs/RNAs/carbohydrates and small molecules.
Development Of Computational Methods To Characterize Carbohydrate Protein Interactions
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Author : Amika Sood
language : en
Publisher:
Release Date : 2016
Development Of Computational Methods To Characterize Carbohydrate Protein Interactions written by Amika Sood and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.
Specific carbohydrate-protein interactions are crucial in numerous physiological processes, disruption of which has been implicated in many different diseases like cancer. This provides researchers an opportunity to utilize carbohydrates as biomarkers and targets for therapeutics for such diseases. There has been a tremendous surge in the research being conducted towards the development of techniques to analyze carbohydrates and their specificity and affinity for different proteins. However, owing to their complex three-dimensional structure, stereochemistry, low binding affinities and broad specificity, carbohydrates have proven to be challenging to study. Therefore, new techniques and improvements in the existing methodologies are required. Here, we show that the incorporation of experimental data into molecular modeling can be used as a powerful combination to gain an understanding of the structural features of proteins and carbohydrates leading to the specificity in their interactions. Firstly, hydroxyl radical protein footprinting (HRPF) was used to establish a relationship between the oxidation of amino acids exposed on the surface of a protein and their solvent accessible surface area (SASA). Oxidation, as well as SASA, are both directly proportional to the exposure of an amino acid to the solvent. This relationship was used to estimate SASA of residues of a protein in solution, which was then successfully utilized as a score to quantify the quality of models generated through a molecular dynamics (MD) simulation and homology modeling. This relationship can also be used to study protein- carbohydrate interactions, which remains to be tested. Secondly, the functional groups of a monosaccharide essential for forming protein-carbohydrate interactions were identified by using co-crystal structures and per-atom binding energy analysis, which shows that not all chemically-equivalent functional groups are equally significant for binding. Lastly, the 3D structure of a group of monosaccharides was analyzed and it was observed that two monosaccharides can possess structural similarities depending on their alignment, which can be used to explain cross-reactivity between a protein and more than one carbohydrate.
Carbohydrate Protein Interactions
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Author : D. Wade Abbott
language : en
Publisher: Springer Nature
Release Date : 2023-05-06
Carbohydrate Protein Interactions written by D. Wade Abbott and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-05-06 with Science categories.
This second edition provides new and updated tools for studying protein-carbohydrate interactions ranging from traditional biochemical methods to state-of-the-art techniques. This book focuses on four different research themes detailing methods for screening and quantifying CAZyme activity, investigating the interactions between proteins, carbohydrate ligands, methods for the visualization of carbohydrates, protein-carbohydrate complexes, structural and “omic” approaches for studying systems of CAZymes. 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 methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Carbohydrate- Protein Interactions: Methods and Protocols, Second Edition aims to be comprehensive guide for researchers in the field.
Computational Prediction And Analysis Of Protein Carbohydrate And Protein Protein Interactions
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Author : Chaitanya A. K. Koppisetty
language : en
Publisher:
Release Date : 2010
Computational Prediction And Analysis Of Protein Carbohydrate And Protein Protein Interactions written by Chaitanya A. K. Koppisetty and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with categories.
Carbohydrate Protein Interaction
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Author : Adrienne E. Clarke
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-03-09
Carbohydrate Protein Interaction written by Adrienne E. Clarke and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-03-09 with Science categories.
Carbohydrate as the primary product of photosynthesis has a vital role in the maintenance of life on this planet. Until relatively recently, interest in complex carbohydrates focussed on their structural role in the extracellular matrix/ cell wall of animal, plant, and microbial cells and on their role as energy sources (e.g., starch and glycogen) and struc tural components (e.g., cellulose) in natural products. There was, however, indirect evidence that carbohydrates could play an informational role; this evidence was from the find ing last century that plant lectins caused specific agglutina tion of certain animal cells and, more recently, that the agglutination was mediated by interactions between the plant lectin and cell surface carbohydrates. It is now clear that endogenous carbohydrate binding proteins are important in cell-cell recognition phenomena in animal systems. Recently, impressive evidence has been presented that complex oligosaccharides, derived from cell walls, are also important in plant recognition events, for example in signalling the defence mechanisms of a plant to respond to attack by insects and microbial pathogens.
Computational Protein Protein Interactions
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Author : Ruth Nussinov
language : en
Publisher: CRC Press
Release Date : 2009-06-26
Computational Protein Protein Interactions written by Ruth Nussinov and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-06-26 with Science categories.
Often considered the workhorse of the cellular machinery, proteins are responsible for functions ranging from molecular motors to signaling. The broad recognition of their involvement in all cellular processes has led to focused efforts to predict their functions from sequences, and if available, from their structures. An overview of current resear
Conformation Of Carbohydrates
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Author : V. S. R. Rao
language : en
Publisher: CRC Press
Release Date : 2019-08-22
Conformation Of Carbohydrates written by V. S. R. Rao and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-08-22 with Medical categories.
This text will give the reader a firm understanding of all aspects of carbohydrate conformation by describing and explaining the importance of interactions between carbohydrates and interactions of carbohydrates with proteins, nucleic acids or any other macromolecule., The authors have gathered a wealth of information on carbohydrate structures, different methods of conformational analysis, the role of carbohydrates as recognition molecules in biological systems and their industrial applications., Whether you are a student, teacher or a basic researcher, this text book is a ‘one-stop’ source of current information on carbohydrate conformation and the potential use of conformational properties in industry and also of their crucial role in important biological events such as cell-cell interaction, cell adhesion, cellular signaling mechanism.
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.
Computational Analysis Of Protein Carbohydrate Interactions
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Author : Chiara Taroni
language : en
Publisher:
Release Date : 1998
Computational Analysis Of Protein Carbohydrate Interactions written by Chiara Taroni and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1998 with categories.