A Structural Characterization Of Protein Carbohydrate Interactions
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A Structural Characterization Of Protein Carbohydrate Interactions
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Author : David Forrest Thieker
language : en
Publisher:
Release Date : 2017
A Structural Characterization Of Protein Carbohydrate Interactions written by David Forrest Thieker 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.
Although carbohydrates are most commonly associated with metabolism, these molecules are involved in a variety of other critical processes that range from cellular trafficking to transcriptional regulation. Alterations in carbohydrate sequence are linked to a host of diseases ranging from cancer to dementia, yet progress in structural glycobiology has been slow compared to that of proteins and DNA. The following work pushes the boundary of our understanding of carbohydrate interactions at the atomic level. First, a 3D adaptation of the Symbol Nomenclature for Glycans (SNFG) was developed as a cartoon representation for carbohydrates to improve the communication of complex structural features to both glycobiologists and non-specialists. Second, the prediction of protein-carbohydrate complexes was improved by including a scoring term within docking programs that accounts for the linkage between glycan residues. Third, the crystal structure of a silayltransferase is presented with a docked model for the sugar donor. Fourth, a significant binding preference was identified between an enzyme within the heparan sulfate biosynthetic pathway and downstream products, with implications for protein localization in vivo. Lastly, a study of the intra-molecular interactions of a glycoprotein suggests a regulatory mechanism in which glycosylation affects intrinsic protein dynamics. Collectively, these efforts contribute to our understanding of the glycan structure-function relationship and facilitate future efforts in glycobiology.
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.
Protein Carbohydrate Interactions
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Author : D. Wade Abbott
language : en
Publisher: Humana Press
Release Date : 2017-05-02
Protein Carbohydrate Interactions written by D. Wade Abbott and has been published by Humana Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-05-02 with Science categories.
This volume is a wide-ranging tool for studying protein-carbohydrate interactions that extend from traditional biochemical methods to state-of-the-art techniques. This book focuses on four different research themes: Part I describes methods for screening and quantifying CAZyme activity; Part II contains methods for investigating the interactions between proteins and carbohydrate ligands; Part III discusses methods for the visualization of carbohydrates and protein-carbohydrate complexes; and Part IV focuses on structural and “omic” approaches for studying systems of CAZymes. 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 tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Protein-Carbohydrate Interactions: Methods and Protocols is a valuable resource to the glycomics research community. In this continuously advancing field, the methods in this book highlight the biology of glycomics, thus driving biotechnological innovation and solutions for human health and sustainable resources within the emerging green community.
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.
Non Lectin Type Protein Carbohydrate Interactions
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Author : Veer Sandeep Bhatt
language : en
Publisher:
Release Date : 2011
Non Lectin Type Protein Carbohydrate Interactions written by Veer Sandeep Bhatt and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011 with categories.
Abstract: Protein-carbohydrate interactions are critical in a multitude of life processes such as bioenergetics, inflammation, cell-cell recognition, cell differentiation, embryonic development, signal transduction and host-pathogen interactions. However, the events leading to protein-carbohydrate recognition and the modulation of protein activity by glycosylation are poorly understood at molecular level. The primary objective in this work is to enrich our understanding of protein-carbohydrate interactions at a molecular level using three model systems. The first system is that of hemoglobin. The modulation of oxygen affinity by various interactions at the quaternary level is first presented in an investigation of the high oxygen affinity Greyhound hemoglobin. This is followed by a structural investigation of bovine hemoglobin carrying different lengths and types of oligosaccharides. These investigations indicate that glycosylation can increase the intrinsic oxygen affinity of hemoglobin by modifying its quaternary structure. The second system is that of a carbohydrate processing enzyme, a uridine 5'-diphospho N-acetylgalactosamine 4-epimerase. An elaborate investigation of structure and activity of this enzyme reveals several novel details of substrate recognition that may have been overlooked previously. Notably, this investigation highlights the complexities of protein-carbohydrate recognition and provides evidence that carbohydrates by themselves may induce global changes in multi-domain proteins. It further indicates that non-polar interactions are also critical in mediating protein-carbohydrate interactions and should be given due consideration in applications such as carbohydrate-based drug discovery. Thirdly, a complex system comprising of a multi-protein machinery that regulates the size of a hetero-polysaccharide called O-antigen, is presented. This system is an essential part of lipopolysaccharide biosynthesis in Gram-negative bacteria. This investigation strongly suggests that a protein called Wzz serves as a trap for nascent oligosaccharide chains while interacting with another protein called Wzy that is responsible for polymerization of these nascent oligosaccharide chains to form the mature O-antigen. Protein X-ray crystallography and routine experimental methods of modern molecular biology such as gene cloning, expression, protein purification and characterization have been used as primary techniques in this work. In addition, computational analysis, especially to perform protein-ligand docking is also used to investigate the third system.
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.
Protein Carbohydrate Interactions
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Author : D. Wade Abbott
language : en
Publisher:
Release Date : 2017
Protein Carbohydrate Interactions written by D. Wade Abbott and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with Carbohydrates categories.
"This volume is a wide-ranging tool for studying protein-carbohydrate interactions that extend from traditional biochemical methods to state-of-the-art techniques. This book focuses on four different research themes: Part I describes methods for screening and quantifying CAZyme activity; Part II contains methods for investigating the interactions between proteins and carbohydrate ligands; Part III discusses methods for the visualization of carbohydrates and protein-carbohydrate complexes; and Part IV focuses on structural and "omic" approaches for studying systems of CAZymes. 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 tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Protein-Carbohydrate Interactions: Methods and Protocols is a valuable resource to the glycomics research community. In this continuously advancing field, the methods in this book highlight the biology of glycomics, thus driving biotechnological innovation and solutions for human health and sustainable resources within the emerging green community. ."--Prové de l'editor.
Deciphering The Molecular Basis Of The Specificity Of Protein Carbohydrate Interactions By Statistical Analysis Of 3d Structural Data From The Protein Data Bank
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Author : Miguel Ángel Rojas Macías
language : en
Publisher:
Release Date : 2014
Deciphering The Molecular Basis Of The Specificity Of Protein Carbohydrate Interactions By Statistical Analysis Of 3d Structural Data From The Protein Data Bank written by Miguel Ángel Rojas Macías 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.
Structural Analysis Of Carbohydrate Protein Interactions Under Special Consideration Of Lipopolysaccharide Fragments Hyaluronic Acid Sulfated Polysaccharides And Sialic Acids
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Author : Ruiyan Zhang
language : de
Publisher:
Release Date : 2017
Structural Analysis Of Carbohydrate Protein Interactions Under Special Consideration Of Lipopolysaccharide Fragments Hyaluronic Acid Sulfated Polysaccharides And Sialic Acids written by Ruiyan Zhang 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.
Deciphering The Molecular Basis Of The Specificity Of Protein Carbohydrate Interactions By Statistical Analysis Of 3d Structural Data From The Protein Data Bank
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Author : Miguel Angel Rojas Macias
language : en
Publisher:
Release Date : 2016
Deciphering The Molecular Basis Of The Specificity Of Protein Carbohydrate Interactions By Statistical Analysis Of 3d Structural Data From The Protein Data Bank written by Miguel Angel Rojas Macias 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.