Development Of Computational Methods To Characterize Carbohydrate Protein Interactions
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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 Interactions
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Author : M.Michael Gromiha
language : en
Publisher: World Scientific Publishing Company
Release Date : 2020-03-05
Protein Interactions written by M.Michael Gromiha and has been published by World Scientific Publishing Company this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-03-05 with Protein-protein interactions categories.
The 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.
Advances In Carbohydrate Chemistry And Biochemistry
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Author :
language : en
Publisher: Academic Press
Release Date : 2014-12-02
Advances In Carbohydrate Chemistry And Biochemistry written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-12-02 with Science categories.
Since its inception in 1945, this serial has provided critical and informative articles written by research specialists that integrate industrial, analytical, and technological aspects of biochemistry, organic chemistry, and instrumentation methodology in the study of carbohydrates. The articles provide a definitive interpretation of the current status and future trends in carbohydrate chemistry and biochemistry. Features contributions from leading authorities and industry experts Informs and updates on all the latest developments in the field
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 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...
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.
Structural And Computational Glycobiology Immunity And Infection
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Author : Elizabeth Yuriev
language : en
Publisher: Frontiers Media SA
Release Date : 2015-08-04
Structural And Computational Glycobiology Immunity And Infection written by Elizabeth Yuriev 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 2015-08-04 with Immunologic diseases. Allergy categories.
Interest in understanding the biological role of carbohydrates has increased significantly over the last 20 years. The use of structural techniques to understand carbohydrate-protein recognition is still a relatively young area, but one that is of emerging importance. The high flexibility of carbohydrates significantly complicates the determination of high quality structures of their complexes with proteins. Specialized techniques are often required to understand the complexity of carbohydrate recognition by proteins. In this Research Topic, we will focus on structural and computational approaches to understanding carbohydrate recognition by proteins involved in immunity and infection. Particular areas of focus include cancer immunotherapeutics, carbohydrate-lectin interactions, glycosylation and glycosyltransferases.
Glycobiology And Human Diseases
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Author : Gherman Wiederschain
language : en
Publisher: CRC Press
Release Date : 2016-02-22
Glycobiology And Human Diseases written by Gherman Wiederschain and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-02-22 with Medical categories.
This book discusses glycobiology and various forms of human diseases. Topics covered include immunoglobulins, inflammation and glycosylation, the role and therapeutic significance of natural anti-glycan antibodies in malignancies and in normal and aberrant pregnancy, identifying urinary glycans as a possible method for the diagnosis of lysosomal st
The Glycome
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Author : Adeel Malik
language : en
Publisher: CRC Press
Release Date : 2021-07-07
The Glycome written by Adeel Malik and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-07-07 with Science categories.
This volume provides a comprehensive understanding of the enigmatic identity of the glycome, a complex but important area of research that has been largely ignored due to its complexity. The authors thoroughly deal with almost all aspects of the glycome, i.e., elucidation of the glycan identity enigma and its role in regulation of the cellular process, and in disease etiology. The book bridges the knowledge gap in understanding the glycome, from being a cell signature to its applications in disease etiology. In addition, it details many of the major insights regarding the possible role of the glycome in various diseases as a therapeutic marker. The book systematically covers the major aspects of the glycome, including the significance of substituting the diverse monosaccharide units to glycoproteins, the role of glycans in disease pathologies, and the challenges and advances in glycobiology. The authors stress the significance and huge encoding power of carbohydrates as well as provide helpful insights in framing the bigger picture. The Glycome: Understanding the Diversity and Complexity of Glycobiology details state-of-the-art developments and emerging challenges of glycome biology, which are going to be key areas of future research, not only in the glycobiology field but also in pharmaceutics.
Carbohydrates In Drug Design And Discovery
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Author : Jesús Jímenez-Barbero
language : en
Publisher: Royal Society of Chemistry
Release Date : 2015-04-10
Carbohydrates In Drug Design And Discovery written by Jesús Jímenez-Barbero and has been published by Royal Society of Chemistry this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-04-10 with Science categories.
In recent years there has been increasing evidence of the importance of carbohydrates and glycoconjugates in biomedical applications, and the use of synthetic ligands based on carbohydrates as drugs has received much attention. Focussing on drug discovery from key targets and placing an emphasis on the multi-disciplinary approaches necessary to challenge these issues, this book comprehensively covers the new and recent discoveries in the area of carbohydrate drug discovery. Carbohydrates in Drug Design and Discovery is split into five sections, beginning with a introduction and perspective on the current market. The book then goes on to discuss new synthetic methods in glycobiology, the use of glycobiology in chemical biology and glycobiology in drug discovery. Providing a worldwide perspective on this broad area, and providing examples of therapeutics already developed using these methods, this book provides a comprehensive introduction, discussion and update on this fast developing field for medicinal chemists and biochemists working in industry and academia.