Database Development And Analysis Of Carbohydrate Protein Interactions
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Database Development And Analysis Of Carbohydrate Protein Interactions
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Author : Sonu Kumar
language : en
Publisher:
Release Date : 2012
Database Development And Analysis Of Carbohydrate Protein Interactions written by Sonu Kumar and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012 with categories.
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 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.
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.
Bioinformatics For Glycobiology And Glycomics
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Author : Claus-Wilhelm von der Lieth
language : en
Publisher: John Wiley & Sons
Release Date : 2009-10-01
Bioinformatics For Glycobiology And Glycomics written by Claus-Wilhelm von der Lieth and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-10-01 with Medical categories.
This book is the first to be dedicated to the bioinformatics of carbohydrates and glycoproteins. It provides an introduction to this emerging field of science both for the experimentalist working in glycobiology and glycomics, and also for the computer scientist looking for background information for the development of highly sophisticated algorithmic approaches. The book provides an overview of the state-of-the-art in the field, with reviews on databases, and the tools in use for analysis, interpretation, and prediction of the structures of complex carbohydrates, and demonstrates the value of bioinformatics for glycobiology. The availability of comprehensive databases and corresponding bioinformatics tools, to access and analyse the large amounts of experimental data relating to the structure of carbohydrates, will be a prerequisite for the success of the large-scale glycomics projects that aim to decipher new, so far unknown, biological functions of glycans. Efficient bioinformatics descriptions and tools can considerably enhance the efficiency of glycomics research, in terms of data quality, analysis and experimental costs. For a complete understanding of the molecular processes in which carbohydrates are involved, such as protein–carbohydrate interactions and the impact of glycosylation on protein function, knowledge of the 3D structure of the carbohydrate, the protein–carbohydrate complex, or the glycoprotein is often indispensable. This book provides a thorough introduction into methods used for conformational analysis of carbohydrates. Key features: Describes bioinformatic approaches to handle carbohydrate-active enzymes and glycosylation. Provides an overview on bioinformatics tools that facilitate analysis of carbohydrate structures. Gives introduction into molecular modelling of carbohydrate 3D structure and carbohydrates contained in the Protein Databank. Assumes only a basic knowledge of biology and bioinformatics.
Advances In Carbohydrate Chemistry And Biochemistry
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Author :
language : en
Publisher: Elsevier
Release Date : 2023-11-10
Advances In Carbohydrate Chemistry And Biochemistry written by and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-11-10 with Science categories.
Advances in Carbohydrate Chemistry and Biochemistry, Volume 83, the latest release in a serial that highlights new advances in the field, includes a variety of highly sourced chapters written by an international board of authors. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in Advances in Carbohydrate Chemistry and Biochemistry serials Edited by leading scientists in the field
Carbohydrate Based Interactions At The Molecular And The Cellular Level
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Author : Kieran L. Hudson
language : en
Publisher: Springer
Release Date : 2018-05-28
Carbohydrate Based Interactions At The Molecular And The Cellular Level written by Kieran L. Hudson and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-05-28 with Science categories.
This book offers a clearly written and highly accessible account of two different aspects of carbohydrate chemistry. Carbohydrates are an essential component of life and have many important biological functions, but the details of how carbohydrates interact with other biomolecules to mediate biological signalling remain unclear. Firstly, this thesis details innovative methods to mine protein structural data to uncover new features of carbohydrate-based interactions. It also explains these findings using physical chemistry, specifically CH–pi interactions associated with the properties of the interacting partners. Carbohydrates are also critical for tissue growth and development, yet are underexploited in the materials science that underpins much of regenerative medicine. As such, the second part of this thesis describes a diverse array of techniques ranging from synthetic chemistry and enzymatic synthesis to prepare a wide variety of carbohydrates, and materials chemistry to prepare glycosylated hydrogels, to cell biology to determine the effects on cellular development for tissue engineering applications.
Omics
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Author : Debmalya Barh
language : en
Publisher: CRC Press
Release Date : 2013-03-26
Omics written by Debmalya Barh and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-03-26 with Medical categories.
With the advent of new technologies and acquired knowledge, the number of fields in omics and their applications in diverse areas are rapidly increasing in the postgenomics era. Such emerging fields-including pharmacogenomics, toxicogenomics, regulomics, spliceomics, metagenomics, and environomics-present budding solutions to combat global challeng
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.
The Development And Application Of In Silico Mapping Techniques For The Study Of Carbohydrate Protein Interactions
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Author : Mark Agostino
language : en
Publisher:
Release Date : 2011
The Development And Application Of In Silico Mapping Techniques For The Study Of Carbohydrate Protein Interactions written by Mark Agostino 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.
Carbohydrate-protein interactions are exquisitely specific, and underpin many biological and biochemical processes. In particular, carbohydrate-antibody recognition is the initial step in transplant rejection across ABO blood group and species barriers. Such interactionsare difficult to structurally characterize, due to the high flexibility of carbohydrates. In silico techniques can be used to fill the gaps in structural knowledge, but must be thoroughly validated prior to use. In this project, novel in silico mapping techniques were developed and validated for investigating carbohydrate-protein recognition, with a focus on carbohydrate-antibody recognition. Anti-[alpha]Gal antibodies, which recognize the [alpha]Gal epitope on porcine tissues and are involved in the rejection of pig-to-human xenografts, were used as a test system throughout the project. A selection of docking programs were evaluated for their ability to reproduce the carbohydrate binding modes of a series of high resolution carbohydrate-antibody crystal structure complexes. Of the programs investigated, it was found that Glide performed the best at this task. The results also highlighted that interaction-based approaches could beuseful in identifying likely binding modes. A "site mapping" technique was developed, which utilizes information from a given docking ensemble to identify protein residues likely to be involved in ligand recognition. The technique was validated for carbohydrate-antibody recognition using poses generated by Glide. Application of the technique to a panel of anti-[alpha]Gal antibodiesestablished the structurally conserved nature of carbohydrate recognition by these antibodies. Since site mapping alone cannot be used to infer likely binding modes, ligand-based mapping approaches were developed. The "epitope mapping" technique is used to determine ligand atoms likely to be involved in protein interaction. The "conformation mapping" technique is used to identify likely torsion angles of carbohydrate glycosidic linkages. Both of these techniques utilize the same docking ensemble as the site mapping technique. By combining the output from the three mapping techniques, likely carbohydrate binding modes of the anti-[alpha]Gal antibodies were determined. These binding modes demonstrated the structural basis of the observed carbohydrate selectivity by two of these antibodies. The site mapping technique was applied to investigate peptide-antibody recognition, highlighting its potential application in the design of carbohydrate-mimetic peptides. The technique was validated using a series of high resolution peptide-antibody crystal structure complexes. The recognition of peptide mimics of the [alpha]Gal epitope by the anti-[alpha]Gal antibodies was investigated using the site mapping technique. By comparing the carbohydrate- and peptide-derived site maps for each of the antibodies, it was determined that the peptides largely act as structural mimics of the carbohydrates. Carbohydrate-lectin recognition was also investigated using molecular docking and the site mapping technique. Although molecular docking could usually identify the crystal bound carbohydrate conformation, it was rarely ranked highly. This highlights the need for alternative scoring approaches when studying carbohydrate-lectin recognition using molecular docking. Site mapping was shown to identify lectin residues involved in carbohydrate recognition with improved consistency and accuracy over the top ranked docking pose, and thus, mapping techniques may be useful for these structurally investigating these challenging systems. The in silico mapping techniques developed in this project are likely to be generally useful for studying ligand-protein recognition, as well as being valuable tools for drug design.