Characterisation And Engineering Of Protein Carbohydrate Interactions
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Characterisation And Engineering Of Protein Carbohydrate Interactions
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Author : Michael Lienemann
language : en
Publisher:
Release Date : 2010
Characterisation And Engineering Of Protein Carbohydrate Interactions written by Michael Lienemann and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with Carbohydrates categories.
Protein-carbohydrate interactions play a crucial role in many biological processes such as cell-cell recognition and receptor-ligand interactions and catalysis. This thesis explores the possibilities of engineering the protein-carbohydrate interactions between carbohydrate-binding proteins and their ligands. Protein-carbohydrate interactions were characterised using different techniques, such as atomic force microscopy (AFM) and surface plasmon resonance (SPR). Two different chitinoligosaccharide-binding proteins were used in the presented experiments, i.e. the plant lectin wheat germ agglutinin (WGA) and a neolectin created by inactivation of the fungal chitin-degrading enzyme Chit42. The structures of WGA and Chit42, which were available as X-ray diffraction data and a homology model, respectively, revealed differences between their binding site architectures. The interaction of monomeric and polymeric N-acetyl-D-glucosamine (GlcNAc) with WGA, that normally binds chitinoligosaccharides on cell surfaces, was investigated with nanomechanical force measurements using AFM. These measurements aimed at determining the effect of ligand length and binding site clustering (multivalent binding) on binding strength between the protein and the carbohydrate ligand. Here, the GlcNAc ligand was presented at the surface of a planar self-assembled monolayer (SAM) of neoglycoconjugates and in a polymeric form as chitin beads. In adsorption measurements using the quartz crystal microbalance (QCM) it was shown that alkanethiols adsorb rapidly to a gold surface, covering it completely within a few minutes as an SAM. In AFM force measurements, GlcNAc-specific binding events were detected with a WGA-modified probe on a GlcNAcneoglycoconjugate SAM at bond rupture forces of 47 ± 15 pN. When this experiment was repeated on a polymeric substrate, manyfold higher forces were detected. This indicated a high increase of affinity with additional binding subsites which were able to interact with the chitinous ligand. SPR measurements confirmed that WGA has higher affinity towards the immobilized GlcNAcneoglycoconjugate SAM than towards the soluble free monosaccharide providing evidence of a significant affinity increase as a result of binding site cooperativity. Furthermore, two different SAM formats have been tested for their suitability for studying protein-carbohydrate interactions. Here, non-specific adhesion was identified as a critical factor that was mainly related to the hydrophobic parts of the neoglycoconjugates and could be attenuated by the introduction of a tetraethylene glycol spacer into the neoglycoconjugate. The binding measurements on neoglycoconjugate SAMs demonstrated that this type of carbohydrate presentation is a useful reference for interactions on naturally occurring two-dimensional glycan arrays and demonstrated that the minimization of non-specific adhesion of proteins is often required in order to obtain meaningful binding data. In addition to WGA-carbohydrate interactions this thesis also deals with the carbohydrate binding cleft of the glycoside hydrolase Trichoderma harzianum chitinase Chit42, which in the wild-type form, solubilises polymeric crystalline chitin (composed of [beta]-4 linked GlcNAc units). Nine different catalytically inactive Chit42 variants were created, carrying amino acid alterations along the binding site cleft (at sugar-binding subsites -4 to +2). These Chit42 variants were characterised with regard to their affinity towards chitinous and non-chitinous oligosaccharides by SPR. As a result, hydrogen bonding between subsites -2/-3 and particularly stacking interactions by tryptophanes at subsites -3 and +2 were seen to be very important for the carbohydrate binding. The exchange of the corresponding amino acids did not cause a change of binding specificity, although the selective binding of GlcN[beta]-4(GlcNAc)4 could be improved by providing a counter charge through an amino acid substitution at subsite -3, replacing threonine with aspartic acid. In addition the introduction of glutamine and particularly an asparagine residue at this position appeared to broaden the substrate preference towards Gal[beta]-4(GlcNAc)4, and the site was thereby implicated as a binding groove hot spot for creating binding proteins, or hydrolytic enzymes with novel substrate specificity towards e.g. structurally related and medically significant oligosaccharides. Analysis of the Chit42 variants with modified active sites showed how the binding selectivity and affinity of neolectins can be engineered and may thereby function as a model for further neolectins and glycoside hydrolases with new ligand and substrate specificities, respectively.
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.
Engineering Protein Carbohydrate Interactions
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Author :
language : en
Publisher:
Release Date : 2012
Engineering Protein Carbohydrate Interactions written by 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.
Handbook Of Carbohydrate Engineering
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Author : Kevin J. Yarema
language : en
Publisher: CRC Press
Release Date : 2005-05-27
Handbook Of Carbohydrate Engineering written by Kevin J. Yarema and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-05-27 with Medical categories.
The Handbook of Carbohydrate Engineering provides an overview of the basic science, theory, methods, and applications of this broad, interdisciplinary field. The text provides background information along with practical knowledge for current and future research methodologies used in the characterization and synthesis of various carbohydrates. This
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.
Glycoscience
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Author : Bertram O. Fraser-Reid
language : en
Publisher: Springer Science & Business Media
Release Date : 2008-04-14
Glycoscience written by Bertram O. Fraser-Reid 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 2008-04-14 with Science categories.
As a reflection of the quantum leap that has been made in the study of glycostructures, the first edition of this book has been completely revised and updated. The editors give up-to-date information on glycostructures, their chemistry and chemical biology in the form of a completely comprehensive survey. Glycostructures play highly diverse and crucial roles in a myriad of organisms and important systems in biology, physiology, medicine, bioengineering and technology. Only in recent years have the tools been developed to partly understand the highly complex functions and the chemistry behind them. While many facts remain undiscovered, this MRW has been contributed to by a large number of the world’s leading researchers in the field.
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.
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.
Interactions Between Proteins And Biomacromolecules Tools And Applications
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Author : Qunye Zhang
language : en
Publisher: Frontiers Media SA
Release Date : 2021-08-02
Interactions Between Proteins And Biomacromolecules Tools And Applications written by Qunye Zhang 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 2021-08-02 with Science categories.