[PDF] Analysis Of Noncovalent And Covalent Protein Ligand Complexes By Electrospray Ionisation Mass Spectrometry eBook

Author : Christoph A. Schalley
Publisher : John Wiley & Sons
Page : 593 pages
File Size : 16,26 MB
Release : 2009-09-08
Category : Science
ISBN : 0470131152

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Details the many benefits of applying mass spectrometry to supramolecular chemistry Except as a method for the most basic measurements, mass spectrometry (MS) has long been considered incompatible with supramolecular chemistry. Yet, with today's methods, the disconnect between these two fields is not warranted. Mass Spectrometry and Gas-Phase Chemistry of Non-Covalent Complexes provides a convincing look at how modern MS techniques offer supramolecular chemists a powerful investigatory toolset. Bringing the two fields together in an interdisciplinary manner, this reference details the many different topics associated with the study of non-covalent complexes in the gas phase. The text begins with brief introductions to supramolecular chemistry and such relevant mass spectrometric methods as ionization techniques, analyzers, and tandem MS experiments. The coverage continues with: How the analyte's transition into the gas phase changes covalent bonding How limitations and pitfalls in analytical methods may produce data misinterpretations Artificial supramolecular aggregates and their examination Biomolecules, their complexes, and their examination After the general remarks making up the first section of the book, the following sections describe specific experimental procedures and are illustrated with numerous examples and short tutorials. Detailed citations end each chapter. Mass spectrometrists, supramolecular chemists, students in these fields, and interested readers from other disciplines involving the study of non-covalent bonds will all value Mass Spectrometry and Gas-Phase Chemistry of Non-Covalent Complexes as an innovative and practical resource.

Author : Yixuan Zhang
Publisher :
Page : 123 pages
File Size : 30,77 MB
Release : 2013
Category : Carbohydrates
ISBN :

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This thesis describes the development and application of electrospray ionization mass spectrometry (ESI-MS) based techniques to investigate protein-carbohydrate interactions in vitro. A catch-and-release electrospray ionization mass spectrometry (CaR-ESI-MS) assay was developed for the identification of specific interactions between water-soluble multisubunit proteins and glycosphingolipids (GSL). The assay is of high sensitivity and specificity, and demonstrates the potential for discovering biologically relevant protein-GSL interactions. Collision-induced dissociation (CID) experiments and molecular dynamic simulations were performed to investigate the dissociation pathways of multisubunit protein-ligand complexes in the gas phase. The observation of multiple dissociation pathways suggests that collisional activation of multisubunit protein-ligand complexes in the gas phase is likely to induce significant changes to the nature of the protein-ligand interactions.

Author : Andrey Dyachenko
Publisher :
Page : 163 pages
File Size : 40,20 MB
Release : 2013
Category :
ISBN :

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In the present thesis we have explored different factors that impede accurate quantitative description of non-covalent protein-protein and protein-ligand interactions and design of new potent and specific binders from the scratch. Firstly, we addressed the role of solvent in the mechanism of non-covalent interactions. Secondly, we tackled the question about the intrinsic conformational flexibility of the protein molecules and the part it plays in weak interactions between proteins. In the first part of the thesis we studied the interactions of vascular endothelial growth factor (VEGF) protein with five cyclic peptides in solution and gas phase. The results showed that affinities of five ligands to VEGF in solution and gas phase are ranked in inversed order. That is, the that has the highest affinity in solution (as shown by chemical shift perturbation NMR and isothermal titration calorimetry) forms the weakest complex with VEGF in gas phase, and vice versa. We compared gas-phase and solution binding affinities of of five peptides and made qualitative conclusions about the role of the solvent in protein-ligand interactions. In order to obtain more quantitative information about the gas-phase behavior of non-covalent complexes we have developed a combined experimental/theoretical approach to study the energetics of collisional activation of the ion prior to dissociation. We applied developed strategy to model CID in traveling wave ion guide (TWIG) collision cell. We validated the model on the CID of leu-enkephalin peptide and then applied developed strategy to five non-covalent protein-peptide complexes and found activation energies of their dissociation reactions. Next we applied ESI native MS to study the allosteric interactions between the molecular chaperonin GroEL and ATP. The obtained data allowed to construct a scheme of conformational transition of GroEL upon binding of ATP and distinguish between two different cooperativity models, providing strong arguments in favor of Monod-Wyman-Changeux (MWC) model. Finally, be studied the backbone dynamics of VEGF with a combination of NMR relaxation and all-atom force-field based normal mode analysis (NMA). We showed that combination of experimental and computational approach allows to identify flexible zones with higher level of confidence. We also found out that residues, that are involved VEGF-receptor interactions, reside in or close to the flexible zones, suggesting the critical role conformational plasticity plays in the non-covalent protein-protein interactions.

Author : Mowei Zhou
Publisher :
Page : 242 pages
File Size : 18,74 MB
Release : 2013
Category :
ISBN :

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Abstract: There is a growing interest in application of mass spectrometry as a high throughput technique for quaternary structure studies of protein complexes. One way to study protein complexes by mass spectrometry is to specifically label peptides segments that carry critical structural information, and after protein digestion subsequently identify the labeled peptides using liquid chromatography - mass spectrometry. A chemical crosslinker forms covalent bonds at specific amino acid sidechains that are in proximity in the protein structure. This approach is used to probe the binding interface of LexA/RecA proteins in Escherichia coli (Chapter 3). In contrast, intact noncovalent protein complexes can be directly transferred into the gas phase, while retaining memory of their solution structures. Accurate molecular weight measurement by mass spectrometry can be used for stoichiometry determination of protein-protein and protein-ligand systems, as manifested by the two examples of stoichiometry determination of differently treated adiponectin oligomers (Chapter 4), and the silver binding properties of the N-terminal region of a bacterial protein CusB (Chapter 5).