Download or read book Photoaffinity Labeling for Structural Probing Within Protein written by Yasumaru Hatanaka and published by Springer. This book was released on 2017-09-25 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers the most up-to-date photoaffinity labeling method to tackle the key loop module involved in the binding process of a bioactive small molecule to its host protein. The book introduces rational points for preparing powerful photoaffinity probes, keys for the efficient analysis of labeled products, and recent successful applications for protein probing. Regarding drug design, the unique topics of the book are the special consideration of the crosslinking potential of recent probes and their application of important receptor proteins . This book presents emerging technologies of photoaffinity labeling to readers who are working in the fields of proteomics, molecular recognition, and drug discovery and development.

Download or read book Photooxidative Crosslinking and Photoaffinity Labeling of Proteins Using Naphthalene Imides and Diimides written by Stacey Sova and published by . This book was released on 2018 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein structures and interactions are key to understanding their biological function. The current techniques to probe structure have limitations that can be overcome with the use of photoaffinity labeling. Traditional labeling uses benzophenone and diazarine derivatives, which require long irradiation times or photoisomerize into less reactive species, which causes non-specific crosslinking on the target protein. This study used carboxylic-acid functionalized naphthalene diimides as a new type of photoaffinity label. Nonspecific photoaffinity labeling has been achieved with these compounds. The mechanism was probed with steady-state photolysis and transient absorbance spectroscopy. The proposed labeling mechanism of these compounds involves generating a biradical upon irradiation that photodecarboxylates. This biradical can react with proteins via a hydrogen abstraction followed by radical recombination to produce a crosslink between the naphthalimide and amino acid in the protein. These naphthalene diimide compounds were then functionalized to interact with the active site of alcohol dehydrogenase.

Download or read book Activity Based Protein Profiling written by Stephan A. Sieber and published by Springer Science & Business Media. This book was released on 2012-02-21 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt: ABPP Methodology: Introduction and Overview, by Matthew B. Nodwell und Stephan A. Sieber Activity-Based Protein Profiling for Natural Product Target Discovery, by Joanna Krysiak und Rolf Breinbauer Photoaffinity Labeling in Activity-Based Protein Profiling, by Paul P. Geurink, Laurette M. Prely, Gijs A. van der Marel, Rainer Bischoff und Herman S. Overkleeft Application of Activity-Based Protein Profiling to the Study of Microbial Pathogenesis, by William P. Heal und Edward W. Tate Functional Analysis of Protein Targets by Metabolomic Approaches, by Yun-Gon Kim und Alan Saghatelian

Download or read book Probing Phosphoinositide and Isoprenoid Binding Proteins by Photoaffinity Labeling written by Li Feng and published by . This book was released on 1999 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Activity Based Protein Profiling written by Benjamin F. Cravatt and published by Springer. This book was released on 2019-01-25 with total page 417 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a collection of contemporary perspectives on using activity-based protein profiling (ABPP) for biological discoveries in protein science, microbiology, and immunology. A common theme throughout is the special utility of ABPP to interrogate protein function and small-molecule interactions on a global scale in native biological systems. Each chapter showcases distinct advantages of ABPP applied to diverse protein classes and biological systems. As such, the book offers readers valuable insights into the basic principles of ABPP technology and how to apply this approach to biological questions ranging from the study of post-translational modifications to targeting bacterial effectors in host-pathogen interactions.

Download or read book Target Discovery and Validation written by Alleyn T. Plowright and published by John Wiley & Sons. This book was released on 2020-02-18 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: The modern drug developers? guide for making informed choices among the diverse target identification methods Target Discovery and Validation: Methods and Strategies for Drug Discovery offers a hands-on review of the modern technologies for drug target identification and validation. With contributions from noted industry and academic experts, the book addresses the most recent chemical, biological, and computational methods. Additionally, the book highlights techologies that are applicable to ?difficult? targets and drugs directed at multiple targets, including chemoproteomics, activity-based protein profiling, pathway mapping, genome-wide association studies, and array-based profiling. Throughout, the authors highlight a range of diverse approaches, and target validation studies reveal how these methods can support academic and drug discovery scientists in their target discovery and validation research. This resource: -Offers a guide to identifying and validating targets, a key enabling technology without which no new drug development is possible -Presents the information needed for choosing the appropriate assay method from the ever-growing range of available options -Provides practical examples from recent drug development projects, e. g. in kinase inhibitor profiling Written for medicinal chemists, pharmaceutical professionals, biochemists, biotechnology professionals, and pharmaceutical chemists, Target Discovery and Validation explores the current methods for the identification and validation of drug targets in one comrpehensive volume. It also includes numerous practical examples.

Download or read book Development of Photoaffinity Labelling Technologies for Small Molecule Drug Discovery a Case Study Targeting Bromodomains written by David Fallon and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of this work was to investigate how the photoaffinity labelling (PAL) approach can positively impact and complement current methods of small molecule target-based drug discovery. For this broad application, an operationally simple and versatile synthetic protocol was required. An Ugi multicomponent reaction protocol for the expedient one-step synthesis of PAL probes was developed. The reaction couples an amine affinity function (compound of interest) with commonly used photoreactive groups and a variety of handle functionalities. Each component can be independently changed, providing access to a wide variety of PAL probes. For proof-of-concept studies, a series of pan-BET selective bromodomain PAL probes were obtained by parallel synthesis. Subsequent studies on the effect of different photoreactive groups, linker lengths, and irradiation wavelengths on photocrosslinking efficiency provided valuable insights into photoaffinity probe design. The observed trends in labelling were interpreted with additional consideration of the protein topology surrounding the active site, guided by crystallography and LC-MSMS studies. Optimal probes were progressed to MS-based proteomics to capture the BET family of proteins from live cells and reveal their potential on- and off-target profiles. From the optimisation studies above, PAL probes with high labelling efficiencies of recombinant BRD4 BD1 and BD2 protein were identified. The most promising probe was used to develop a novel biochemical PAL displacement assay, where the affinities of other competitor compounds to both BD1 and BD2 could be determined in the same experiment. This dual-domain PAL displacement assay represents the exciting and unexplored potential for PAL probes in biochemical assays. Additionally, preliminary investigations into the impact of PAL on fragment-based biochemical screening were performed. A series of photoreactive BET-targeting fragments were prepared and their labelling efficiencies to recombinant BRD4 BD1 were found to be concentration-dependent and correlated well with the affinity of the fragment. Overall, this work demonstrates new and exciting ways that the PAL approach can assist small-molecule target-based drug discovery, such as photoreactive fragment hit finding and novel biochemical PAL screening methods with recombinant protein. Additionally, the synthetic aspect of PAL-based chemoproteomics is made more accessible through the described one-step Ugi protocol and the information obtained regarding optimal probe design.

Download or read book Advances in Heterocyclic Chemistry written by and published by Academic Press. This book was released on 2019-03-19 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Heterocyclic Chemistry, Volume 129 is the definitive series in the field—one of great importance to organic chemists, polymer chemists and many biological scientists. Because biology and organic chemistry increasingly intersect, the associated nomenclature also is being used more frequently in explanations. Written by established authorities in the field from around the world, this comprehensive, updated release includes chapters on Metal-Catalyzed Direct Arylation of 1,2-Azoles, The Literature of Heterocyclic Chemistry, Part XVII, 2017, Pyrrolo-, Imidazoquinolines and Pyrroloquinazolines with a Bridgehead Nitrogen, Synthesis and Reactions of Arsole, Stibole, and Bismole, Advances in Synthesis and Chemistry of Aziridines, and more. Considered the definitive serial in the field of heterocyclic chemistry Serves as the go-to reference for organic chemists, polymer chemists and many biological scientists Provides the latest comprehensive reviews written by established authorities in the field Combines descriptive synthetic chemistry and mechanistic insight to enhance understanding of how chemistry drives the preparation and useful properties of heterocyclic compounds

Download or read book Photochemical Probes in Biochemistry written by Peter E. Nielsen and published by Springer. This book was released on 1989-04-30 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proceedings of the NATO Advanced Research Workshop, Copenhagen, Denmark, August 14-19, 1988

Download or read book Photochemical Probes in Biochemistry written by Peter E. Nielsen and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: The concept of using photochemical probes in the study of biological systems was developed by Westheimer who published the first photoaffinity labeling experiments more than twenty years ago (J.Bio1. Chem. 237, (1962) 3006). Since then the concept has been used successfully in various areas of biochemistry and recently several new interesting and exciting aspects of the concept have been developed. It is the general opinion by scientists in the "field" that the full potential of photochemical probes in biochemical studies has far from been exploited yet. This is mostly due to the interdisciplinary character of the concept involving photochemistry, synthetic chemistry as well as biochemistry/molecular biology. The perspective of the NATO advanced workshop on "Photochemical Probes in Biochemistry", held in Holte (Copenhagen) Denmark 14-19, August, 1988, was several fold. The workshop was to give an account of the "state of the art" of using photochemical probes in biochemistry as well as to bring together specialists in photochemistry, syn thetic chemistry and molecular biology in order to analyze advantages as well as the inherent problems and pitfalls of the concept and provide suggestions and guidelines for fu ture research. Furthermore, it is the hope of the editor that the present publication which gives an account of the lectures presented at the workshop, will provide an introduction to scientists who are not familiar with photochemical probes, but to whom these could help answer central and pertinent questions.

Download or read book Design Synthesis and Application of New Heterobifunctional Photoaffinity Probe for the Studies of Protein protein Interactions Involved in the Actin linked Calcium regulated System of Muscle Contraction microform written by Pele Choi-sing Chong and published by National Library of Canada. This book was released on 1983 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the rabbit skeletal muscle system previous studies suggested that sulfhydryl (SH) groups might be in the proximity of the sites of interaction of the following protein complexes: troponin C - troponin I, troponin-tropomyosin, actin-actin, actin-tropomyosin, and actin-myosin. Therefore a bifunctional cross-linking reagent that could be specifically attached to these SH groups would be invaluable for the identification of the proteins in the vicinity of the labelled SH group and enable the determination at the molecular level of amino acid residues involved in the site of interactions. This information would aid us in understanding how the Ca 2+ -induced conformational changes in troponin C can be transmitted from troponin C to all other components of the regulatory complex. For this reason we have designed and synthesized a new heterobifunctional photoaffinity probe, N-(4-azidobenzoylglycyl)-S-(2-thiopyridyl)cysteine (AGTC) from cysteine via a coupling of the N-hydroxysuccinimide ester of 4-azidobenzoylglycine to S-(2-thiopyridyl)cysteine. The chemical stability and reactivity of AGTC have been characterized. AGTC is readily dissolved in an aqueous buffer at pH 7.5 and is stable at room temperature ranging in pH from 3 to 9. The disulfide bridge moiety of AGTC is stable to the conditions of photolysis used to activate the arylazido group for crosslinking. AGTC is readily incorporated (90%-100%) within 2 hr into such proteins as rabbit skeletal troponin C, tropomyosin, and actin through disulfide bridge formation. The degree of incorporation of AGTC into proteins can be monitored by spectrophotometric determination of the release of pyridine-2-thionine at 343 nm. AGTC has a cross-linking distance of 14 A. The aryl azide moiety is inert until photolysis, permitting the removal of the excess reagents from the modified proteins and control experiments to ensure the correct protein-protein interaction. Also the aryl azide is nonspecific, in that it does not require the presence of a particular reactive functional group at the binding site for cross-linking to occur. Demonstration of the general utility of AGTC to study protein-protein interactions has been carried out in three different protein complexes: the interactions involving troponin C and troponin I, tropomyosin and troponin, and the subunits of troponin complex. Troponin C was labelled specifically at cysteine 98 with radioactive AGTC to form AGC-TnC which was used to form a binary complex with S-carboxamidometnylated troponin I (CM-Tnl) in benign media. Photolysis of CM-TnI-AGC-TnC complex resulted in the formation of a 1:1 covalently cross-linked complex in 30% yield. The radiolabelled CM-TnI-AGC was isolated from the cross-linked complex by reduction of the disulfide bridge between AGC and TnC using DEAE-Sephadex chromatography in the presence of 8M urea and 1 mM EGTA. These results indicated that CM-Tnl was within 14 A of cysteine 98 of TnC. AGC-TM (AGTC was attached to cysteine 190 of TM via disulfide bond formation) was used to determine which component of rabbit skeletal troponin (CM-Tn) was in close proximity to cysteine 190 of TM. Photolysis of the CM-Tn-AGC-TM complex in the presence of Ca 2+ resulted in formation of a 1:1 covalently cross-linked complex in 7% yield. The radiolabelled troponin (CM-Tn-AGC) was isolated by hydroxylapatite chromatography. CM-Tn-AGC was further separated into its individual components on DEAE-Sephadex chromatography. Radioactive measurements and SDS-urea gel electrophoresis indicated that only troponin T (TnT) was radiolabelled. A limited (15 min) chymotryptic digest of CM-Tn-AGC resulted in the isolation of T2-AGC (residues 159-259 of TnT). More extended proteolysis of CM-Tn-AGC allowed the isolation of T2'-AGC (residues 159-227 of TnT). When the CM-Tn-AGC-TM complex was photolyzed in the absence of Ca 2 + compared to the presence of Ca 2+ there was 1.7 fold increase in the cross-linking yield. This result suggested that there was a Ca 2+ -sensitive conformational change in the binding region of TnT around cysteine 190 . A tightening of the complex about cysteine 190 in the absence of Ca 2+ could explain the decrease in reaction of the arylnitrene with solvent. Nevertheless, region 159-227 of TnT is in the vicinity of cysteine 190 of TM in both the presence and absence of Ca 2 + . The topographical relationship of the SH groups of rabbit skeletal troponin has been investigated to provide information for the specific labelling of the SH groups with AGTC for the purpose of monitoring the Ca 2+ -induced conformational changes in the troponin complex. The approach involved the reaction of 14 C-iodoacetamide with SH groups in native troponin and various binary complexes of troponin components in the presence and absence of Ca 2+ . The SH groups involved in interaction sites and those exposed were identified by peptide mapping using two dimensional paper electrophoresis and autoradiography. In the presence and absence of Ca 2+ cysteine 133 of Tnl in native troponin was exposed while cysteines 48 and 64 of Tnl and cysteine 98 of TnC were inaccessible to modification. Differential labelling of the Tnl-TnT complex showed that cysteine 133 of Tnl was again exposed and cysteines 48 and 64 were inaccessible. 14 C-S-carboxamidomethylation of the Tnl-TnC complex showed that all three cysteine residues of Tnl (48, 64, and 133) were accessible to modification in the absence of Ca 2+ while cysteine 48 and 133 were only partially accessible in the presence of Ca 2+ . Cysteine 98 of TnC was inaccessible to modification in both the presence and absence of Ca 2+ . These studies indicated that in native troponin, TnT was solely responsible for the inaccessibility of cysteines 48 and 64 of Tnl in absence of Ca 2+ , and 64 of Tnl in the presence of Ca 2+ . The inaccessibility of cysteine 48 of Tnl in native troponin in the presence of Ca 2+ may be due to a combined effect of conformational changes in Tnl induced by TnC upon Ca 2+ binding and the interaction with TnT. These studies have provided the information for selective and specific attachment of AGTC into Tnl for the study of Ca 2+ -induced conformational changes in the troponin complex itself or troponin in the thin filament. AGTC was attached to cysteines 48 and 64 of skeletal Tnl to determine which component of troponin was in close proximity to these cysteines. The reconstituted troponin complex (AGTC labelled CM-Tnl, TnT, and TnC) was photolyzed and separated using DEAE-Sephadex chromatography in the absence of reducing agent. Radioactive measurements indicated that 12% of the cross-linker reacted with solvent and 88% with proteins. The percentage radiolabel found in Tnl, Tnl-TnT, and Tnl-TnC complexes was 35%, 55%, and 10%, respectively. These results have indicated that both TnT and TnC are in the vicinity of one or both cysteines 48 and 64 of Tnl. Of the total radiolabel found in TnT, 33% and 23% was located in two CNBr fragments, CB4 (residues 176-230) and CB2 (residues 71-151). The most likely interpretation of the cross-linking results is that one of the interaction sites between Tnl and TnT is an ionic interaction involving the region around cysteines 48 and 64 of Tnl (residues 28-82) with the CB5 region of TnT (residues 135-185). Finally, combining the present photochemical cross-linking results and all other studies, a working model of the regulatory complex (TM-Tn) was constructed to aid us in future experimental design to expand our knowledge on how the Ca 2+ -induced conformational changes in TnC can be transmitted from TnC to all other components of the regulatory complex.

Download or read book Photoaffinity Labeling Studies on a Promoter of Dendritic Spine Formation written by Kevin Sibucao and published by . This book was released on 2017 with total page 126 pages. Available in PDF, EPUB and Kindle. Book excerpt: The small molecule BTA-EG4 has been shown to be a promoter of dendritic spine formation. The mechanism behind this phenomenon, however, is not well understood. The work in this dissertation is motivated by this gap in knowledge. The first part of this dissertation focuses on photoaffinity labeling studies to identify the cellular targets of BTA-EG4. Chapter 1 provides a summary of Alzheimer's disease, the rational design of BTA-EG4, and methods to determine targets of small molecules. In Chapter 2, the synthesis of a BTA-EG4-based photoaffinity labeling probe and photodegradation studies are presented. Kinetic studies demonstrate that the probe photolyzes rapidly under UV light. In Chapter 3, photoaffinity labeling studies and subsequent protein identification experiments are reported. Competition experiments with the photoaffinity labeling probe and BTA-EG4 demonstrate that the probe labels a 55-kDa protein specifically. Tandem mass spectrometry revealed that the 55-kDa protein is the actin binding protein fascin 1. The second part of this dissertation focuses on the major protein identified from photoaffinity labeling studies, fascin 1. Chapter 4 provides a brief survey of the structure and function of fascin 1. In Chapter 5, characterizations of the interaction between BTA-EG4 and fascin 1 are reported. Isothermal titration calorimetry confirms the physical binding between fascin 1 and BTA-EG6, a BTA-EG4 analog. Slow speed sedimentation assays reveal that BTA-EG4 does not affect the actin-bundling activity of fascin 1. However, GST pull-down experiments show that BTA-EG4 inhibits the binding of fascin 1 with the GTPase Rab35. In addition, this work demonstrates that BTA-EG4 may be mechanistically distinct from the known fascin inhibitor G2.

Download or read book Design and Synthesis of Photoaffinity Labeling Probes Based on Clinically Approved CFTR Modulators written by Christopher Michael Hamilton and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cystic fibrosis (CF) is caused by loss-of-function mutations to the cystic fibrosis transmembrane conductance regulator protein (CFTR). The last decade has seen the development and clinical implementation of small-molecule therapies, termed CFTR modulators, which restore mutant CFTR activity. The CFTR modulators were discovered using functional assays, irrespective of any information of putative binding sites on CFTR. Characterizing the binding sites of the approved CFTR modulators will aid in structure-based drug design of new more effective CFTR treatments. To determine the binding sites of the clinically approved CFTR modulators, photoaffinity labeling (PAL) analogues were designed, synthesized, and characterized. One of the probes based on the structure of ivacaftor has been successfully used in photolabeling studies to identify two binding sites on CFTR. Photolabeling studies utilizing probes based on the structures of lumacaftor and elexacaftor are underway.

Download or read book Cumulated Index Medicus written by and published by . This book was released on 1999 with total page 1846 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Mass Spectrometry Based Chemical Proteomics written by W. Andy Tao and published by John Wiley & Sons. This book was released on 2019-07-10 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: PROVIDES STRATEGIES AND CONCEPTS FOR UNDERSTANDING CHEMICAL PROTEOMICS, AND ANALYZING PROTEIN FUNCTIONS, MODIFICATIONS, AND INTERACTIONS—EMPHASIZING MASS SPECTROMETRY THROUGHOUT Covering mass spectrometry for chemical proteomics, this book helps readers understand analytical strategies behind protein functions, their modifications and interactions, and applications in drug discovery. It provides a basic overview and presents concepts in chemical proteomics through three angles: Strategies, Technical Advances, and Applications. Chapters cover those many technical advances and applications in drug discovery, from target identification to validation and potential treatments. The first section of Mass Spectrometry-Based Chemical Proteomics starts by reviewing basic methods and recent advances in mass spectrometry for proteomics, including shotgun proteomics, quantitative proteomics, and data analyses. The next section covers a variety of techniques and strategies coupling chemical probes to MS-based proteomics to provide functional insights into the proteome. In the last section, it focuses on using chemical strategies to study protein post-translational modifications and high-order structures. Summarizes chemical proteomics, up-to-date concepts, analysis, and target validation Covers fundamentals and strategies, including the profiling of enzyme activities and protein-drug interactions Explains technical advances in the field and describes on shotgun proteomics, quantitative proteomics, and corresponding methods of software and database usage for proteomics Includes a wide variety of applications in drug discovery, from kinase inhibitors and intracellular drug targets to the chemoproteomics analysis of natural products Addresses an important tool in small molecule drug discovery, appealing to both academia and the pharmaceutical industry Mass Spectrometry-Based Chemical Proteomics is an excellent source of information for readers in both academia and industry in a variety of fields, including pharmaceutical sciences, drug discovery, molecular biology, bioinformatics, and analytical sciences.

Download or read book Chemical Probes in Biology written by Manfred P. Schneider and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 403 pages. Available in PDF, EPUB and Kindle. Book excerpt: This NATO Advanced Study Institute (co-sponsored by FEBS and INTAS) under the title "Chemical Probes in Biology" was designed to summarize and disseminate recent expert knowledge regarding a deeper understanding ofbiological phenomena on a molecular level. Such scientific activities -frequently termed Bio-organic Chemistry or Chemical Biology are constituting a highly interdisciplinary branch of chemistry beyond the traditional ways in which chemists and biologists have been working in the past. Thus, on this occasion we were bringing together senior experts from the disciplines of Chemistry and Biology in order to amalgamate their diverse yet basically common interests in this area. Ultimate goal was - next to an exchange of information between the two scientific cultures - the communication ofexciting possibilities in interdisciplinary research to the young scientists present. The meeting was held in the Anargyros and Korgialenios School on the Island ofSpeteses, Greece from 18-30 August 2002. The ASI was attended by a total of 91 scholars from 23 different countries. A group of 27 speakers presented a series of 34 highly stimulating, informative and educational lectures covering a broad range of topics relevant to the general theme ofthis meeting: Science at the InteifaceofChemistry, Biology and Medicine. The lectures were complemented by a total of 89 posters presented by the young scholars and a series of short lectures derived thereof This was clearly one ofthe highlites of the meeting creating a lively atmosphere of interaction and intellectual creativity - typical phenomena for the whole meeting.

Download or read book Design and Synthesis of a Bifunctional Photoaffinity Probe for Labeling Target Protein in H1N1 Virus written by 黃瑋 and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: