Site Specific Protein Labeling

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Site-Specific Protein Labeling

Author : Arnaud Gautier
Publisher : Humana Press
ISBN 13 : 9781493922710
Total Pages : 0 pages
Book Rating : 4.9/5 (227 download)

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Book Synopsis Site-Specific Protein Labeling by : Arnaud Gautier

Download or read book Site-Specific Protein Labeling written by Arnaud Gautier and published by Humana Press. This book was released on 2015-01-06 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume provides in-depth protocols for protein labeling techniques and applications, with an additional focus on general background information on the design and generation of the organic molecules used for the labeling step. Chapters provide protocols for labeling techniques and applications, with an additional focus on general background information on the design and generation of the organic molecules used for the labeling step. 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. Authoritative and practical, Site-Specific Protein Labeling: Methods and Protocols provides a comprehensive overview on the most relevant and established labeling methodologies, and helps researchers to choose the most appropriate labeling method for their biological question.

Site-Specific Protein Labeling

Author : Arnaud Gautier
Publisher : Humana
ISBN 13 : 9781493944170
Total Pages : 0 pages
Book Rating : 4.9/5 (441 download)

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Book Synopsis Site-Specific Protein Labeling by : Arnaud Gautier

Download or read book Site-Specific Protein Labeling written by Arnaud Gautier and published by Humana. This book was released on 2016-09-24 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume provides in-depth protocols for protein labeling techniques and applications, with an additional focus on general background information on the design and generation of the organic molecules used for the labeling step. Chapters provide protocols for labeling techniques and applications, with an additional focus on general background information on the design and generation of the organic molecules used for the labeling step. 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. Authoritative and practical, Site-Specific Protein Labeling: Methods and Protocols provides a comprehensive overview on the most relevant and established labeling methodologies, and helps researchers to choose the most appropriate labeling method for their biological question.

Bioconjugate Techniques

Author : Greg T. Hermanson
Publisher : Academic Press
ISBN 13 : 0080568726
Total Pages : 1233 pages
Book Rating : 4.0/5 (85 download)

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Book Synopsis Bioconjugate Techniques by : Greg T. Hermanson

Download or read book Bioconjugate Techniques written by Greg T. Hermanson and published by Academic Press. This book was released on 2010-07-26 with total page 1233 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioconjugate Techniques, 2nd Edition, is the essential guide to the modification and cross linking of biomolecules for use in research, diagnostics, and therapeutics. It provides highly detailed information on the chemistry, reagent systems, and practical applications for creating labeled or conjugate molecules. It also describes dozens of reactions with details on hundreds of commercially available reagents and the use of these reagents for modifying or cross linking peptides and proteins, sugars and polysaccharides, nucleic acids and oligonucleotides, lipids, and synthetic polymers. A one-stop source for proven methods and protocols for synthesizing bioconjugates in the lab Step-by-step presentation makes the book an ideal source for researchers who are less familiar with the synthesis of bioconjugates More than 600 figures that visually describe the complex reactions associated with the synthesis of bioconjugates Includes entirely new chapters on the latest areas in the field of bioconjugation as follows: Microparticles and nanoparticlesSilane coupling agentsDendrimers and dendronsChemoselective ligationQuantum dotsLanthanide chelatesCyanine dyesDiscrete PEG compoundsBuckyballs,fullerenes, and carbon nanotubesMass tags and isotope tagsBioconjugation in the study of protein interactions

Site-specific Protein Labeling Via Sortase A and Its Applications

Author : Maximilian Wei-Lin Popp
Publisher :
ISBN 13 :
Total Pages : 414 pages
Book Rating : 4.:/5 (745 download)

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Book Synopsis Site-specific Protein Labeling Via Sortase A and Its Applications by : Maximilian Wei-Lin Popp

Download or read book Site-specific Protein Labeling Via Sortase A and Its Applications written by Maximilian Wei-Lin Popp and published by . This book was released on 2011 with total page 414 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technological improvements in the assays and equipment used for biological, biochemical, biophysical and microscopy purposes have ensured that methods for labeling of proteins with reporter molecules remain in high demand. Standard chemical labeling methods using entities that react with amino acid side chains lack the specificity to ensure precise placement of reporter groups. Genetic methods, although specific, lack the versatility afforded by chemical synthesis-most reporters are limited to protein sized domains or peptide tags to which corresponding antibody based reagents are available. The first portion of this work is devoted to the establishment of a system that allows for the site-specific labeling of proteins with a wide variety of chemically synthesized probes. This system exploits sortases, a class of bacterial transpeptidases, that recognize a small five amino acid tag genetically fused to the protein of interest and catalyze the formation of an amide bond between the protein to be studied and the probe. The second part of this thesis describes how this sortase mediated protein labeling method has been implemented to explore enzyme structure and function, improve the physical properties of therapeutic proteins, study glycoproteins important for innate immune responses in living cells (Appendix A), and visualize influenza glycoproteins in living, infected cells. Finally, a protocol is included for this system (Appendix B), which is both versatile and easy to establish in any lab. The synthetic chemistry demanded is minimal, requiring only standard, readily available reagents, making the system amenable to labs equipped for cell and molecular biology experiments.

Noncanonical Amino Acids

Author : Edward A. Lemke
Publisher :
ISBN 13 : 9781493975747
Total Pages : 411 pages
Book Rating : 4.9/5 (757 download)

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Book Synopsis Noncanonical Amino Acids by : Edward A. Lemke

Download or read book Noncanonical Amino Acids written by Edward A. Lemke and published by . This book was released on 2018 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Total Chemical Synthesis of Proteins

Author : Ashraf Brik
Publisher : John Wiley & Sons
ISBN 13 : 3527346600
Total Pages : 626 pages
Book Rating : 4.5/5 (273 download)

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Book Synopsis Total Chemical Synthesis of Proteins by : Ashraf Brik

Download or read book Total Chemical Synthesis of Proteins written by Ashraf Brik and published by John Wiley & Sons. This book was released on 2021-06-08 with total page 626 pages. Available in PDF, EPUB and Kindle. Book excerpt: How to synthesize native and modified proteins in the test tube With contributions from a panel of experts representing a range of disciplines, Total Chemical Synthesis of Proteins presents a carefully curated collection of synthetic approaches and strategies for the total synthesis of native and modified proteins. Comprehensive in scope, this important reference explores the three main chemoselective ligation methods for assembling unprotected peptide segments, including native chemical ligation (NCL). It includes information on synthetic strategies for the complex polypeptides that constitute glycoproteins, sulfoproteins, and membrane proteins, as well as their characterization. In addition, important areas of application for total protein synthesis are detailed, such as protein crystallography, protein engineering, and biomedical research. The authors also discuss the synthetic challenges that remain to be addressed. This unmatched resource: Contains valuable insights from the pioneers in the field of chemical protein synthesis Presents proven synthetic approaches for a range of protein families Explores key applications of precisely controlled protein synthesis, including novel diagnostics and therapeutics Written for organic chemists, biochemists, biotechnologists, and molecular biologists, Total Chemical Synthesis of Proteins provides key knowledge for everyone venturing into the burgeoning field of protein design and synthetic biology.

Rational Design and Directed Evolution of Probe Ligases for Site-specific Protein Labeling and Live-cell Imaging

Author : Katharine Alice White
Publisher :
ISBN 13 :
Total Pages : 241 pages
Book Rating : 4.:/5 (831 download)

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Book Synopsis Rational Design and Directed Evolution of Probe Ligases for Site-specific Protein Labeling and Live-cell Imaging by : Katharine Alice White

Download or read book Rational Design and Directed Evolution of Probe Ligases for Site-specific Protein Labeling and Live-cell Imaging written by Katharine Alice White and published by . This book was released on 2012 with total page 241 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical fluorophores have superior photophysical properties to fluorescent proteins and are much smaller. However, in order to use these probes for live-cell protein imaging, highly specific labeling methods are required. Here, we will describe three efforts to re-engineer the E. coli enzyme, lipoic acid ligase (LplA), to catalyze the ligation of small-molecule probes onto recombinant proteins. We call this collection of methods the PRIME (PRobe Incorporation Mediated by Enzymes) methodologies. First, we describe the structure-guided mutagenesis of LplA and the identification of an LplA variant that can ligate a blue coumarin fluorophore onto a 13-amino acid LplA acceptor peptide (LAP2). This "coumarin ligase" can be used to image cellular proteins with high specificity, sensitivity, and minimal perturbation of the biology of the protein of interest. We also demonstrate how subpopulations of a protein of interest can be labeled using genetically targeted coumarin ligase. Second, we describe our attempts to use yeast display evolution and fluorescence activated cell sorting (FACS) to evolve a truncated LplA enzyme. The original truncated enzyme had severely decreased activity for LplA's natural substrate, lipoic acid. We created a 107 library of LplA mutants and, after four rounds of selection, produced a truncated LplA mutant with lipoylation activity equivalent to full-length LplA. We next sought to evolve activity for an unnatural small molecule probe, but found that this strategy was limited by both increased hydrophobic probe sticking when using the truncated enzyme and some enzyme-dependent nonspecificity. Finally, from a library of 107 LplA mutants, we evolved a full-length LplA capable of ligating an unnatural picolyl azide (pAz) substrate. We demonstrated improved activity of the "pAz ligase" in the secretory pathway and cell surface, two regions where coumarin ligase is inactive. This enzyme can also be used to image cell surface protein-protein interactions as well as label proteins as they are trafficked through the endoplasmic reticulum. These probe ligases will be useful tools for cell biologists interested in studying protein function or protein-protein interactions in the context of living cells.

Chemical Ligation

Author : Luca D. D'Andrea
Publisher : John Wiley & Sons
ISBN 13 : 1119044103
Total Pages : 492 pages
Book Rating : 4.1/5 (19 download)

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Book Synopsis Chemical Ligation by : Luca D. D'Andrea

Download or read book Chemical Ligation written by Luca D. D'Andrea and published by John Wiley & Sons. This book was released on 2017-04-03 with total page 492 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presenting a wide array of information on chemical ligation – one of the more powerful tools for protein and peptide synthesis – this book helps readers understand key methodologies and applications that protein therapeutic synthesis, drug discovery, and molecular imaging. • Moves from fundamental to applied aspects, so that novice readers can follow the entire book and apply these reactions in the lab • Presents a wide array of information on chemical ligation reactions, otherwise scattered across the literature, into one source • Features comprehensive and multidisciplinary coverage that goes from basics to advanced topics • Helps researchers choose the right chemical ligation technique for their needs

Molecular Biology of the Cell

Author :
Publisher :
ISBN 13 : 9780815332183
Total Pages : 0 pages
Book Rating : 4.3/5 (321 download)

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Book Synopsis Molecular Biology of the Cell by :

Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Mass Spectrometry-Based Chemical Proteomics

Author : W. Andy Tao
Publisher : John Wiley & Sons
ISBN 13 : 1118970217
Total Pages : 448 pages
Book Rating : 4.1/5 (189 download)

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Book Synopsis Mass Spectrometry-Based Chemical Proteomics by : W. Andy Tao

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.

PET Chemistry

Author : P.A. Schubiger
Publisher : Springer Science & Business Media
ISBN 13 : 3540495274
Total Pages : 348 pages
Book Rating : 4.5/5 (44 download)

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Book Synopsis PET Chemistry by : P.A. Schubiger

Download or read book PET Chemistry written by P.A. Schubiger and published by Springer Science & Business Media. This book was released on 2007-01-19 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: Personalized medicine employing patient-based tailor-made therapeutic drugs is taking over treatment paradigms in a variety of ?elds in oncology and the central nervous system. The success of such therapies is mainly dependent on ef?cacious therapeutic drugs and a selective imaging probe for identi?cation of potential responders as well as therapy monitoring for an early bene?t assessment. Molecular imaging (MI) is based on the selective and speci?c interaction of a molecular probe with a biological target which is visualized through nuclear, magnetic resonance, near infrared or other methods. Therefore it is the method of choice for patient selection and therapy monitoring as well as for speci?c e- point monitoring in modern drug development. PET (positron emitting tomography), a nuclear medical imaging modality, is ideally suited to produce three-dimensional images of various targets or processes. The rapidly increasing demand for highly selective probes for MI strongly pushes the development of new PET tracers and PET chemistry. ‘PET chemistry’ can be de?ned as the study of positron-emitting compounds regarding their synthesis, structure, composition, reactivity, nuclear properties and processes and their properties in natural and - natural environments. In practice PET chemistry is strongly in?uenced by the unique properties of the radioisotopes used (e. g. , half-life, che- cal reactivity, etc. ) and integrates scienti?c aspects of nuclear-, organic-, inorganic- and biochemistry.

Site-specific Labeling of Cellular Proteins with Unnatural Substrates of Biotin Ligases

Author : Irwin Chen
Publisher :
ISBN 13 :
Total Pages : 616 pages
Book Rating : 4.:/5 (224 download)

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Book Synopsis Site-specific Labeling of Cellular Proteins with Unnatural Substrates of Biotin Ligases by : Irwin Chen

Download or read book Site-specific Labeling of Cellular Proteins with Unnatural Substrates of Biotin Ligases written by Irwin Chen and published by . This book was released on 2007 with total page 616 pages. Available in PDF, EPUB and Kindle. Book excerpt: (cont.) Selections did not enrich for BirA mutants that could catalyze ligation of the azide analog to the AP, but instead highlighted the technical difficulties of our in vitro compartmentalization strategy. We used phage display to engineer a new and orthogonal biotin ligase-acceptor peptide pair for site-specific protein labeling. Yeast biotin ligase (yBL) does not biotinylate the AP, but we discovered a new 15-amino acid substrate for yBL, which we call the yeast acceptor peptide (yAP). The yAP is not biotinylated by BirA, and thus we were able to specifically label AP and yAP fusion proteins co-expressed in the same cell with differently colored quantum dots. We fused the yAP to a variety of recombinant proteins and demonstrated biotinylation by yBL at the N-terminus, C-terminus, and within a flexible internal region. yBL is also very sequence-specific, as endogenous proteins on the surface of yeast and HeLa cells are not biotinylated. This new methodology expands the scope of biotin ligase labeling to two-color imaging and yeastbased applications.

Proximity Labeling

Author : Murat Sunbul
Publisher : Humana
ISBN 13 : 9781493995394
Total Pages : 231 pages
Book Rating : 4.9/5 (953 download)

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Book Synopsis Proximity Labeling by : Murat Sunbul

Download or read book Proximity Labeling written by Murat Sunbul and published by Humana. This book was released on 2020-08-14 with total page 231 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides detailed protocols and untold tips and tricks regarding the most well-known examples of proximity labeling methods, in which the protein of interest is genetically fused to or labeled with an enzyme that can generate short-lived reactive species to non-specifically label molecules within a certain radius of up to twenty nanometers. Beginning with peroxidase-based proximity labeling methods, the volume continues with BioID, proximity labeling methods that describe the proximity ligation assay to detect RNA-DNA interactions, UV cross-linking to demonstrate RNA-protein interactions, and how chemical and enzymatic reactivities can be improved upon DNA-DNA and protein-protein interactions, as well as “proximity-induced self-labeling,” where the radius of labeling is zero. Written for the highly successful Methods in Molecular Biology series, 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. Authoritative and practical, Proximity Labeling: Methods and Protocols serves as an ideal guide for researchers exploring the crucial roles that proximity-driven reactions play in biological systems.

Activity-Based Protein Profiling

Author : Benjamin F. Cravatt
Publisher : Springer
ISBN 13 : 3030111431
Total Pages : 417 pages
Book Rating : 4.0/5 (31 download)

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Book Synopsis Activity-Based Protein Profiling by : Benjamin F. Cravatt

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.

Subcellular Proteomics

Author : Eric Bertrand
Publisher : Springer Science & Business Media
ISBN 13 : 1402059434
Total Pages : 397 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Subcellular Proteomics by : Eric Bertrand

Download or read book Subcellular Proteomics written by Eric Bertrand and published by Springer Science & Business Media. This book was released on 2007-08-29 with total page 397 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume summarizes the new developments that made subcellular proteomics a rapidly expanding area. It examines the different levels of subcellular organization and their specific methodologies. In addition, the book includes coverage of systems biology that deals with the integration of the data derived from these different levels to produce a synthetic description of the cell as a system.

Hydrazide Reactive Peptide Tags for Site-specific Protein Labeling

Author : Glenn Michael Eldridge
Publisher :
ISBN 13 : 9781267075307
Total Pages : 170 pages
Book Rating : 4.0/5 (753 download)

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Book Synopsis Hydrazide Reactive Peptide Tags for Site-specific Protein Labeling by : Glenn Michael Eldridge

Download or read book Hydrazide Reactive Peptide Tags for Site-specific Protein Labeling written by Glenn Michael Eldridge and published by . This book was released on 2011 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: Tools that enable visualization of one protein inside of a living cell allow biologists to study the localization and concentration of that one protein over the course of the life of a cell. Currently, it is not possible to develop a visual probe that specifically targets each and every protein, although this would be ideal for the visualization of multiple proteins. Many general tools have recently been developed for the specific modification of any protein of interest (POI) with a visualization probe; a technology termed site-specific protein labeling (SSPL). However, not all of these methods will be ideal for each and every protein and still new methods for SSPL are needed. One SSPL approach matches bioorthogonal reagents with complementary peptides. Here, hydrazide reactive peptides were selected from M13 phage-displayed libraries using reaction-based selections. After selection from phage displayed peptide libraries, the selected peptides were screened for interaction with hydrazide probes through fusion to T4 lysozyme. A peptide-lysozyme protein fusion demonstrated specific, covalent labeling by the Hydrazide Reactive (HyRe) peptides both in purified form and in crude bacterial cell lysates, sufficient for specific detection of protein fusion over-expression. Spot-synthesis helped identify smaller yet still functional variants of the selected peptides for future solution based experiments. The assay of spot synthesized peptides was iteratively improved by first using an insoluble colorimetric assay, then by synthesizing peptides in duplicate, and finally by using a one step fluorescent probe for hydrazide binding. Chemical synthesis of nine HyRe tag variants and subsequent reaction with two structurally distinct hydrazide probes produced covalent adducts observable by MALDI-TOF MS and MS/MS. Reaction of hydrazide-containing probes with peptides 114, amino acid sequence HKSNHSSKNRE, and MS/MS analysis of the peptide-probe conjugates revealed that a peptide nucleophile near the N-terminus attacks the hydrazide carbonyl. At low pH, an imine-containing product is formed that is capable of reduction with sodium cyanoborohydride. Further optimization of the novel bimolecular reaction described here would be a useful tool for in vivo protein labeling and bioconjugate synthesis.

Protein Prenylation Reactions as Tools for Site-specific Protein Labeling and Identification of Prenylation Substrates

Author : Thi Thanh Uyen Nguyen
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (724 download)

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Book Synopsis Protein Prenylation Reactions as Tools for Site-specific Protein Labeling and Identification of Prenylation Substrates by : Thi Thanh Uyen Nguyen

Download or read book Protein Prenylation Reactions as Tools for Site-specific Protein Labeling and Identification of Prenylation Substrates written by Thi Thanh Uyen Nguyen and published by . This book was released on 2009 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: