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E-raamat: Kinomics - Approaches and Applications: Approaches and Applications [Wiley Online]

Edited by (University of Saskatchewan, Canada), Edited by
  • Formaat: 368 pages
  • Ilmumisaeg: 23-Sep-2015
  • Kirjastus: Blackwell Verlag GmbH
  • ISBN-10: 3527683038
  • ISBN-13: 9783527683031
Teised raamatud teemal:
  • Wiley Online
  • Hind: 185,03 €*
  • * hind, mis tagab piiramatu üheaegsete kasutajate arvuga ligipääsu piiramatuks ajaks
Kinomics - Approaches and Applications: Approaches and ApplicationsSuurem pilt
  • Formaat: 368 pages
  • Ilmumisaeg: 23-Sep-2015
  • Kirjastus: Blackwell Verlag GmbH
  • ISBN-10: 3527683038
  • ISBN-13: 9783527683031
Teised raamatud teemal:
Wiley Online e-raamatudRohkem infot Wiley Online kohta
Raamatu kodulehekülg: https://onlinelibrary.wiley.com/doi/book/10.1002/9783527683031
Authored by the world's leading kinase experts, this is a comprehensive introduction to current knowledge and practice within this emerging field.
Following an overview of the major players and pathways that define the kinome, the major part of this work is devoted to current strategies of kinome investigation and manipulation. As such, kinase engineering, peptide substrate engineering, co-substrate design and kinase inhibitor design are discussed in detail, and their potential applications in kinome analysis and kinome-based pharmacotherapy are shown.
The result is a toolbox for every kinase researcher: By addressing and comparing current approaches to the study of kinase action, both novice and established researchers will benefit from the practical knowledge contained in this invaluable reference.
List of Contributors
xiii
Preface xix
Part I Protein Kinases Cell Signaling
1(136)
1 Global Approaches to Understanding Protein Kinase Functions
3(44)
Jennifer L. Gorman
James R. Woodgett
1.1 A Brief History of the Structure of the Human Kinome
3(7)
1.1.1 AGC Kinases
3(2)
1.1.2 The CaMK Family
5(1)
1.1.3 CMGC Family Kinases
5(2)
1.1.4 STE Family Kinases
7(1)
1.1.5 Tyrosine Kinases
7(1)
1.1.6 Casein Kinases
8(1)
1.1.7 Tyrosine Kinase-Like Family
9(1)
1.1.8 RGC Kinases
9(1)
1.1.9 Atypical/Other Protein Kinases
9(1)
1.2 Why Study Protein Kinases -- Their Roles in Disease
10(6)
1.2.1 Neurodegenerative Disease
10(3)
1.2.2 Hallmarks of Cancer
13(3)
1.3 Methodology for Assessment of Protein Kinase Functions
16(12)
1.3.1 Mass Spectrometry
16(2)
1.3.2 Fluorescence Resonance Energy Transfer
18(2)
1.3.3 Assessment of Kinase Functions in vitro: Genetic and Chemical
20(2)
1.3.4 Functional Assessment of Kinase Function in vivo: Animal Models
22(3)
1.3.5 CRISPR/Cas9 Genomic Recombineering
25(3)
1.4 Final Thoughts
28(19)
Acknowledgments
29(1)
References
29(18)
2 "Genuine" Casein Kinase (Fam20C): The Mother of the Phosphosecretome
47(16)
Giorgio Cozza
Vincent S. Tagliabracci
Jack E. Dixon
Lorenzo A. Pinna
2.1 Introduction
47(1)
2.2 Early Detection of the pS-x-E Motif in Secreted Phosphoproteins
48(2)
2.3 CK1 and CK2 are Not Genuine Casein Kinases
50(1)
2.4 Polo-Like Kinases: Newcomers in the Club of False "Casein Kinases"
51(1)
2.5 Characterization of an Orphan Enzyme: The Spectacular Performance of a Peptide Substrate
51(2)
2.6 Catalytic Activity of Fam20C: Mechanistic Aspects
53(1)
2.7 A Kinase in Need of Control
54(3)
2.7.1 Constitutively Active or Inactive?
54(1)
2.7.2 A Potential Mediator of Sphingosine Signaling
55(1)
2.7.3 Fam20c as a Novel Regulator of Blood Phosphate Homeostasis
56(1)
2.7.4 Does it Make Sense to Develop Fam20C Inhibitors?
56(1)
2.8 Outlook
57(6)
Funding
58(1)
References
58(5)
3 Chemical Biology of Protein Kinases
63(22)
David Mann
3.1 The Basis of Chemical Genetics
63(2)
3.2 Protein Kinase Chemical Genetics
65(3)
3.3 Applications for AS Kinases
68(9)
3.3.1 Substrate Identification: General Phosphoproteomics
69(1)
3.3.2 Substrate Identification: Refinements through the Use of AS Kinases
70(3)
3.3.3 Substrate Identification in Action: What Have We Learned?
73(2)
3.3.4 Use of Specific Inhibitors for AS Kinases
75(2)
3.4 Current Challenges
77(3)
3.5 Conclusions
80(5)
Acknowledgments
81(1)
References
81(4)
4 Protein Kinases and Caspases: Bidirectional Interactions in Apoptosis
85(30)
Stephanie A. Zukowski
David W. Litchfield
4.1 Introduction
85(1)
4.2 Apoptosis: Caspase-Dependent Pathways
86(2)
4.2.1 Extrinsic Apoptosis
86(1)
4.2.2 Caspase-Dependent Intrinsic Apoptosis
87(1)
4.3 Functional Crosstalk between Protein Kinases and Caspases
88(11)
4.3.1 Direct Phosphorylation of Caspases by Protein Kinases
89(1)
4.3.1.1 Initiator Caspases
89(2)
4.3.1.2 Executioner Caspases
91(1)
4.3.2 Cleavage of Caspase Substrates is Positively and Negatively Regulated by Protein Kinase Phosphorylation
91(3)
4.3.3 Caspase-Mediated Degradation of Kinases and Apoptotic Progression
94(1)
4.3.3.1 Rho-Associated Coiled-Coil-Containing Protein 1 (ROCK1)
94(2)
4.3.3.2 p21-Activated Protein Kinase 2 (PAK2)
96(1)
4.3.3.3 Focal Adhesion Kinase (FAK)
97(1)
4.3.3.4 Protein Kinase Akt
97(1)
4.3.3.5 Protein Kinase Cδ (PKC5)
97(2)
4.4 Strategies to Investigate Global Crosstalk between Protein Kinases and Caspases
99(4)
4.4.1 Computational Approaches and Bioinformatics: Investigating Overlap between Protein Kinase Consensus Sites and Caspase Recognition Motifs
99(2)
4.4.2 Proteomics-Based Strategies to Investigate Crosstalk within the Phosphoproteome and the Caspase Degradome
101(2)
4.4.3 Reporters to Monitor the Spatial and Temporal Dynamics of Phosphorylation and Caspase Cleavage in Living Cells
103(1)
4.5 Implications and Future Prospects
103(12)
References
104(11)
5 The Kinomics of Malaria
115(22)
Mathieu Brochet
Andrew B. Tobin
Oliver Billker
Christian Doerig
5.1 Introduction
115(2)
5.1.1 Malaria Parasites: Highly Divergent Eukaryotes
115(1)
5.1.2 Posttranslational Modifications of Proteins: An Essential Multiplier of Proteome Complexity
116(1)
5.2 The Plasmodium Kinome: Salient Features
117(3)
5.3 Reverse Genetics of the Plasmodium Kinome
120(3)
5.4 Lessons from Phosphoproteomics
123(4)
5.4.1 Phosphorylation Cascades
124(1)
5.4.2 Evidence for Tyrosine Phosphorylation Plasmodium
124(3)
5.5 Host Cell Kinomics in Malaria Infection
127(1)
5.6 Targeting Protein Kinases in Antimalarial Drug Discovery
128(2)
5.6.1 Targeting the Parasite Kinome for Curative and Transmission-Blocking Intervention
128(1)
5.6.2 Targeting Host Kinases?
129(1)
5.7 Concluding Remarks
130(7)
References
130(7)
Part II ATP Co-substrate Design
137(56)
6 ATP Analogs in Protein Kinase Research
139(30)
Thilani M. Anthony
Pavithra M. Dedigama-Arachchige
D. Maheeka Embogama
Todd R. Faner
Ahmed E. Fouda
Mary Kay H. Pflum
6.1 Base-Modified ATP Analogs
140(8)
6.1.1 C2, C6, and C8-Modified ATP Analogs
141(1)
6.1.2 N6-Modified ATP Analogs
141(2)
6.1.2.1 Gatekeeper as-Kinase Mutants
143(1)
6.1.2.2 Multiply Mutated as-Kinases
144(1)
6.1.3 Pyrazolopyrimidine ATP Analogs
145(1)
6.1.4 Triazole and Imidazole ATP Analogs
146(1)
6.1.5 Applications of as-Kinases and Base-Modified ATP Analogs
147(1)
6.2 Sugar-Modified ATP Analogs
148(1)
6.3 α- and β-Phosphate-Modified ATP Analogs
149(3)
6.3.1 AMP-PCP ISO
6.3.2 AMP-PNP
151(1)
6.3.3 AMP-CPP
151(1)
6.4 γ-Phosphate-Modified ATP Analogs
152(9)
6.4.1 ATPγS
153(2)
6.4.2 ATP-Biotin
155(2)
6.4.3 ATP-Fluorophore Analogs
157(1)
6.4.4 ATP-Ferrocene
158(1)
6.4.5 ATP-Arylazide and ATP-Benzophenone
158(1)
6.4.6 γ-Alkenyl-, γ-Alkynyl-, γ-Azido-ATP
159(1)
6.4.7 Bifunctional C8-Azido- and γ-Arylazido-ATP
160(1)
6.4.8 ATP-Acyl-Biotin
160(1)
6.5 Conclusions
161(8)
References
163(6)
7 Electrochemical Detection of Protein Kinase-Catalyzed Phosphorylations
169(24)
Sanela Martic
Soha Ahmadi
Zhe She
Heinz-Bernhard Kraatz
7.1 Introduction
169(18)
7.1.1 Label-Free Detection of Phosphorylation
169(1)
7.1.1.1 Gold NPs
169(4)
7.1.1.2 Silver Nanoparticles (AgNPs)
173(1)
7.1.1.3 Solution-Based Redox Probes
173(2)
7.1.2 Labeled Detection of Phosphorylation
175(1)
7.1.2.1 Ferrocene -- ATP Cosubstrate
175(2)
7.1.2.2 Probing Protein Kinase Binding Pocket
177(4)
7.1.2.3 Probing Phosphoprotein Binding
181(1)
7.1.2.4 Probing Phosphoprotein Conformational Change
182(1)
7.1.2.5 Detection of Protein Kinase Inhibitors
183(4)
7.1.2.6 Utility of Fc--ATP Beyond Electrochemistry
187(1)
7.2 Conclusions
187(6)
References
190(3)
Part III New Methodologies for Kinomics
193(88)
8 Phos-tag Technology for Kinomics
195(16)
Emiko Kinoshita-Kikuta
Eiji Kinoshita
Tohru Koike
8.1 Introduction
195(1)
8.2 Kinomics and Phosphoproteomics
196(1)
8.3 Phos-tag Technology
196(1)
8.4 Highly Sensitive Detection of Phosphopeptides and Phosphoproteins by the Phos-tag Biotin Method
197(4)
8.4.1 Outline
197(1)
8.4.2 Application of Phos-tag Biotin in Peptide Microarrays
197(3)
8.4.3 Application of Phos-tag Biotin in Western Blotting
200(1)
8.5 Protein Kinase Assay with Phos-tag Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis
201(7)
8.5.1 Outline
201(1)
8.5.2 Quantitative Analysis of Abl Tyrosine Kinase Activity
202(2)
8.5.3 Simultaneous Detection of the Activation/Inactivation of Extracellular Signal-Regulated Kinases
204(2)
8.5.4 Differential Analysis of the Phosphorylation Statuses of Cellular Proteins in Combination with Two-Dimensional Difference Gel Electrophoresis
206(2)
8.6 Conclusion
208(3)
References
208(3)
9 Development of Species- and Process-Specific Peptide Kinome Arrays with Priority Application to Investigations of Infectious Disease
211(22)
Ryan Arsenault
Brett Trost
Anthony Kusalik
Scott Napper
9.1 Phosphorylation-Mediated Signal Transduction
211(2)
9.1.1 Kinome versus Phosphoproteome Analysis
212(1)
9.2 Peptide Arrays for Kinome Analysis
213(5)
9.2.1 Species-Specific Peptide Arrays for Kinome Analysis
214(3)
9.2.2 Analysis of Data from Kinome Microarrays
217(1)
9.3 Infectious Disease
218(10)
9.3.1 Human Infectious Agents
220(1)
9.3.1.1 Monkey Pox
220(1)
9.3.1.2 Prion Disease
221(1)
9.3.2 Livestock Pathogens
222(1)
9.3.2.1 Cattle
222(3)
9.3.3 Application of Arrays to Samples of Greater Biological Complexity
225(1)
9.3.3.1 Kinome Profiling of M AP-Infected Calf Intestinal Tissues
226(1)
9.3.3.2 Poultry
226(1)
9.3.3.3 Honeybees and Colony Collapse Disorder (CCD)
227(1)
9.4 Conclusions
228(5)
References
229(4)
10 New Approaches to Understanding Bacterial Histidine Kinase Activity and Inhibition
233(22)
Kaelyn E. Wilke
Erin E. Carlson
10.1 Introduction to Two-Component System Signaling
233(2)
10.2 Focus on Bacterial HKs
235(1)
10.3 Bacterial HK Activity
235(7)
10.3.1 Significance of Understanding HK Activity
235(1)
10.3.1.1 Detection of HK Activity: The Major Obstacle
236(1)
10.3.2 Current Methods for Studying HK (and TCS) Activity
237(1)
10.3.2.1 Genetic Characterization
237(1)
10.3.2.2 Elucidation of TCS Activity at the Protein Level
237(1)
10.3.3 Thiophosphorylation as a Stable Alternative
238(1)
10.3.4 BODIPY-FL-ATPγS Probe
239(1)
10.3.5 Future Challenges and Developments
240(2)
10.4 Bacterial HK Inhibition
242(6)
10.4.1 Significance
242(1)
10.4.2 HK Inhibitors: Past and Present
242(3)
10.4.3 Repurposing Unsuccessful Inhibitors
245(3)
10.4.4 Future HK Inhibitor Developments
248(1)
10.5 Outlook on Tools for the Study and Inhibition of Bacterial HKs
248(7)
References
248(7)
11 Methods for Large-Scale Identification of Protein Kinase Substrate Networks
255(26)
KassaDee J. Ketelaar
Ian S. Wallace
11.1 Introduction
255(1)
11.2 Computational Prediction of Phosphorylation Sites and Protein Kinase -- Substrate Relationships
256(3)
11.3 The Role of Mass Spectrometry in Identifying Posttranslational Modifications
259(5)
11.4 Analog-Sensitive Kinases and Other Specific Inhibitors
264(2)
11.5 Array-Based Methods
266(3)
11.6 Solution-Based Methods
269(2)
11.7 Future Perspectives
271(10)
References
272(9)
Part IV Kinase Inhibition
281(50)
12 Developing Inhibitors of STAT3: Targeting Downstream of the Kinases for Treating Disease
283(18)
Andrew M. Lewis
Daniel P. Ball
Rahul Rana
Ji Sung Park
David Rosa
Ping-Shan Lai
Rodolfo F. Gomez-Biagi
Patrick T. Gunning
12.1 Introduction
283(1)
12.2 STAT3 Structure and Signaling
284(4)
12.2.1 The Role of STAT3 in Cancer
287(1)
12.2.2 STAT3 in Inflammatory Disease
287(1)
12.2.3 STAT3 in Alzheimer's Disease
287(1)
12.3 Methods for Directly Inhibiting STAT3
288(8)
12.3.1 Peptide Inhibitors of STAT3
288(2)
12.3.2 Small-Molecule Inhibitors of STAT3
290(1)
12.3.2.1 Inhibitors of the SH2 Domain
290(4)
12.3.2.2 Natural Product Inhibitors of STAT3
294(2)
12.3.3 Oligonucleotide Decoys of STAT3 Transcription
296(1)
12.4 Conclusion
296(5)
References
298(3)
13 Metal Compounds as Kinase and Phosphatase Inhibitors in Drug Development: The Role of the Metal and Ligands
301(30)
Maria V. Babak
Margaux Airey
Christian G. Hartinger
13.1 Introduction
301(1)
13.2 Kinase Inhibitors: From Ideal 3D Shapes to Kinase Inhibitor-Derived Ligands in Metal Complexes
302(17)
13.2.1 Metal-Based Kinase Inhibitors: Taking Advantage of the Unique 3D Structure of Metal Complexes
302(7)
13.2.2 Non-ATP Binding Site Targeting Kinase Inhibitors
309(2)
13.2.3 Metal-Based Paullones, Indoloquinolines, and Quinoxalinones: Coordination of Bioactive Ligands to Metal Centers
311(6)
13.2.4 Flavonol- and Hydroxypyridone-Derived Complexes: Toward Multimodal Anticancer Agents
317(1)
13.2.5 Exploiting Metal Compounds for Selective Activation and Targeted Release of Kinase Inhibitors
318(1)
13.3 Phosphatases and Metal Compounds
319(4)
13.3.1 Therapeutic Potential of Metal-Based PTP Inhibitors
319(1)
13.3.2 Inorganic Vanadium Salts as Reversible and Irreversible PTP Inhibitors
320(2)
13.3.3 Vanadium Coordination Compounds as Phosphatase Inhibitors
322(1)
13.4 Conclusions
323(8)
Acknowledgments
323(1)
References
324(7)
Index 331
Heinz-Bernhard Kraatz received his Ph.D. from the University of Calgary in 1993. He is a Professor of Chemistry in the Department of Physical and Environmental Sciences and the Department of Chemistry at the University of Toronto. He received a number of awards for his work in biological chemistry. His research is focused on the design surface-supported functional bioconjugates for the study of biological interactions and enzymatic activities including protein kinase catalyzed phosphorylations. His current research interests are in the area of biomaterials and biochemical transformations and analysis.

Sanela Martic is an Assistant Professor of Chemistry at Oakland University, USA, since 2012. Dr. Martic received her Ph.D. degree in 2009 from Queen's University at Kingston, under the supervision of Prof. Suning Wang and co-supervision of Prof. Gang Wu. Her Ph.D. dissertation was on the synthesis of fluorescent nucleosides and their self-assembly. Jointly with her colleague, Heinz-Bernhard Kraatz, she focused on the synthesis of the redox active bioconjugates for protein kinase phosphorylations. Her current research interests include the self-assembly of peptides and proteins towards new biomaterials and bioanalytical methods.
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