Biomathematical and Biomechanical Modeling of the Circulatory and Ventilatory Systems

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2 Biomathematical and Biomechanical Modeling of the Circulatory and Ventilatory Systems Volume 4 For further volumes:

3 Marc Thiriet Intracellular Signaling Mediators in the Circulatory and Ventilatory Systems 123

4 Marc Thiriet Project-team INRIA-UPMC-CNRS REO Laboratoire Jacques-Louis Lions, CNRS UMR 7598 Université Pierre et Marie Curie Place Jussieu 4 Paris Cedex 05 France ISSN ISSN (electronic) ISBN ISBN (ebook) DOI / Springer New York Heidelberg Dordrecht London Library of Congress Control Number: Springer Science+Business Media New York 2013 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Printed on acid-free paper Springer is part of Springer Science+Business Media (

5 1 Introduction Signaling Lipids Lipids in Signal Transduction Phosphoinositides PI(4,5)P PI(3,4,5)P PI(5)P Nuclear Phosphoinositides Phosphoinositide-Dependent Enzymatic Activity Phosphoinositide Influence on Ion Carriers (Non-Lipid) Inositol Phosphates I(1,4,5)P Main Enzymes of the Metabolism of Inositol Polyphosphates Choline-Containing Phospholipids Sphingolipids Ceramide Sphingomyelinases Sphingosine Kinases Sphingosine 1-Phosphate Cardiac Effects of Sphingolipids Sphingolipid Effects on Smooth Muscle Cells Sphingolipid Effects on Endothelial Cells Arachidonic Acid and Eicosanoids Arachidonic Acid Cyclooxygenases Lipoxygenases Cytochrome-P450 Monooxygenases Arachidonic Acid Metabolites in Lungs v

6 vi Prostaglandins Hydroxy- and Epoxyeicosatrienoic Acids Lipases Hormone-Sensitive Lipase Adipose Triglyceride Lipase Hepatic Lipase Endothelial Lipase Lipoprotein Lipase Lipase-H Phospholipases Phospholipases-A Phospholipases-A Superfamily of Phospholipases-A Phospholipase-B Phospholipase-C Phospholipase-D Phosphoinositide Kinases Phosphatidylinositol 3-Kinases Other Phosphoinositide Kinases Phosphoinositide Phosphatases Phosphatase and Tensin Homolog Myotubularins and Myotubularin-Related Phosphoinositide 3-Phosphatases Phosphoinositide 4-Phosphatases Phosphoinositide 5-Phosphatases Other Lipid Phosphatases Phosphotransferases (Ecto)Nucleotide Pyrophosphatase Phosphodiesterases Substrates and Functions of ENPPs Production Regulation ENPP ENPP2 (Autotaxin) ENPP Preamble to Cytoplasmic Protein Kinases Protein Kinase Classification Superfamily 0 (Miscellaneous) AGC Superfamily of Protein Kinases CAMK Superfamily of Protein Kinases CK1 Superfamily of Protein Kinases CMGC Superfamily of Protein Kinases STE Superfamily of Protein Kinases TK Superfamily of Protein Kinases TKL Superfamily of Protein Kinases RGC Superfamily of Protein Kinases

7 vii Superfamily of Atypical Protein Kinases TATA-Binding Factor-Associated Factor Agents of Kinase Activity Alternatively Spliced Variants Intracellular Pseudokinases CASK Pseudokinase GCN2 Pseudokinase ILK Pseudokinase Janus Pseudokinases Pseudokinase Kinase Suppressors of Ras Sterile 20-Related Adaptors Tribbles Pseudokinases TrrAP Pseudokinase Cytoplasmic Protein Tyrosine Kinases Receptor and Cytosolic Protein Tyrosine Kinases Family of Abl Kinases Abl1 Kinase (Abl) Abl2 Kinase (Arg) Abl-Binding Proteins ACK Kinases BrK Kinase (Protein Tyr Kinase-6; FRK Subfamily) CSK Kinase Focal Adhesion Kinases FeS and FeR Kinases (FPS/FES Subfamily) Fyn-Related Kinase Janus Kinases Canonical and Non-Canonical Pathways of JaK Activation Signal Transducers and Activators of Transcription Other Regulation of JaK Activity Janus Kinases in Heart Inhibitors of the JaK STAT Pathway MATK Kinase or CSK Homologous Kinase (CSK Subfamily) SRMS Kinase (FRK Subfamily) Kinases of the SRC Family SRC Family Kinases during Hypoxia BLK Kinase (SRCB Subfamily) BMX Kinase (TEC Family) BTK Kinases (TEC Family) FGR Kinase (SRCA Subfamily) Fyn Kinase (SRCA Subfamily) Hemopoietic Cell Kinase (SRCB Subfamily)

8 viii ITK Kinase (TEC Family) Leukocyte-Specific Cytosolic Kinase (SRCB Subfamily) Lyn Kinase (SRCB Subfamily) Src Kinase TEC Kinase TXK Kinase (TEC Family) Yes Kinase (SRCA Subfamily) From Src to SYK Spleen Tyrosine Kinase Cytoplasmic Protein Serine/Threonine Kinases Superfamily of Ser/Thr Sterile-20-Related Kinases Ste20-like Kinase Germinal Center Kinase Family MAP4Ks of GCK Subfamilies 1 and 4 of the Ste20-like Kinase Superfamily Kinases of GCK Subfamilies 2 and3 MST Kinases STK25 of the GCK Subfamily Other Kinases of the GCK Subfamily Kinases of the GCK Subfamily Kinases of the GCK Subfamily Kinases of the GCK Subfamily Kinases of the GCK Subfamily AGC Superfamily Nuclear DBF2-Related Protein Kinases and Large Tumor Suppressors Phosphoinositide-Dependent Kinase Protein Kinase-A Family Protein Kinase-X Protein Kinase-Y Protein Kinase-B Family Protein Kinase-C Family Protein Kinase-D Family Protein Kinase-G Family CDC42-Binding Protein Kinases G-Protein-Coupled Receptor Kinase Family Microtubule-Associated Ser/Thr Kinase Family P21-Activated Kinase Family RoCK Kinase Family Other Members of the ROCK Family P90 Ribosomal S6 Kinase Family P70 Ribosomal S6 Kinase Family

9 ix Serum- and Glucocorticoid-Regulated Kinase Family Diacylglycerol Receptors and Kinases CAMK Superfamily Calmodulin-Dependent Protein Kinase (CamK) Family Myosin Light-Chain Kinase Family AMP-Activated Protein Kinases AMPK-Related Kinases Checkpoint Kinase Family Death-Associated Protein Kinase Family Death Receptor-Associated Protein-Related Apoptotic Kinase Family PIM Kinase Family Protein kinase-d Family PIKK Superfamily Ataxia Telangiectasia Mutated and ATM and Rad3-Related Kinases DNA-Dependent Protein Kinase Target of Rapamycin CK1 Superfamily Casein Kinase-1 Family Vaccinia-Related Kinase Family Tau Tubulin Kinase Family Family-2 Casein Kinases Catalytic CK2α1andCK2α2Subunits) Regulatory CK2β Subunit CMGC Superfamily Cyclin-Dependent Kinase Family Homeodomain-Interacting Protein Kinase Family TKL Superfamily Integrin-Linked Kinase Interleukin-1 Receptor-Associated Kinase Family LIM Domain-Containing Kinase Subfamily (LISK [LIMK TESK] Family) Testis-Specific Kinase Subfamily (LISK [LIMK TESK] Family) Receptor-Interacting Protein Kinase Family Aurora Kinase Family Aurora Kinase-A Polo-like Kinase Family Polo-like Kinase PLK Polo-like Kinase PLK Polo-like Kinase PLK Polo-like Kinase PLK

10 x 5.12 With-No-K Kinase Family WNK WNK WNK WNK Regulation of Ion Transport in Nephron Other Types of Ser/Thr Kinases Doublecortin-like Kinase Haspin Liver Kinase-B1 (STK11) Never in Mitosis Gene-A-Related Expressed Kinases NEMo-like Kinase PTen-Induced Kinase Protein Kinase-R Slicing Factor Protein Kinase TANK-Binding Kinase Mitogen-Activated Protein Kinase Module Main Features of MAPK Signaling Basic Three-Tiered MAPK Module Double Phosphorylation Cycle MAPK Pathway MAPK Stimuli MAPK Cascade Regulation Auto-Inhibition Scaffold Proteins Transcription Factor Substrates of MAPK Modules Subcellular Compartmentation MAPK Modules in Cell Metabolism Insulin and Glucagon Signaling MAPKs in Adipocytes MAPKs in Metabolic Syndrome Mitogen-Activated Protein Kinase Kinase Kinase Kinases Other Regulators of the MAPK Module Small GTPases of the Ras Hyperfamily Heterotrimeric G Proteins Mitogen-Activated Protein Kinase Kinase Kinases Family of Raf Kinases Moloney Sarcoma Viral Mos Proto- Oncogene Kinase (Mos) Family of Mixed Lineage Kinases Family of MAP/ERK Kinase Kinases (MEKK)

11 xi Family of Mitogen-Activated Protein Kinase Kinase Kinases-5/ Mitogen-Activated Protein Kinase Kinase Kinase-7 (TAK1) Family of Thousand and One Kinases (TAOK) Mitogen-Activated Protein Kinase Kinase Kinase-8 (TPL2) Mitogen-Activated Protein Kinase Kinase Kinase MAP3K Mitogen-Activated Protein Kinase Kinases MAP2K MAP2K MAP2K MAP2K MAP2K MAP2K MAP2K Mitogen-Activated Protein Kinases JNKs and P38MAPKs in Cardiovascular Diseases Family of Extracellular Signal-Regulated Kinases Family of Jun N-Terminal Kinases Family of P38 Mitogen-Activated Protein Kinases Stress-Activated Protein Kinases Kinase Substrates of MAPKs MAPK-Activated Protein Kinases MAPK-Interacting Ser/Thr Kinases Mitogen- and Stress-Activated Protein Kinases Dual-Specificity Protein Kinases Mitogen-Activated Protein Kinase Kinase Glycogen Synthase Kinase Dual-Specificity Tyrosine Phosphorylation-Regulated Kinases DYRK1a DYRK1b DYRK DYRK DYRK Cell Division Cycle-like Kinases CLK CLK CLK CLK

12 xii 7.5 Wee1 Kinase Membrane-Associated Tyr/Thr Protein Kinase Raf Kinase Inhibitory Protein Cytosolic Protein Phosphatases Pseudophosphatases Catalytically Active Protein Phosphatases Cytosolic Protein Serine/Threonine Phosphatases Protein Phosphatase Protein Phosphatase Protein Phosphatase Protein Phosphatase Protein Phosphatase Protein Phosphatase Protein Phosphatase Magnesium-Dependent Protein Phosphatase Cytosolic Protein Tyrosine Phosphatases Protein Tyrosine Phosphatase Regulation by Reversible Oxidation Classical Cytosolic Protein Tyrosine Phosphatases PEST Family Phosphatases in Inflammation and Immunity Dual-Specificity Protein Phosphatases Infraclass-2 Protein Tyrosine Phosphatase Infraclass-3 PTP Cell-Division Cycle-25 Phosphatases Infraclass Aspartate-Based Protein Tyrosine Phosphatases Guanosine Triphosphatases and Their Regulators Heterotrimeric G Proteins (Gαβγ GTPases) Set of Gα Subunits Set of Gβ Subunits Set of Gγ Subunits G Protein and Myogenic Response Regulators of Heterotrimeric G Proteins Nucleoside Diphosphate Kinases Regulators of G-Protein Signaling Gα Guanine Nucleotide-Exchange Factors Activators of G-Protein Signaling GPCR-Interacting Proteins G-Protein-Coupled Receptor Kinases Monomeric (Small) GTPases Superfamily of ARF GTPases CDC42 GTPase (RHO Superfamily)

13 xiii Superfamily of Rab GTPases Rac GTPases Rad GTPase Rag GTPases Ral GTPases Ran GTPases Rap GTPases Ras GTPases RHEB GTPase Superfamily of RHO GTPases (CDC42, Rac, and Rho) Family of RHO GTPases (RhoA, RhoB, and RhoC) Atypical RhoBTB GTPases Classical RhoD GTPase Classical RhoF GTPase Atypical RhoG GTPase Atypical RhoH GTPase Atypical RhoJ GTPase Atypical RhoQ GTPase RhoT GTPase Atypical RhoT1/2 GTPases (Miro-1/2) Atypical RhoU GTPase Atypical RhoV GTPase RGK (Rad Gem/Kir Rem) Family of GTPases RND Family of Atypical GTPases Family of RIN and RIT GTPases Phosphoinositide 3-Kinase Enhancer: GTPase and GAP Regulators of Monomeric Guanosine Triphosphatases Guanine Nucleotide-Exchange Factors GTPase-Activating Proteins Guanine Nucleotide-Dissociation Inhibitors Other Major Types of Signaling Mediators Gaseous Neurotransmitters Carbon Monoxide and Heme Oxygenases Carbon Monoxide Synthesis and its Regulation Vasodilation and Other Effects Carbon Monoxide and Nitric Oxide Nitric Oxide, Nitric Oxide Synthases, Nitrite, and Nitrate Nitric Oxide Synthases Nitric Oxide Production from Nitrite and Nitrate Nitric Oxide and Hypoxic Vasodilation

14 xiv Reduction Oxidation Reaction Products of Nitric Oxide NO Transfer NO Effects Interaction between Nitric Oxide and Hydrogen Sulfide Hydrogen Sulfide Hydrogen Sulfide Production Hydrogen Sulfide Effects Hydrogen Sulfide in Mitochondria NADPH and Dual Oxidases Structure Subtypes Activity NOx ROS Axis Redox Signaling and Reactive Oxygen and Nitrogen Species Signaling by Reactive Oxygen Species Signaling by Reactive Nitrogen Species Hippo Signaling (STK3 STK4 Pathway) Hippo Signaling Components Coregulators Receptors for Activated C-Kinase G-Kinase-Anchoring Protein Scaffolds of Synapses of the Central Nervous System A-Kinase-Anchoring Proteins Annexins Transcription Factors Involved in Stress Responses Nuclear Factor-κB Signaling Module Hypoxia-Inducible Factor Forkhead Box Transcription Factors P53 Family of Transcription Factors Transcription Factor p Signaling Pathways camp Signaling Crosstalk between Calcium and camp Signalings Crosstalk between the ERK and camp Signaling Pathways camp Response Element-Binding Protein and Cofactors Adenylate Cyclases Phosphodiesterases

15 xv 11.2 cgmp Signaling Signaling via Cell Junctions Elastin Laminin Receptor Adhesion Molecules Discoidin Domain Receptors Signaling via Focal Adhesions Signaling via Gap Junctions Interactions between Ion Channels and Small GTPases Calcium Signaling Calcium-Induced Calcium Release Calcium Signaling and Myocyte Contraction Instantaneous and Long-Lasting Responses to Calcium Calcium Signaling Components Types of Calcium Signalings Calcium-Mobilizing Mediators cadpr and NAADP Calcium and Nervous Control of Blood Circulation Calcium Signaling and Immunity Calcium Signaling and Intracellular Transport Calcium Signaling and Cell Fate Oxygen Delivery and Hypoxia Transduction Hypoxia-Inducible Factor Axis Hypoxia-Inducible Factor-Independent Axis VEGF Signaling Insulin Pathway Inflammasome Mechanotransduction Basic Components of Vascular Mechanotransduction Mechanotransduction Signaling Mechanotransduction in Arterial Compartments Conclusion References Notation Rules: Aliases and Symbols List of Currently Used Prefixes and Suffixes List of Aliases Complementary Lists of Notations Index