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Tertiary Structure Prediction of Adenosine A3 Receptor

Tertiary Structure Prediction of Adenosine A3 Receptor. Presented by Lindsay Riley Goddard Group, Caltech SoCalBSI , CalStateLA 20 August 2009.

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Tertiary Structure Prediction of Adenosine A3 Receptor

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  1. Tertiary Structure Prediction of Adenosine A3 Receptor Presented by Lindsay Riley Goddard Group, Caltech SoCalBSI, CalStateLA 20 August 2009 MPNNSTALSLANVTYITMEIFIGLCAIVGNVLVICVVKLNPSLQTTTFYFIVSLALADIAVGVLVMPLAIVVSLGITIHFYSCLFMTCLLLIFTHASIMSLLAIAVDRYLRVKLTVRYKRVTTHRRIWLALGLCWLVSFLVGLTPMFGWNMKLTSEYHRNVTFLSCQFVSVMRMDYMVYFSFLTWIFIPLVVMCAIYLDIFYIIRNKLSLNLSNSKETGAFYGREFKTAKSLFLVLFLFALSWLPLSIINCIIYFNGEVPQLVLYMGILLSHANSMMNPIVYAYKIKKFKETYLLILKACVVCHPSDSLDTSIEKNSEPNNSTALSLANVTYITMEIFIGLCAIVGNVLVICVVKLNPSLQTTTFYFIVSLALADIAVGVLVMPLAIVVSLGITIHFYSCLFMTCLLLIFTHASIMSLLAIAVDRYLRVKLTVRYKRVTTHRRIWLALGLCWLVSFLVGLTPMFGWNMKLTSEYHRNVTFLSCQFVSVMRMDYMVYFSFLTWIFIPLVVMCAIYLDIFYIIRNKLSLNLSNSKETGAFYGREFKTAKSLFLVLFLFALSWLPLSIINCIIYFNGEVPQLVLYMGILLSHANSMMNPIVYAYKIKKFKETYLLILKAC VVCHPSDSLDTSIEKNSE

  2. Significance of Adenosine A3 Receptor • BACKGROUND • G-protein-coupled receptor (GPCR) • 7 transmembranehelices • exterior  interior •  Involved in many cell signaling pathways drug therapy • Good target for •  Important to know structure • for drug specification http://www.biomedcentral.com/content/figures/1471-2105-8-177-1-l.jpg

  3. Significance of Adenosine A3 Receptor • FUNCTION • Prevents restriction of blood flow in brain and heart • Anti-inflammatory, anti-cancer effects • Protection of spinal cord and bone marrow • THERAPEUTIC IMPLICATIONS • A3 ligand(IB-MECA) in Phase II clinical trials for treatment of • rheumatoid arthritis and metastatic colorectal tumors Kim, S. , Jacobson, K. “Three-Dimensional Quantitative Structure – Activity Relationship of Nucleosides Acting at the A3 Adenosine Receptor: Analysis of Binding and Relative Efficacy.” J. Chem. Inf. Model. 2007, 47, 1225-1233

  4. HINDRANCES • Difficult to perform X-ray crystallography on • transmembrane proteins • Only 2 / 800 human GPCR structures • determined via X-ray crystallography: • Bovine rhodopsin • Squid rhodopsin • Turkey β1-adrenergic receptor • Human β2-adrenergic receptor • HumanA2a-adenosine receptor

  5. SOLUTION • Predict structure using all-atom based first • principles methods GEnSeMBLE Homology Helix Hydrophobicity profile OptHelix Align to template BiHelix Combihelix Analyze top structures SuperBiHelix Final Structure Align and homologize Optimize helices BiHelix CombiHelix Analyze top structures SuperBiHelix Final Structure

  6. MPNNSTALSLANVTYITMEIFIGLCAIVGNVLVICVVKLNPSLQTTTFYFIVSLALADIAVGVLVMPLAIVVSLGITIHFYSCLFMTCLLLIFTHASIMSLLAIAVDRYLRVKLTVRYKRVTTHRRIWLALGLCWLVSFLVGLTPMFGWNMKLTSEYHRNVTFLSCQFVSVMRMDYMVYFSFLTWIFIPLVVMCAIYLDIFYIIRNKLSLNLSNSKETGAFYGREFKTAKSLFLVLFLFALSWLPLSIINCIIYFNGEVPQLVLYMGILLSHANSMMNPIVYAYKIKKFKETYLLILKAC VVCHPSDSLDTSIEKNSE Homology Helix GEnSeMBLE Align and homologize Optimize helices BiHelix CombiHelix Analyze top structures SuperBiHelix

  7. CLUSTAL 2.0.11 multiple sequence alignmentsp|P33765|AA3R_HUMAN MPNNSTALSLANVTYITMEIFIGLCAIVGNVLVICVVKLNPSLQTTTFYF 50sp|P29274|AA2AR_HUMAN MP------IMGSSVYITVELAIAVLAILGNVLVCWAVWLNSNLQNVTNYF 44 ** :.. .***:*: *.: **:***** .* **..**..* **sp|P33765|AA3R_HUMAN IVSLALADIAVGVLVMPLAIVVSLGITIHFYSCLFMTCLLLIFTHASIMS 100sp|P29274|AA2AR_HUMAN VVSLAAADIAVGVLAIPFAITISTGFCAACHGCLFIACFVLVLTQSSIFS 94 :**** ********.:*:**.:* *: :.***::*::*::*::**:*sp|P33765|AA3R_HUMAN LLAIAVDRYLRVKLTVRYKRVTTHRRIWLALGLCWLVSFLVGLTPMFGWN 150sp|P29274|AA2AR_HUMAN LLAIAIDRYIAIRIPLRYNGLVTGTRAKGIIAICWVLSFAIGLTPMLGWN 144 *****:***: :::.:**: :.* * :.:**::** :*****:***sp|P33765|AA3R_HUMAN ---MKLTSEYHRN---VTFLSCQFVSVMRMDYMVYFSFLTWIFIPLVVMC 194sp|P29274|AA2AR_HUMAN NCGQPKEGKNHSQGCGEGQVACLFEDVVPMNYMVYFNFFACVLVPLLLML 194 .: * : ::* * .*: *:*****.*:: :::**::* sp|P33765|AA3R_HUMAN AIYLDIFYIIRNKLSLNLSN---SKETGAFYGREFKTAKSLFLVLFLFAL 241sp|P29274|AA2AR_HUMAN GVYLRIFLAARRQLKQMESQPLPGERARSTLQKEVHAAKSLAIIVGLFAL 244 .:** ** *.:*. *: .:.: : :*.::**** ::: ****sp|P33765|AA3R_HUMAN SWLPLSIINCIIYFN---GEVPQLVLYMGILLSHANSMMNPIVYAYKIKK 288sp|P29274|AA2AR_HUMAN CWLPLHIINCFTFFCPDCSHAPLWLMYLAIVLSHTNSVVNPFIYAYRIRE 294 .**** ****: :* ...* ::*:.*:***:**::**::***:*::sp|P33765|AA3R_HUMAN FKETYLLILKACVV-----------------CHPSDSLDTSIEKNSE--- 318sp|P29274|AA2AR_HUMAN FRQTFRKIIRSHVLRQQEPFKAAGTSARVLAAHGSDGEQVSLRLNGHPPG 344 *::*: *::: *: .* **. :.*:. *.. sp|P33765|AA3R_HUMAN --------------------------------------------------sp|P29274|AA2AR_HUMAN VWANGSAPHPERRPNGYALGLVSGGSAQESQGNTGLPDVELLSHELKGVC 394sp|P33765|AA3R_HUMAN ------------------sp|P29274|AA2AR_HUMAN PEPPGLDDPLAQDGAGVS 412

  8. Alignment of A3 sequence to A2a template Top View Side View

  9. MPNNSTALSLANVTYITMEIFIGLCAIVGNVLVICVVKLNPSLQTTTFYFIVSLALADIAVGVLVMPLAIVVSLGITIHFYSCLFMTCLLLIFTHASIMSLLAIAVDRYLRVKLTVRYKRVTTHRRIWLALGLCWLVSFLVGLTPMFGWNMKLTSEYHRNVTFLSCQFVSVMRMDYMVYFSFLTWIFIPLVVMCAIYLDIFYIIRNKLSLNLSNSKETGAFYGREFKTAKSLFLVLFLFALSWLPLSIINCIIYFNGEVPQLVLYMGILLSHANSMMNPIVYAYKIKKFKETYLLILKAC VVCHPSDSLDTSIEKNSE GEnSeMBLE GEnSeMBLE • Hydrophobicityprofile • OptHelix • Align to template • BiHelix • CombiHelix • Analyze top structures • SuperBiHelix

  10. GEnSeMBLE Homology Helix

  11. Secondary Structure Prediction TM2 & TM3 70 80 90 100 110 120 | | | | | | SEQ: VGVLVMPLAIVVSLGITIHFYSCLFMTCLLLIFTHASIMSLLAIAVDRYLRVKLTVRYKR PORTER: HHHccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccc PSIPRED: HHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEcccccccE OLD_RAW: HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------- OLD_CAP: HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------- TM6 190 200 210 220 230 240 | | | | | | SEQ: SFLTWIFIPLVVMCAIYLDIFYIIRNKLSLNLSNSKETGAFYGREFKTAKSLFLVLFLFA PORTER: HHHHHcHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHH PSIPRED: HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHH OLD_RAW: HHHHHHHHHHHHHHHHHHHH--------------------------------HHHHHHHH OLD_CAP: HHHHHHHHHHHHHHHHHHHHHHHHH------------------------HHHHHHHHHHH

  12. OptHelix * Proline and Glycine residues displayed

  13. Alignment of A3 helices to A2a template

  14. GEnSeMBLE Homology Helix Hydrophobicity profile OptHelix Align to template BiHelix Combihelix Analyze top structures SuperBiHelix Final Structure Align and homologize Optimize helices BiHelix CombiHelix Analyze top structures SuperBiHelix Final Structure

  15. BiHelix: energy minimization of helix pairs

  16. CombiHelix Output

  17. or Dock Ligands DarwinDock Matching GEnSeMBLE Homology Helix Final Structure Final Structure

  18. or Dock Ligands DarwinDock Matching GEnSeMBLE Homology Helix Final Structure Final Structure

  19. DarwinDock: adenosine Important residues involved in agonist binding (based on mutation experiments) 6 ASP 3 HIS 7 HIS 7 SER adenosine

  20. Matching: adenosine

  21. Also working on… • analyzing A3 adenosine docking • analyzing A3 SuperBiHelix output • A2a structure and ligand docking • A1 structure and ligand docking • A2b structure and liganddocking • docking agonists: ClIBMECA & NECA • docking antagonists: MRS1292 & NMeClIBMECA • To do list… • add loops to final structure • simulate lipid bilayer

  22. Acknowledgements Goddard Group at California Institute of Technology Dr. Soo-Kyung Kim Dr. RavinderAbrol Professor William A. Goddard III Biogroup SoCalBSI at California State University, Los Angeles Dr. JamilMomand Dr. Sandy Sharp Dr. Nancy Warter-Perez Dr. WendieJohnston Ronnie Cheng The lovely interns Funding NIH, Pfizer, PharmSelex

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