tertiary structure prediction of adenosine a3 receptor
DESCRIPTION
Tertiary Structure Prediction of Adenosine A3 Receptor. Presented by Lindsay Riley Goddard Group, Caltech SoCalBSI , CalStateLA 20 August 2009. - PowerPoint PPT PresentationTRANSCRIPT
MPNNSTALSLANVTYITMEIFIGLCAIVGNVLVICVVKLNPSLQTTTFYFIV
SLALADIAVGVLVMPLAIVVSLGITIHFYSCLFMTCLLLIFTHASIMSLLAIA
VDRYLRVKLTVRYKRVTTHRRIWLALGLCWLVSFLVGLTPMFGWNMKL
TSEYHRNVTFLSCQFVSVMRMDYMVYFSFLTWIFIPLVVMCAIYLDIFYII
RNKLSLNLSNSKETGAFYGREFKTAKSLFLVLFLFALSWLPLSIINCIIYFN
GEVPQLVLYMGILLSHANSMMNPIVYAYKIKKFKETYLLILKACVVCHPS
DSLDTSIEKNSEPNNSTALSLANVTYITMEIFIGLCAIVGNVLVICVVKLN
PSLQTTTFYFIVSLALADIAVGVLVMPLAIVVSLGITIHFYSCLFMTCLLLI
FTHASIMSLLAIAVDRYLRVKLTVRYKRVTTHRRIWLALGLCWLVSFLVG
LTPMFGWNMKLTSEYHRNVTFLSCQFVSVMRMDYMVYFSFLTWIFIPL
VVMCAIYLDIFYIIRNKLSLNLSNSKETGAFYGREFKTAKSLFLVLFLFAL
SWLPLSIINCIIYFNGEVPQLVLYMGILLSHANSMMNPIVYAYKIKKFKET
YLLILKAC VVCHPSDSLDTSIEKNSE
Tertiary Structure Prediction of Adenosine A3 Receptor
Presented by Lindsay RileyGoddard Group, Caltech
SoCalBSI, CalStateLA20 August 2009
Significance of Adenosine A3 Receptor
Good target for Important to know structure for drug specification
BACKGROUND• G-protein-coupled receptor (GPCR)
7 transmembrane helices exterior interior
Involved in many cell signaling pathways drug therapy
http://www.biomedcentral.com/content/figures/1471-2105-8-177-1-l.jpg
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
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
THERAPEUTIC IMPLICATIONS• A3 ligand (IB-MECA) in Phase II clinical trials for treatment
of rheumatoid arthritis and metastatic colorectal tumors
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• Human A2a-adenosine receptor
SOLUTION• Predict structure using all-atom based
first principles methods
GEnSeMBLEHomology Helix1. Align and homologize2. Optimize helices3. BiHelix4. CombiHelix5. Analyze top
structures6. SuperBiHelix
Final Structure
1. Hydrophobicity profile2. OptHelix3. Align to template4. BiHelix5. Combihelix6. Analyze top structures7. SuperBiHelix
Final Structure
MPNNSTALSLANVTYITMEIFIGLCAIVGNVLVICVVKLNPSLQ
TTTFYFIVSLALADIAVGVLVMPLAIVVSLGITIHFYSCLFMTCLL
LIFTHASIMSLLAIAVDRYLRVKLTVRYKRVTTHRRIWLALGLC
WLVSFLVGLTPMFGWNMKLTSEYHRNVTFLSCQFVSVMRMD
YMVYFSFLTWIFIPLVVMCAIYLDIFYIIRNKLSLNLSNSKETGAF
YGREFKTAKSLFLVLFLFALSWLPLSIINCIIYFNGEVPQLVLYMG
ILLSHANSMMNPIVYAYKIKKFKETYLLILKAC
VVCHPSDSLDTSIEKNSE
GEnSeMBLE
1. Align and homologize
2. Optimize helices3. BiHelix4. CombiHelix5. Analyze top structures6. SuperBiHelix
Homology Helix
CLUSTAL 2.0.11 multiple sequence alignment
sp|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 394
sp|P33765|AA3R_HUMAN ------------------sp|P29274|AA2AR_HUMAN PEPPGLDDPLAQDGAGVS 412
Alignment of A3 sequence to A2a template
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MPNNSTALSLANVTYITMEIFIGLCAIVGNVLVICVVKLNPSLQ
TTTFYFIVSLALADIAVGVLVMPLAIVVSLGITIHFYSCLFMTCLL
LIFTHASIMSLLAIAVDRYLRVKLTVRYKRVTTHRRIWLALGLC
WLVSFLVGLTPMFGWNMKLTSEYHRNVTFLSCQFVSVMRMD
YMVYFSFLTWIFIPLVVMCAIYLDIFYIIRNKLSLNLSNSKETGAF
YGREFKTAKSLFLVLFLFALSWLPLSIINCIIYFNGEVPQLVLYMG
ILLSHANSMMNPIVYAYKIKKFKETYLLILKAC
VVCHPSDSLDTSIEKNSE
GEnSeMBLE
1. Hydrophobicity profile
2. OptHelix3. Align to template4. BiHelix5. CombiHelix6. Analyze top
structures7. SuperBiHelix
GEnSeMBLE
GEnSeMBLE
Homology Helix
Secondary Structure Prediction
70 80 90 100 110 120 | | | | | |
SEQ: VGVLVMPLAIVVSLGITIHFYSCLFMTCLLLIFTHASIMSLLAIAVDRYLRVKLTVRYKR PORTER: HHHccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccPSIPRED: HHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEcccccccEOLD_RAW: HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------------OLD_CAP: HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------------
190 200 210 220 230 240 | | | | | | SEQ: SFLTWIFIPLVVMCAIYLDIFYIIRNKLSLNLSNSKETGAFYGREFKTAKSLFLVLFLFA PORTER: HHHHHcHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHPSIPRED: HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHOLD_RAW: HHHHHHHHHHHHHHHHHHHH--------------------------------HHHHHHHHOLD_CAP: HHHHHHHHHHHHHHHHHHHHHHHHH------------------------HHHHHHHHHHH
TM2 & TM3
TM6
OptHelix
* Proline and Glycine residues displayed
Alignment of A3 helices to A2a template
GEnSeMBLEHomology Helix1. Align and homologize2. Optimize helices3. BiHelix4. CombiHelix5. Analyze top
structures6. SuperBiHelix
Final Structure
1. Hydrophobicity profile2. OptHelix3. Align to template4. BiHelix5. Combihelix6. Analyze top structures7. SuperBiHelix
Final Structure
BiHelix: energy minimization of helix pairs
CombiHelix Output
Homology HelixH1 H2 H3 H4 H5 H6 H7 Energy0 0 0 15 0 0 0 2930 0 0 0 0 0 0 3000 0 15 15 0 15 0 3100 0 0 0 0 30 345 3120 0 0 15 0 15 0 3150 0 15 345 0 15 0 3240 0 0 15 0 30 0 3250 0 0 0 0 15 0 3250 0 0 330 0 15 0 3380 0 0 345 0 30 345 339
Dock Ligands
DarwinDock Matching
GEnSeMBLEHomology Helix
Final Structure Final Structure
or
Dock Ligands
DarwinDock Matching
GEnSeMBLEHomology Helix
Final Structure Final Structure
or
DarwinDock: adenosine
adenosine
Important residues involved in agonist binding (based on mutation experiments)
6 ASP
7 HIS3 HIS
7 SER
Matching: adenosine
Also working on…• analyzing A3 adenosine docking• analyzing A3 SuperBiHelix output• A2a structure and ligand docking• A1 structure and ligand docking• A2b structure and ligand docking• docking agonists: ClIBMECA & NECA• docking antagonists: MRS1292 &
NMeClIBMECA
To do list…• add loops to final structure• simulate lipid bilayer
Acknowledgements
Funding
Goddard Group at California Institute of Technology
Dr. Soo-Kyung KimDr. Ravinder AbrolProfessor William A. Goddard IIIBiogroup
SoCalBSI at California State University, Los Angeles
Dr. Jamil MomandDr. Sandy SharpDr. Nancy Warter-PerezDr. Wendie JohnstonRonnie ChengThe lovely interns
NIH, Pfizer, PharmSelex