Construction of an A2aGPCR Model using Homology Comparative Protein Modeling Gabrielle Roberts  Biology Department, Long I...
Introduction  <ul><li>Brief overview of protein structure  </li></ul><ul><li>GPCR  </li></ul><ul><li>New Age of Bioinforma...
PROTEINS  <ul><li>Diverse range of bio molecules which play important structural and functional roles within cells   </li>...
Protein structure   <ul><li>Protein is a polymer made up of amino acid monomers.  </li></ul>The  variable R-group accounts...
 
Protein Structural levels   Primary structure  Secondary structure  Tertiary structure  Quaternary structure  Polypeptide ...
Secondary Structure :  Beta pleated Sheets  <ul><li>Hydrogen bond between N-H and carboxylic group on the backbone of adja...
Parallel  Anti-Parallel
Beta structural motifs <ul><li>Beta hairpin  </li></ul><ul><li>Adjacent strands in anti-parallel arrangement  </li></ul><u...
Secondary Structure : Alpha Helix <ul><li>Hydrogen bond between N-H and carboxylic groups on backbone  </li></ul><ul><li>H...
Tertiary Structure   <ul><li>Interaction of R groups:  </li></ul><ul><li>Hydrophobic : phenylalanine, valine, tryptophan <...
Serum albumin Homo sapiens  Pilin Neisseria gonorrhoeae
Tertiary structural domains <ul><li>Domain is the stable part of the protein  </li></ul><ul><li>Has a particular function:...
GPCR   <ul><li>7 transmembrane domains that bind to molecules such as hormones, neurotransmitters </li></ul><ul><li>Molecu...
New Age of Bioinformatics   <ul><li>Allows scientists to virtually screen possible drug targets to protein.  </li></ul><ul...
<ul><li>PROBLEM   </li></ul><ul><li>Difficult to crystallize GPCR  </li></ul><ul><li>SOLUTION </li></ul><ul><li>Use compar...
OBJECTIVE  <ul><li>To construct a theoretical model of an A2a GPCR using homology modeling </li></ul>
Method  <ul><li>Select protein template :  </li></ul><ul><li>Align target sequence(A2a) with template sequence(A2b). Alter...
Results:   Protein alignment   <ul><li>Protein sequence obtained from NCBI website  </li></ul>A2b is 60% identical to A2a ...
Results:  Homology Modeling   <ul><li>Modeller : computer program that uses altered sequence and A2b PDB file to make a A2...
A2a Theoretical Model vs. A2b Model   Models viewed using Ras win
Future Considerations  <ul><li>To attempt model assessment with molecular docking of known A2a ligand antagonists/ agonist...
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Construction of an A2a GPCR Model using Homology Comparative Protein Modeling

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Experimental procedures such as X-ray diffraction are key in the development of three dimensional structures representing several protein molecules. However, the three dimensional structures of some proteins have yet to be determined. Adenosine G-protein coupled receptor A2a is an example of a protein whose molecular structure does not exist within the protein database. We attempt to find out the three dimensional structure of A2a using the Homology modeling program “Modeller”.

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Construction of an A2a GPCR Model using Homology Comparative Protein Modeling

  1. 1. Construction of an A2aGPCR Model using Homology Comparative Protein Modeling Gabrielle Roberts Biology Department, Long Island University, Brooklyn, NY
  2. 2. Introduction <ul><li>Brief overview of protein structure </li></ul><ul><li>GPCR </li></ul><ul><li>New Age of Bioinformatics </li></ul><ul><li>A2a GPCR Model Prediction </li></ul>
  3. 3. PROTEINS <ul><li>Diverse range of bio molecules which play important structural and functional roles within cells </li></ul>Hair & Nails: Keratin Cytoskeleton: Microtubules, intermediate filaments, microfilaments Muscle Tissues: Actin and Myosin
  4. 4. Protein structure <ul><li>Protein is a polymer made up of amino acid monomers. </li></ul>The variable R-group accounts for the presence of 20 different amino acids
  5. 6. Protein Structural levels Primary structure Secondary structure Tertiary structure Quaternary structure Polypeptide chain Alpha helix or beta sheets Functional protein* Interactions between more than one polypeptide
  6. 7. Secondary Structure : Beta pleated Sheets <ul><li>Hydrogen bond between N-H and carboxylic group on the backbone of adjacent beta strands </li></ul>
  7. 8. Parallel Anti-Parallel
  8. 9. Beta structural motifs <ul><li>Beta hairpin </li></ul><ul><li>Adjacent strands in anti-parallel arrangement </li></ul><ul><li>Connected by 2-5 amino acids </li></ul><ul><li>Greek key motif </li></ul><ul><li>4 anti parallel stands linked by hairpins </li></ul>B-meander motif 2 or more anti parallel strands linked by hair pins Psi-loop motif - 2 anti parallel stands with one in between connected to both by hydrogen bonds
  9. 10. Secondary Structure : Alpha Helix <ul><li>Hydrogen bond between N-H and carboxylic groups on backbone </li></ul><ul><li>Helical twists </li></ul>
  10. 11. Tertiary Structure <ul><li>Interaction of R groups: </li></ul><ul><li>Hydrophobic : phenylalanine, valine, tryptophan </li></ul><ul><li>Hydrophilic : glutamic acid, asparagines </li></ul><ul><li>Salt bridges : charged amino acids </li></ul><ul><li>Disulfide bridges </li></ul><ul><li>Larger motifs </li></ul>
  11. 12. Serum albumin Homo sapiens Pilin Neisseria gonorrhoeae
  12. 13. Tertiary structural domains <ul><li>Domain is the stable part of the protein </li></ul><ul><li>Has a particular function: </li></ul><ul><li>Binding to ligand, DNA, or another protein </li></ul><ul><li>Spanning plasma membrane </li></ul><ul><li>Catalytic site </li></ul>
  13. 14. GPCR <ul><li>7 transmembrane domains that bind to molecules such as hormones, neurotransmitters </li></ul><ul><li>Molecular binding activates signal transduction pathways </li></ul>
  14. 15. New Age of Bioinformatics <ul><li>Allows scientists to virtually screen possible drug targets to protein. </li></ul><ul><li>X-ray diffraction is used to make a crystallized structure of protein. The structure is stored in a Protein Data Bank. </li></ul><ul><li>http://www.pdb.org/pdb/home/home.do </li></ul><ul><li>Molecular docking </li></ul><ul><li>design drugs targets that fit conformation of proteins or have affinity for protein receptors. </li></ul>
  15. 16. <ul><li>PROBLEM </li></ul><ul><li>Difficult to crystallize GPCR </li></ul><ul><li>SOLUTION </li></ul><ul><li>Use comparative homology modeling to construct a theoretical 3 dimensional model </li></ul><ul><li>“domains are conserved” </li></ul><ul><li>“proteins from the same family have significant similarities in tertiary structures” </li></ul>
  16. 17. OBJECTIVE <ul><li>To construct a theoretical model of an A2a GPCR using homology modeling </li></ul>
  17. 18. Method <ul><li>Select protein template : </li></ul><ul><li>Align target sequence(A2a) with template sequence(A2b). Altering sequence of A2a to match A2b. </li></ul><ul><li>Use homology modeling program Modeller to create 3D structure of A2a </li></ul><ul><li>View protein structure using Ras win. </li></ul>A2b: GPCR family, PDB
  18. 19. Results: Protein alignment <ul><li>Protein sequence obtained from NCBI website </li></ul>A2b is 60% identical to A2a sequence 191 residues of A2a matched A2b
  19. 20. Results: Homology Modeling <ul><li>Modeller : computer program that uses altered sequence and A2b PDB file to make a A2a model. </li></ul>“ spartial restraints” and the “position of atoms in space”
  20. 21. A2a Theoretical Model vs. A2b Model Models viewed using Ras win
  21. 22. Future Considerations <ul><li>To attempt model assessment with molecular docking of known A2a ligand antagonists/ agonists </li></ul><ul><li>Specific pocket binding residues </li></ul>

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