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Protein structure Visualization Molecular Story

Protein structure Visualization Molecular Story

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Protein structure Visualization Molecular Story

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  1. Protein structureVisualizationMolecular Story

  2. Review “Central Dogma”: Sequence  Structure  function Sequence based analysis Structure based analysis Gene Sequence Protein Structure Protein Function (Genomics) (Structural Genomics) (Functional Genomics) Primary Structure Protein - Protein Secondary Structure Protein-DNA/RNA Tertiary Structure Protein-Lipids Quaternary Structure Protein-Small Molecules Determine Structure Drug Development Sequence similarity Conserved domain Predict structure Predict function

  3. Bio-information data collection methods and major databases Genome sequencing  Genbank (www.ncbi.nih.gov) Genechip  gene expression database X-ray crystallography, NMR  protein structure database ( www.pdb.org) 2D gel, mass spectrometry  proteomics database Literature db  PubMed (www.pubmed.org) Inherent genetic disease db  OMIM (www.ncbi.nih.gov)

  4. Structure based analysis  Molecular profile and story Protein structure: Primary Secondary Tertiary -Folding quaternary Protein structure determination: X-ray crystallography NMR spectroscopy Protein structure prediction: Secondary structure prediction Homology modeling Protein structure analysis: The structure character of the individual protein The structural basis of the protein function Protein family (based on conserved domain, motifs to predict their functions) Write the molecular profile and story

  5. Protein Molecular Structure a) Protein is a polymer of amino acids. 20 Amino Acids ( Functional Groups) Peptide Bond Formation

  6. c) The Secondary Structure and Tertiary Structure of Protein Elements of Secondary Structure: Helix Loop Turn β-Strand Helix β-Strand in β-Sheet Turn Loop Turn

  7. Secondary Structure & Ramachandran Plot

  8. Ramachandran Plot of CDC42-RhoGDI Complex [PDB Code 1DOA]

  9. Many alpha helices are Amphipathic 100 degree per residue

  10. Molscript Representations of Typical Protein Architectures. β 7 Propellor (2bbkH) α 4-Layer Sandwich (2dnjA) β Barrel (2por) Sandwich (2hlaB)

  11. Molscript Representations of Typical Protein Architectures. α β Barrel (4timA) α Helix Bundle (2ccy) α Horseshoe (1bnh) 2 Solenoid (1tsp)

  12. Schematic Illustrations of Isologous and Heterologous Association between Protein Subunits b a c d d c b a c a b d --b a----b a-----b d a c b a d--c b--a --d b a c---d c---d c- Heterologous Tetramer d c Heterologous Association Isologous Association

  13. Examples of Protein Quarternary Structure. The prealbumin dimer, in which arrows depict the β-strands. The two monomers (left and right) associate to extend the two β-sheets (1bm7). The Isologous tetrameric structure of rabbit skeletal muscle aldolase, with three twofold symmetry axes (1ado).

  14. DNA Quadruplex & G Quartets + K

  15. NMR Spectroscopy Sample-Spectrum-Structure

  16. X-Ray Crystallography Crystal Diffraction Electron Density Structure

  17. Protein Function and Structure (Architecture) a) Binding: Protein-DNA: transcription factors, eg TATA binding protein (PDB 1tgh) Protein-RNA: microRNA-target protein  RNAi function Protein-small molecule: eg: Myoglobin-Heme/O2,Fe (PDB 1a6k) drug-target protein binding Protein-Protein: eg, chaperonin GroEL b) Catalysis: Enzymes Catalyzes biochemical reactions eg: DNA Polymerase catalyzes DNA replication (PDB 1pbx) HIV protease cleaves protein catalyzing the HIV replication (PDB 1a8k) c) Switching: eg: small GTPase Ras is a ‘Molecular switch’ for cell growth, GTP-bound, ‘ON’ (PDB 121p); GDP-bound, “off” (PDB 1pll) d) Structural Proteins: Silk: a stack of anti-parallel beta-sheets (PDB 1slk) within a sheet: covalent bonding and hydrogen bond, between sheets: Van der Waals force F-actin: helical assemblies of actin and actin-associated proteins  muscle contraction, cytoskeleton

  18. The Second Project • Go to www.pdb.org, • Type a protein (or a disease) name, search for the structures • b) Download the structure text file, save it as a text file with .pdb extension. • c) Input the xxx.pdb file to Pymol (download from www.pymol.org) • to see the molecular structure, notice its structural characters. • d) Read the major reference paper (from www.pubmed.org) for this protein structure and the corresponding gene, summarize the connection of the structure and the protein function. Write the molecular story for this gene.