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Amino Acids and Protein Structure

Amino Acids and Protein Structure. Protein structure. Four levels of protein structure Linear Sub-Structure 3D Structure Complex Structure. polarity. Hydrogen Bonding Intermolecular Forces Dipole- Dipole Ion-Dipole Van der Waals. Hydrophobic Effect.

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Amino Acids and Protein Structure

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  1. Amino Acids and Protein Structure

  2. Protein structure • Four levels of protein structure • Linear • Sub-Structure • 3D Structure • Complex Structure

  3. polarity • Hydrogen Bonding • Intermolecular Forces • Dipole-Dipole • Ion-Dipole • Van der Waals

  4. Hydrophobic Effect • Nonpolar molecules disrupt dynamic hydrogen bonds • Hydrophobic amino acids include • alanine, valine, leucine, isoleucine, phenylalanine, tryptophan and methionine

  5. Hydrophobicity in Protein folding • Hydrophobic amino acids face the interior of the protein

  6. Hydrophobicity Number • Hydrophobicity Scale • Physical scales based on surface tension or energy solvation • Wimley-White Scale • Peptide bonds and side chains • Experimentally determined values

  7. Charge • Refers to the total external charge, while polarity refers to the difference in charge

  8. Charge in protein interactions • Opposites attract, so charge can influence protein binding activity

  9. Amino acid size

  10. Summary

  11. Protein folding • Physical structures resulting from amino acid sequences • Predictive techniques • FoldIt

  12. interaction • Binding sites • Chemical bonds from with ligands • Specific molecules and ions

  13. CASP • Critical Assessment of Protein Structure Prediction • Competition structure • Advancing predictive science • Based on structure, complex, domain, function

  14. SCOP • Structural Classification of Proteins • Collaborative classification effort • Based on amino acid sequence, domain structure, and function • Classified into families and superfamilies • Sourced from Protein Data Bank (PDB)

  15. Protein data bank – PDB Useful for low sequence similarity Computational methods X-Ray Crystallography NMR Spectroscopy Protein structure alignment

  16. DALI • Distance alignment matrix based on hexapeptide contact patterns • FSSP (Families of Structurally Similar Proteins) Database • Server-based • DaliLite standalone

  17. Combinatorial extension • Breaks structures into aligned fragment pairs • Originally only structural superpositions and inter-residue distances • Now includes secondary structure, solvent exposure, hydrogen-bonding patterns, and dihedral angles

  18. SSAP • Sequential Structure Alignment Program • Vectors between non-contiguous residues • Optimal local alignments compiled into summary matrix • Dynamic programming

  19. X-Ray Crystallography • Crystal • X-ray diffraction • Angles and intensities • Electron density • Atom positions and chemical bonds • Good resolution

  20. Nuclear magnetic resonance (NMR) • Water solution • Solid methods in development • Sample is placed in magnet • Different nuclei absorb different radio frequencies • Interaction • Determine orientation and structure

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