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Understanding Protein Structure: Secondary Structures, Venn Diagrams, and Comparison Methods

Chapter 8 delves into the intricate structure of proteins, focusing on key concepts such as secondary structure elements like alpha helices and beta sheets. It addresses the importance of hydrogen bonding in stabilizing these structures and presents tools such as the Ramachandran plot for assessing steric conformations. Additionally, it covers the usage of distance matrices, handedness, and torsion angles in structural analysis. Methods for comparing protein structures are discussed, emphasizing a framework for understanding similarities and differences among them.

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Understanding Protein Structure: Secondary Structures, Venn Diagrams, and Comparison Methods

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Presentation Transcript

  1. Chapter 8 – Structure description Chapter 8. Strucure description

  2. Venn diagram Chapter 8. Strucure description

  3. Structures Chapter 8. Strucure description

  4. Coordinates Chapter 8. Strucure description

  5. Alpha or beta coordinates Chapter 8. Strucure description

  6. Distance matrices Chapter 8. Strucure description

  7. Handedness Chapter 8. Strucure description

  8. Torsion angles Chapter 8. Strucure description

  9. Ramachandran plot Chapter 8. Strucure description

  10. Protein secondary structures • Globular proteins which are solvable, packs the hydrophobic side chains inside the molecule. This makes a hydrophobic kernel and hydrophilic surface. • The backbone is polar, hence hydropholic. To neutralize this hydrophility there are hydrogen bindings between NH and CO on the backbone. • This is done by constructing regular secondary structures • Helices, alpha most usual • Beta sheets • They are made by succeeding residues having equal torsion angles Chapter 8. Strucure description

  11. Alpha helix Chapter 8. Strucure description

  12. Beta sheets Chapter 8. Strucure description

  13. DSSP – Define Secondary Structure of Proteins • DSSP identifies both the SSEs and solvent exposure of proteins.It is mainly based on H-bond patterns, and must therefore include a method for identifying those. Chapter 8. Strucure description

  14. Determining helices Chapter 8. Strucure description

  15. Determining beta strands Chapter 8. Strucure description

  16. Structure comparison Chapter 8. Strucure description

  17. Requirement for structure descriptions Chapter 8. Strucure description

  18. Desribing structure pieces Chapter 8. Strucure description

  19. Space based description Chapter 8. Strucure description

  20. Framework for pairwise structure comparison Chapter 8. Strucure description

  21. Cannot use pure dynamic programming for structure comparison Chapter 8. Strucure description

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