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