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