Globular protein (tertiary and quaternary structure)

Similarities of soluble globular proteins

• Mixture of 2nd structures, gotta have irregular to fold

• Hydrophobic cores, hydrophilic exteriors

• Closely packed interiors

• maximized H-bonds in the interior-net energetically favourable

Where are disulphide bonds found? Are there prosthetic groups?

Only in extracellular proteins, some do some don’t

Tertiary structure rules for soluble globular proteins?

• Hydrophobic interactions are critical- need inside and outside (at least 2)

• Extensive H-bonding within 2nd not between them

• No knots

• Elements that are close in 1st are close in 3rd- not other way around

• Connections between B-strands are usually right handed

Right handed connection

Above plane- scoops up and towards you, shorter

What are the three classification systems we use for tertiary structure?

• SCOP- structural classification of proteins

• CATH: class, architecture, topology, and homology

• InterPro

What are some classifying thing we look at with tertiary structure

Structure is better conserved than sequence, common features and relationships

Describe overall structures as a, B, or a/B

Super secondary structures

Motifs/folds, domains

Motifs

recognizable combinations of secondary structure that appear in a number of different proteins

use to generate layers and Barry hydrophobic R groups

A/B barrel is common, or B-a-B loop motif

Domains

Subset, discrete, independently folded compact units within a polypeptide

May be composed of or include motifs

More intradomain interactions than interdomain ones

Elements that depict subportion

Leucine zipper

Coiled coil, two a helices (left handed super helix), with leucine at the helix-helix interface (similar to a-keratin)