Lecture 2 - Domains Flashcards
Hierarchy of protein structure
Secondary structure -> Super-secondary structure -> Motif -> Domain
What is a protein domain
A polypeptide chain or part of a polypeptide that can fold independently to form a stable tertiary structure
Characteristics of domains
- Formed from secondary structures and structural motifs
- Domains are recognisable units of tertiary structure
- If a domain were expressed independently of the rest of a protein, it would form a stable folded structure.
- motifs would not fold correctly
Can domains be whole proteins?
Yes, such as triosephosphate isomerase
Can a domain form part of a protein?
Yes, such as pyruvate kinase
phosphoenolpyruvate to pyruvate in glycolysis
Name the three groups of domains
alpha-domains - formed from a-helical motifs
beta-domains - contain anti-parallel B-sheets
a/B domains - Formed from BaB motifs predominantly
Derived from Michael Levitt and Cyrus Chothia
a-domains
- More general case of leucine zipper motif
- Amphipathic a-helices made up of heptad repeats
H-P-P-H-P-P-P
H - Hydrophobic
P - Polar
- Forms hydrophobic stripe
- Two stripes align to minimise solvent exposure
The coiled coil in a-Domains
3.6 residues per turn in a-helix
Hydrophobic stripes twisted
3.5 residues per tuen in coiled-coil
Hydrophobic stripes align
Three helix bundle a-domain
Modification of coiled-coil theme; three intertwined a-helices
Hydrophobic residues between helices
Helices can run parallel (e.g. fibrinogen) or anti-parallel (Hsc20 heat shock cognate protein - a chaperone)
Four helix bundle a-domain
- Helices not twisted round each other; more cross-over each other (differs to coiled coil)
- Hydrophobic core - hydrophobic residues ‘buried’ between helices
The goblin fold
- Found in large groups of related proteins including myoglobin and hemoglobin
- Helix-loop-helix motifs
- Eight helices wrapped around central core - active site heme
- Helix pairs not adjacent with exception of G and H, form anti-parallel pair
Explain the up and down barrel
b-Domains are made up from b-fold motifs; b-strands in anti-parallel
- A rolled up sheet of b-sheet fold motifs.
Last and first b-strand interact via H-bonds to ‘seal’ the roll - Can be twisted for distorted
The beta-barrel beta-domain
Variation on up and down barrel theme but not a simple ‘roll-up’
Strands 4-6 are flipped riund so order in barrel is 1, 2, 3, 6, 5, 4, 7, 8
Superoxide dismutase is an example
Greek key proteins as B-domain
Two beta-fold motifs are folded in a Greek key motif
Proteins are made up of a succession of Greek key type folds
y-crystallin - Found in lenses of our eyes - Responsible for maintaining a smooth gradient of refractive index of light
The jelly roll as a B-domain
Formed from a series of Greek key motifs, arranged in a different way
e.g. spherical virus coat proteins, concanavalin A
Four continuous b-strands running anti-parallel to a second four
The parallel B-helix
Cylinder/helix of parallel B-sheets
Simplest form contains two sheets e.g. Serratia metalloproteinase - first isolated from the Gram-negative bacterium Serratia
Can also contain three b-sheets e.g. pectate lyase (pectate in cell walls)
The a/B barrel
- Barrel of multiple B-a-B fold motifs
- Core of hydrophobic twisted B-strands surrounded by hydrophilic a-helices
- Centre of barrel full of hydrophobic side chains
- Active site at 1 end of barrel formed by loops which connect carboxy ends of B-strands to amino end of a-helices
The twisted sheet - a/B domain
Unlike the a/b barrel there are a-helices on both sides of the plane of the b-sheet; cannot form a barrel structure
Instead a twisted b-sheet is found at the core of the domain surrounded on all sides by a-helices
a/B domain - The horseshoe fold
Leucine rich motif
X-L-X-X-L-X-X-Z-X-L-X-X-X-X-X-X-X-L-X-X-X-L-X-X-X-X
X- any amino acid
Z- Asparagine or cysteine
L- Leucine
Each motif forms a b-loop-a structure stabilised by the leucine residues in the hydrophobic core which pack against each other
Unlike the a/b barrel one face of each b-strand is exposed to solvent
Protein modifications
co- and post-translational modifications in vivo
- Addition of hydrophobic groups for membrane localization
- C-terminal - myristoylation, a C14 saturated acid
N-terminal glycosylphosphatidylinositol (GPI) - Addition of cofactors for enhanced enzymatic activity
Flavin (FMN or FAD) may be covalently attached
Heme cytochrome attachment via thioether bonds with cysteins - Modification of amino acids
Hydroxylation of proline in collagen
Hypusine formation (on conserved lysine of eIF5A)
Dynamic Phosphorylation
- Common protein modification in eukaryotes
- Dynamic phosphorylation is key mechanism of cell signalling
Phosphorylation occurs on serine (90%), threonine (10%), and tyrosine (<1%) residues
10-30% of the human proteome is phosphorylated
Can effect protein structure, activity and localisation
N-glycosylation
Glycosylation of Asparagine residues occurs co-translationally in the ER
- sequence motif NX(S/T) where X is not proline
N-glycosylation has important structural and functional roles
- increase hydrophillicity
- modulate protein – protein interactions
Ubiquitiylation
Ubiquitin - 8.5kDa protein that covalently attaches to lysine side chains
Polyubiquitination targets proteins for degradation
Dynamic mono-ubiquitinoylation regulates activity, localisation, and protein-protein interaction
Other Ubq-like modifiers are involved in regulation
SUMO (Small Ubq-like Modifier)
NEDD8 (Neural Precursor Developmentally Downregulated 8)
