Lecture 6 - Protein Structure & Protein Folding Flashcards
Building up Protein Tertiary Structure
- Secondary structure
- Supersecondary structure
- Protein domains
- Complete protein structures
Supersecondary structure
helices
strands
connected by turns or by loops or coil
Common motifs of supersecondary structure
- Helix - turn – helix
- b hairpin
- Greek key
- Strand-helix-strand
Helix-turn-helix
2 helices together joined by a loop or turn
Common supersecondary structure
Helix - turn - Helix examples
DNA binding proteins
Calcium binding protein (longer turn) - hand
β hairpin
Strands antiparallel
Length varies
β strand goes up has a turn and back down
β hairpin examples
Bovine pancreatic trypsin inhibitor
Snake venom toxin
Greek key
4 antiparallel strands
Connected starting in centre
Strand, Helix, Strand
Strands Interact with H bonds
Helices above or below
Supersecondary structure elements combine to form
Domains or motifs
Domains or motifs
Independently folded region in a protein that sets apart from other regions
Small protein
1 domain
Long big protein
Multiple domains packed together
Domain size
150 - 200 amino acids stretch
Protein domain has
Hydrophobic core
Hydrophilic parts on surface
Glyceraldehyde 3 phosphate dehydrogenase
2 domains (1 binds NAD cofactor helps coenzyme work) 1 protein chain
Proteins can be grouped into families based on tertiary structure 3 examples
α domain family (helices)
α / β family (Strand helix strand)
Antiparallel β family
α domain family
4 helix bundle
Eg myoglobin
4 helix bundle
Hydrophobic sidechains in middle (up to vanderwaal radius - max energy)
Hydrophilic sidechains outside
Good for stabilisation
Tilted helices (20 degrees) stabilize sidechains & can nestle next to each other
Myoglobin
Globin fold
Wraps around heme group
α / β family
Mix of α and β structure
Strand helix strand
α / β barrel
α / β open twisted sheet
α / β barrel
8 strands 8 helices
Barrel of strands in middle helices on outside
H bond to each other
Hydrophobic interior Hydrophilic outside (asp, lys, glu)
α / β open twisted sheet
a helices and b strands alternating
Sequence determines pathway
Antiparallel β family
Antiparallel β barrel
Hydrophobic interior of barallel
Eg retinal binding protein
Retinal binding protein
Hydrophobic Retinal inside barrel
b strands nestles retinal
Retinal nose hydroxide sticking out
Carries retinal around body
Surround retinal with hydrophobic sidechains, OH sticks out
In nature common structural motifs and domains are repeated and combined to make
different types of proteins
Domains are often reused by nature and combined with other domains to make
proteins with different functions.
Common Protein Domains
EGF (Hexagon)
Chymotrypsin (Oval)
Kringle Protein (K) - held by disulfide bridges
Ca bind protein (Triangle)
Urokinase
3 domains together
EGF, K, Chymotrypsin
Factor IX
4 domains
1 Ca bind protein, Chymotrypsin, 2 EGF
Plasminogen
6 domains
5 K, 1 Chymotrypsin
Proteins are synthesized as
linear polymers that have
to fold into a 3D functional structure
Protein are made at the
ribosome,
fold into active shape spontaneously
Where are the instructions that proteins need?
embedded in amino acid sequence
sequence contains the instructions
Afinsen experiment
in nutshell
Unfold ribonuclease A structure by Urea and b mercaptoethanol
Remove urea and b merca
Amino acids fold themselves up
Made correct disulfide bonds, and tertiary structure, became active
Proteins contain
information that leads to own structure in their sequence
Collectively what makes a significant contribution to protein conformational stability?
Non-covalent interactions, while individually weak in proteins, collectively
covalent bonds (eg. disulfide bonds)
what’s the most important noncovalent contributor
to protein stability in aqueous solution?
hydrophobic core
Protein folding is directed by
internal hydrophobic residues,
hydrophilic residues are solvent exposed.
is protein folding a random process?
Yes
Folding pathways events
(i) Formation of short secondary structure segments
(ii) Nuclei come together, growing cooperatively to form a domain
(iii) Domains come together (but tertiary structure still partly disordered)
(iv) Small conformational adjustments to give compact native structure
Some protein folding is
assisted by
chaperones
Chaperones
(a) ‘chaperone’-independent
(b) Chaperone-dependent eg Hsp70
(c) Chaperonin-dependent eg GroEL-GroES
What can lead to unfolding
and loss of biological function (denaturation)?
Weakening of non-covalent interactions
Unfolding of proteins may result from…
Change pH Heating Detergents Organic solvents Urea Guandium HCL
Proteins in living organisms that are folded normally can
sometimes
change their shape and become misfolded
Some misfolded proteins can cause
other proteins to change
their shape
sometimes with disastrous consequences
In the brain three conditions have been identified as being due to a protein,
PrP changes shape and forms aggregates that cause brain damage
BSE bovine spongiform
encephalopathy
CSD Creutzfeld-Jacob Disease
PrP
abnormal form of prion protein
induces the normal form of this protein to become misfolded
a → b transformation
No treatment, fatal
Kuru The proteins that cause the problem are called
prions for
“proteins infectious agent”
Other diseases in which protein misfolding or
aggregation is thought to contribute:
- Alzheimer’s Disease
- Type 2 Diabetes
amyloid (abnormally folded protein)
Prions not involved
