Lecture 6 - Protein structure and protein folding Flashcards
Supersecondary structure
Super-secondary structure contains 3D secondary elements ie helices and strands that are connected by turns or regions of less ordered structure (loops or coils)
Some examples are helix-turn-helix, beta hairpin, Greek key and strand-helix-strand
Common motifs of super secondary structures
Helix-turn-helix, beta hairpin, Greek key and strand-helix-strand
Helix-turn-helix examples
DNA binding proteins - dimers and have 2 helices each, they dimerise across the helix and then two outer helices fit inside the DNA major groove , calcium binding proteins
What is a beta hairpin and what are the key features?
- What shape is it is most like?
- How many residues?
- Most common AA?
- What % of residues in turn?
- What bonds are common?
- Hairpin like
- involve usually 3 or 4 residues,
- High Gly, Pro content
- Almost 30% of residues involved in turns
- Hydrogen bonds across the turn are common
Also common, antiparallel, length varies, short stretches of beta strands that are antiparallel to each other, beta stand-turn-beta strand
Greek key
N to C
Connected so that the first strand is in the middle connects to 2 and foes to 3 and then goes to 4
4 stranded beta sheet, composed of 4 individual antiparallel strands
Strand helix strand
Helix is depicted as a cylinder
The 2 strands are next to one another and they hydrogen bond to one another and helix is out of the plane
Protein domains and motifs
Super-secondary structure elements combine to form regions with a specific function
Typically, a protein domain has a hydrophobic core and the hydrophilic parts of the protein are arranged on the surface in contact or near solvent.
Small proteins contain usually one domain, larger proteins may have multiple domains.
Three examples of protein families based off tertiary structure
Alpha domain family (alpha helicies dominant)
alpha/beta family
Antiparallel beta family
Alpha domain family
4 helix bundle - connected from N to C, tilted about 20 degrees to each other which has a purpose
Helix - turn - helix - turn - helix - turn - helix - turn
Folds together because it can create its own hydrophobic core, hydrophobic residues are in the core which helps to stabilise the protein
Globin fold - 8 helices that bind around a heme group and there are 2 histodines there that interact with the heme group
alpha/beta family
Mixture of alpha and beta structure - alternating alpha helices and beta strand
alpha/beta barrel - strand-helix-strand-helix (8 strands), all of the strands interact, hydrophobic inside of barrel - next layer of side chains point out (hydrophilic outside the barrel)
alpha/beta open twisted sheet
Alpha/beta horseshoe fold
Antiparallel beta family
No alpha
Mostly antiparallel beta structure … beta strand - turn - beta strand - turn - beta strand
8 strand generally and it forms a barrel with a hydrophobic interior
Retinal binding protein - every atom in retinal is hydrophobic with exception of the terminal hydroxide. Binds retinal and transports it
Hydrophobic inside of barrel
Mostly carrier proteins or binding proteins
Protein folding
Proteins are synthesized as linear polymers that have to fold into a 3-dimensional functional structure
Protein are made at the ribosome, and then generally they fold into their active shape spontaneously
The only “instructions” needed are embedded in the aa sequence
Essentially the sequence contains the instructions!
This was proven by a famous biochemist, Christian Afinsen, in a series of experiments that led to a Nobel Prize
The Afinsen Experiment
Anfinsen treated a ribonuclease enzyme with excess β-mercaptoethanol and 8M urea. This broke all the hydrogen and disulphide bonds and the protein denatured. When the agents were removed, the enzyme eventually reformed its original tertiary structure
Folding pathways
Protein folding is directed largely by its internal hydrophobic residues, which form an internal core, while hydrophilic residues are solvent exposed. Not a random process
A likely sequence of events is:
(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
Stabilisation of protein folding
Non-covalent interactions, while individually weak in proteins, collectively make a significant contribution to protein conformational stability
In some proteins additional covalent bonds (eg. disulfide bonds) may be present that contribute to conformation stability
The hydrophobic core is likely the most important noncovalent contributor to protein stability in aqueous solution.
Metal ion coordination, hydrophobic interactions, electrostatic attraction, side chain hydrogen bonding (non covalent), disulphide bond (covalent)
Some protein folding is assisted by….
Chaperones - prevent aggregation before the final folding can occur
(a) ‘chaperone’-independent
(b) Chaperone-dependent eg Hsp70
(c) Chaperonin-dependent eg GroEL-GroES - these are larger molecules that require ATP to function, hydrophobic core that interacts with the hydrophobic part of the amino acid chain. Prevents incorrect folding from taking place. Quite often gets partially folded by chaperones first.
What is a chaperone and what role do they play?
Chaperones are independent peptides that assist in the correct folding or unfolding of other proteins.
Some chaperones eg Hsp70 are thought to crowd and stabilise the unfolded molecule until it folds properly.
No ATP required for these
What is a chaperoning and what role does it play?
Chaperonins have the same function as chaperones (independent peptides that assist in the correct folding or unfolding of other proteins). but are barrel-shaped and the protein folding happens protected from the cell environment inside the structure.
Unfolding of proteins
Weakening of non-covalent interactions can lead to unfolding and loss of biological function (denaturation)
May result from eg:
- change in pH (lab 1) - detergents - urea
- heating (lab 1) - organic solvents - guanidium HCL
Misfolding of proteins
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 as well, sometimes with disastrous consequences
Can be associated with disease in living organisms
Misfolding of proteins in disease
In the brain three conditions have been identified as being due to a protein, PrP, that changes its shape and then forms aggregates that cause brain damage: bovine spongiform encephalopathy (BSE), Creutzfeld-Jacob Disease (CSD) and Kuru
The proteins that cause the problem are called prions for “proteins infectious agent”
It is thought that the abnormal form of a prion protein, PrP, induces the normal form of this protein to become misfolded
alpha → beta transformation
No treatment available, always fatal.
Other diseases in which protein misfolding or aggregation is thought to contribute:
– Alzheimer’s Disease
– Type 2 Diabetes
Prions are not involved in these ailments
Abnormally folded protein called amyloid is thought to contribute
