C. PROTEIN CHEMISTRY 2 Flashcards
ways to determine protein structure
X-ray crystallography
NMR spectroscopy
Cryo-electron microscopy
AlphaFold
where is animal insulin derived from
cows and pigs
what type of amino acids does evolution conserve
those that are important to a protein’s structure and function across species
(compare sequences through aligning multiple ‘homologue’ sequences of a particular protein in different species)
is insulin highly conserved
YES
Porcine and human insulin only differ in a single amino acid and bovine insulin varies by three amino acid
what covalent forces are present in insulin
peptide bonds
disulphide bonds
what non-covalent bonds are present in insulin
hydrogen bonds
Van Der Waals forces/interactions
hydrophobic interactions
electrostatic interactions
(ionic interactions and salt bridges)
can peptide bonds be broken down
yes by hydrolysis but in very harsh (they are every stable) chemical conditions under 6M acid/alkali or by proteases under physiological conditions hence why storage is important
can disulphide bridges be broken down
yes by reduction with β-mercaptoethanol (reducing agent containing thiols) to re-form cysteines
why do hydrogen bonds contribute most to stability in proteins
they are furthest away from water which would disrupt them
how are hydrogen bonds disrupted
heat or high salt solutions which cause heat
what is optimum orientation of H-bonds
X-H points directly to the lone pairs so that the angle between X, H and Y is 180 degrees
are VDW forces weak
yes but there are many of them and they are short dipole-dipole (δ+ & δ-) interactions between close atoms
how are VDW forces disrupted
heat or denaturing agents like detergents, high salt solutions
where does π-π overlap occur
between π electron clouds delocalised over rings and bonds (eg - aromatic rings)
how are π-π overlaps disrupted
heat
are electrostatic interactions strong
yes, inversely proportional to the distance between 2 charged groups
how are electrostatic interactions broken
changes in pH or high ionic strength
how do hydrophobic interactions occur
non-polar side chains of amino acids forced together in aqueous environments to minimise their disruptive effect on the hydrogen-bonding network of water molecules
what is the distribution of amino acid residues in soluble proteins
charged/polar amino acids map to the surface (glutamic acid, serines, arginine) and non-polar are buried in the core (leucine, phenylalanine, proline)
what is special about membrane proteins
they have extensive hydrophobic regions (ie the helices and sheets)
what drives protein folding into 3D structure
non-polar side chains cluster in interior of protein so contact with water is avoided
polar side chains form hydrogen bonds with surrounding water molecules
how do proteins fold to the native conformation
- go through intermediate states on their way to a stable low energy tertiary structure
- folding begins with formation of local segments of secondary structure. A so-called ‘molten globule’ can form by ‘hydrophobic collapse’ (all hydrophobic side-chains suddenly clump together), a structure in which the secondary structure elements of the protein are mostly formed
- chaperone proteins: assist in the proper folding of proteins in the cell
example of protein that we eat which undergoes denaturation
eggs but re-naturation isn’t possible for eggs (is for others)
how does denaturation occur
extreme changes in pH, temperature or addition of detergents
structure of insulin in mature form
A chain - 21 residues
B chain - 30 residues
molecule linked 2 inter-chain and 1 intra-A-chain disulfide bridges
(C-chain and signal peptide are removed)
how does insulin exist in dilute solutions like circulation
monomers (globular molecule) - can bind to receptor and are biologically active
how does insulin exist in crystals and in β-cell secretory granules
hexamers
(at micromolar concentrations, insulin dimerises, and in the presence of zinc and iron, it further associates into hexamers)
how are the biologically active monomers formed
Hexamers precipitate in crystalline form owing to the pH (around 5.5) and the presence of zinc and calcium ions
Upon extracellular release, the hexamers dissociate into dimers and eventually into monomers
how does insulin form fibrils
occurs when the native state is destabilised, insulin monomer undergoes partial unfolding and the helical polypeptide hormone aggregates to form amyloid fibrils
complications:
when insulin is present at high concentrations ie - at the site of repeated insulin injection in diabetics and in clinical formulations, fibrillations can interfere with the requirement of equal amounts of functional insulin in each dose
insulin surface features
monomer has 2 extensive non-polar surfaces
1. aromatic and buried upon dimer formation
2. buried upon hexamer formation
insulin uses the same surfaces for binding to its cognate receptor that it does for self-assembly
when is rapid-acting forms of insulin used
meal times eg - Insulin lisper, insulin aspart, insulin glulisine
how do rapid-acting insulin analogs work
after subcutaneous injection, the proportion that is bound in the form of dimers and hexamers is lower, which means that the monomeric form of the molecule can be absorbed
at the point of injection more quickly
when is long-acting forms of insulin used
basal requirements
how does insulin aspart work
proline 28 (neutral) in B-chain is substituted with an aspartic acid residue (-vely charged)
there is increased charge repulsion which prevents formation hexamers
