topic 4 - Protein structure Flashcards
what is the protein structure?
there are four levels of structure
the secondary structure is composed of:
the main chain bond angles
alpha helix
beta sheet
others
tertiary and quaternary structure:
supramolecular interactions
coiled coils
structure determination
< 50 residues = peptide, oligopeptide (< ~10)
> 50 residues = polypeptide, protein
what are the four levels of structure to a protein?
primary structure = residue sequence.
secondary structure = local peptide scale regular structural motifs.
tertiary structure= folding of entire protein
quaternary structure= multiple proteins.
describe the secondary structure and what it dominates?
the 2nd structure is dominated by the main chain amide-amide hydrogen bonds
what are Ramachandran plots?
in a polypeptide chain non-amide covalent bonds are relatively free to rotate.
These rotations are represented by the torsion angles of the N-Cα (φ; spelled Phi) and carbonyl-Cα (ψ; spelled Psi) bonds to the amide plane.
Ramachandran used computer models to systematically vary these torsion angles, using Van der Walls radii to find potentially stable conformations, and conformations that were sterically disallowed due to atomic collision.
They tell us what is sterically possible
what is a alpha helix?
360° in 3.5 residues.
Return to same location in 7 residues
Right handed helix
The alpha helix is a rod-like structure whose inner section is formed by a tightly coiled main chain, with its side chains extending outward in a helical array. The alpha helix structure takes advantage of the hydrogen bond between CO and NH groups of the main chain to stabilize.
what is a beta sheet?
Antiparallel Beta Sheet
Pleated Side chains point up and down
Parallel Beta Sheet
Pleated Side chains point up and down
A beta sheet is a secondary structure that occurs in many proteins and consists of two or more parallel adjacent polypeptide chains arranged in such a way that hydrogen bonds can form between the chains.
what are the 4 less common secondary structures?
beta turn
3 to the power of 10 Helix
triple Helix
random coil
what does the tertiary structure involve?
p-p stacking
hydrogen bonding
hydrophobic effect
disulfide bonds
salt bridges
what are disulfide bonds
-SH = thiol, sulfhydryl; mercaptan
Cysteine can form disulphide bonds or “bridges” in a protein, These bring two peptide fragments together.
~250 kJ mol-1 = weak for a covalent bond, but stronger than non-covalent forces.
This happens under oxidative conditions, naturally in the cell.
Disulfides can be broken by exchange with other thiolates. They can be reformed in new ways. Must be the correct arrangement for a protein to work
what are coiled coils and where are they found?
hydrophobic effect
salt bridges
found in:
bee silk
DNA binding
protein nanotechnology
Coiled‐coil domains of some proteins are almost invariant in sequence and length, betraying a structural and functional role for amino acids along the entire length of the coiled‐coil. Other coiled‐coils are divergent in sequence, but conserved in length, thereby functioning as molecular spacers.
what does the quaternary structure do?
Multiple polypeptide chains come together via the same forces which drive tertiary structure.
how can Gel Electorphoresis be used for analysis?
We can use charge/mass ratio to analyse proteins by polyacrylamide gel electrophoresis (PAGE)
Under ‘native’ conditions, movement will depend on protein charge (pKas and pI)
Proteins can be denatured and given uniform negative charge using sodium dodecyl sulfate – SDS-PAGE more common
Dithiothreitol (DTT) can be used to reduce disufides
what method is used to determine structure?
XRD - X-Ray Diffraction
how do we determine structure with NMR?
- more native conditions
- no need for crystallisation
- less precise positions
- less automated
how do we determine structure with Cryo - EM?
- more native conditions
- no need for crystallisation
- lower resolution
- relies on previous models
