Proteins - T&Q, Forces and Folding Flashcards
What is the tertiary structure of proteins?
Describes the folding/organisation of secondary structure elements
Can be a/b or both and is very unique
How can we determine the positions of atoms in proteins?
X-Ray crystallography - A crystal of the molecule is imaged resulting in a diffraction pattern (atomic resolution not achieved)
NMR spectroscopy - interactomic distance measurements and geometric constrainsts are used to build a 3D image
Cryo-electron microscopy - sample is cooled (-196 C) so fast it assumes a vitreous (glasslike) state = retains native state for viewing
Where are amino acids normally found in globular proteins?
Non-polar residues - interior of the protein
Uncharged polar residues - on the surface but also occur in the interior
Charged polar residues - on the surface
Due to the hydrophobic effect
What are groupings of secondary structure elements called?
Supersecondary structures or motifs (special folding)
Name some supersecondary structures/motifs?
- Beta-alpha-Beta (the helix connects two parallel beta strands)
e. g. triose phosphate isomerase - Beta hairpin (antiparallel strands connected by tight turns
e. g. erubotoxin - Alpha-alpha (two successive antiparallel helices packed against each other with their axes inclines
e. g. calmodulin - Greek-key motif (a beta hairpin folded over to form a 4-stranded anti-parallel beta sheet)
How are most proteins classified?
All alpha helices
All beta sheets
But most contain a mixture:
A/B mixed together
A/B with segregated regions
How are the a, b and a/b classes further categorised?
Via topology - according to how their secondary structure elements are connected:
Beta barrels x3
2 are all B with beta hairpin motifs
1 is an a/b barrel with overlapping BaB motifs
What do larger polypeptides form?
Domains
Each domain consists of 40-200 amino acids with an average diameter of 25 Å
e.g. Glyceraldehyde 3-phosphate dehydrogenase
Some domains are structurally independent - can be separated and be stable
Other multi-domain proteins have binding sites occupying clefts between domains
Rossmann folds often act as nucleotide binding sites (identification of this fold = clue to the function of the protein)
Describe quaternary structure?
Many polypeptide chains non-colvalently assembled
Larger than 100 kDa
Describe subunits within quaternary structures?
The subunits associate noncovalently
Proteins with more than one subunit = oligomers and their identical units = protomers
Homo oligomer - one type of protein subunit
Hetero oligomer - different types of protein subunit
How are subunits within quaternary structures arranged?
Symmetrically
Each protomer occupies a geometrically equivalent position in the oligomer
Due to only L residues = rotational symmetry
What are the types of rotational symmetry?
Cyclic symmetry - single axis of rotation
Dihedral symmetry - n-fold rotation axis intersects a twofold rotation axis at right angles
What does protein stability depend on?
Hydrophobic effect Electrostatic interactions Hydrogen bonding Di-sulphide bridges Metal ions
These stabilising forces work against destabilising (entropy)
Why are proteins deemed relatively stable?
Energy needed to denature (100 residue protein) 40 kJ mol-1
Energy required to break H bonds = 20 kJ mol-1
What is the hydrophobic effect?
Causes non-polar substances to minimise their contacts with water
= aggregation of non-polar side chain amino acids in the interior of the protein
