Protein Folding Flashcards
what must you remember about peptide bonds?
they can’t rotate
but the bonds on each side can
to allow rotations around the peptide bond, the phi is… and psi is…
- nearly always negative (except in let hand helix)
- pos / neg
what is phi?
N-C bond
what is psi?
C-Cbond
77% of psi/phi angles are not seen because…
their interactions are unfavourable
clockwise rotation means a …
+ve angle
anticlockwise rotation means a…
-ve angle
in the thermodynamic sink folding goes from a high energy state to a …
lower energy state
what is the problem with the thermodynamic sink?
movement down a thermodynamic landscape
what are the assumptions that have been made about the thermodynamic sink?
- native state = lowest energy conformation
- unfolded state = random coil
- folding path + native state = directed by side chain interactions
- hydrophobic effect = largest driver of protein folding
- organising interactions are maintained in native structure
what is protein denaturation?
loss of native structure
denaturation does not mean …
peptide bond breakage
unfolded (U) structure
diverse population of structures
no structure preference
native (N) structure
one structure
preferential conformation
there are no … interactions in the unfolded state
stabilising
folding is …. driven
thermodynamically
what will happen if we introduce mutations?
we will move up the curve
at midpoint of 50%, molecular population still knows how to fold
remember we are not … or … bonds as we fold
making
breaking
protein folding increases…
whole system entropy by disorganising water mol around unfolded state
when is denaturation only permitted?
when delta G is positive
what does the overall free energy change depend on?
combined effects of exposure of internal polar + non-polar groups + interaction with water together
with consequential changes in water-water interactions on enthalpy and entropy
each phi-psi will fold…
independently of all other phi-psi pairs
except ones immediately next to it
