protein folding and stability Flashcards
intermolecular forces integral to protein folding and stability
-h bonding -van der waals -ionic bonds -covalent bonds (disulphide) HIVd -hydrophobic interactions
Van der Waals
non covalent interactions between eelctrostatically neutral molecules- they arise from electrostatic interactions between permanent dipoles -much weaker than ionic -no positive or negative component -if molecules get too close and electrons overlap repulsion will occur - in terms of VDW, the proteins have to be packed closely to ensure that as many VDW form as possible- this means that the structures aren’t hollow and they fold tightly
why are proteins not hollow
so that as many intermolecular forces can form as possible e.g. optimal length in VDW will ensure that as many form as possible giving stability
proteins are held together by fairly weak forces however..
it it the accumulation of all these forces which increase stability - no protein will fold correctly due to just one of the forces (accept possibly not disulphide bridges)
proteins can be denatured because..
incorrect pH incorrect temp
proteins are used to existing in water and do not like..
organic solvents
proteins fold spontaneously because..
the native conformation is the most energetically stable
example of disease due to a defect in protein folding
CF involves the misfiling of a protein and results in the lack of the protein that involves the CL- transport mem.
proteins fold to their energetically most..
energetically stable conformation
why do proteins fold
proteins do not like organic solvents- therefore when the protein is folded less surface area (contact residues) is exposed to the solvent
what describes the change in proteins being in the folded state to the unfolded state
protein folding is an equilibrium process
hydrophobic interaction
in some proteins the amino acid side chains hydrophobic - these groups like to be on the inside of globular proteins (on the inside of the folded structure) -hydrophobic amino acids have methyl groups e.g. alanine and isoleucine or side chain or ring structures eg. phenylalanine
physical basis from hydrophobic effect
entropically unfavourable- water molecules dislike becoming ordered- therefore the interaction between water an oil is as minimal as possible e.g. drops of old come together to make bigger droplets and therefore have less contact wit water - less hate rmoecule scan fit around it
hydrophobic effect is driven by..
entropy
three types of VDW
1) london dispersion forces 2) dipole induced dipole interactions (stronger) 3) interaction between permanent dipoles (strongest)
london dispersion forces
due to one group having a greater attraction to electrons than the other- just dealt charges ( e.g. oxygen being more electronegative than carbon)
hydrogen bonding
electrostatic interactions between weakly acidic donor groups and acceptor atoms that bear a lone pari of electrons -many H bonds in alpha and beta pleated sheets -O or N any molecule that can form hydrogen bonds to each other can also bond with water- therefore H bonds are found within folded and non-folded proteins - therefor their effect is only marginal
ideal H bond length
2.7-3.1 A
H bonds only have a marginal effect because…
folded and unfolded proteins have H bonds
ionic interactions
electrostatic interactions between -ve and +ve charge amino acid like lysine and arginine. Can be many or single interactions
in ionic bonding water must be stripped, otherwise the molecules would be salvage day water and this has a price to pay:
enthalpically unfavourable- energy must be provided and this is relayed by the forming of thee ionic binds
disulphide bridges
only covalent bonds involve in protein structure
- e.g. 2 cysteine produce cystine
- mainly found in proteins which are secreted
- not found in cytoplasm which is a reducing environment.
- proteins with disulphide binding are very stable
what are disulphide bridges also called
cysteine residues
strongest intermolecular force
disulphide bridges
mechanism of protein folding: the levinthal paradox
Lets assume that each amino acid has approx 10 possible diff conformations- a polypeptide of n amino acid therefore has 10n possible conformation -if a protein could try every possible combination the time period of 10^-14 seconds. -the time for a protein of n residues to explore all of it conformations would take 10^13 seconds. Therefore for a protein of 100 amino acid this would take 10^87 second–> the age of the universe is only 10^18sec. Therefore impossible to try out all diff conformations
why is it impossible of a protein to try out all its confrmatons
-the time for a protein of n residues to explore all of it conformations would take 10^13 seconds. Therefore for a protein of 100 amino acid this would take 10^87 second–> the age of the universe is only 10^18sec. Therefore impossible to try out all diff conformations
evidence for protein folding being a directive process and not random
the levinthal paradox
Afisens experiment
- when B-mercatoethanol and urea were removed slowly the protein refolded and the correct disulphide bonds were reformed- 100% activity
- however when the B-mecatoethanol was removed, the cysteine formed random disulphides. Upon subsequent removal of urea only 1% of activity was restored. Scrambled ribonuclease spontaneously refolds and the sequence dictates its structure. If you only removed B mercatoethanol there is only 1% chance it will reform correctly.
- 1/105 is the odd of getting the right disulphide to reform. Only those proteins who had the right disulphide combination could function properly.
- However if you added slightly more b-mecaptoethanol the disulphide bonds will be re-broken and then reform to give the correct conformation and therefore now the protein will have 100% activity
chaperones and protein folding
if there are many unfolded molecules, they can join together, which would prevent them from being functional. Chaperones job is to stop this from happening. They give the unfolded protein a nice environment in which they can fold on their own, without giving any direction. it protects them from unfolded molecules with which they may aggravate with.
many ionic interactions
multiple charges from different amino acids forming interactions together
example of ionic interaction between two amino acids
lysince and arginine
cystine residues are formed as a result of
a condensation reaction: two cysteine are brought together and water is lost
