Protein Folding Flashcards
What is Protein Folding?
the process by which a protein adopts its correct conformation.
During the folding process the polypeptide adopts its three-dimensional structure from random coil which is essential for function
Every protein is produced as an unfolded polypeptide (random coil) when first translated from a sequence to a chain of amino acids within the ribosome.
What does intrinsically disordered mean?
The correct three-dimensional structure is usually essential to function, although large parts of functional proteins may remain unfolded (intrinsically disordered) which means the protein may NOT BE ACTIVE.
could also mean protein becomes TOXIC.
List techniques that can be used to look at the folding pathway.
1) NMR
2) EPR
3) Fluorscence
4) FIR
Denaturants, temperature and pressure used to fold and unfold the protein.
Issues encountered are with accuracy and time needed to study
The protein FLip35 shows two pathways; how was this modelled?
inital protein allowed to move in a controlled temperature and monitored.
Pathways are predicted using the amino acid sequence of the protein.
List four forces that influence folding and protein interactions.
1) Covalent
These can be backbone, or side chain bonds
2) Hydrogen bonding
3) Hydrophobic (entropic)
4) electrostatic
Describe COVALENT backbone bonds
There are partially double peptide bond (which are not free) and therefore planar. They can be in the low energy trans conformation or the higher energy cis conformation that show different orientations.
There are also PHI and PSI bonds on the peptide that are single and ROTATE (1-360 degrees) Such rotation is dictated by STERIC interactions across these bonds
Describe the difference between single bonds and double bonds in terms of rotation.
Single bonds are FREE to rotate
Double bonds are not free to rotate instead they are said to be PLANAR (and lie in a plane) but given enough energy they can flip
What does a Ramachandran plot show?
It is a plot of PHI against PSI that helps to visualize the bonds conformation.
The conformational space owned by different combinations of Phi and Psi rotations (ie, the min and max energy conformations.)
Se
PSI can be pos or neg
PHI mostly negative
Describe how backbone bonds for BETA sheets and alpha helix
The beta sheet formed form parallel or ANTIparallel beta strands joined together with hydrogen bonds.
The sheet is still flat, with side chains sticking out.
Mixed strands are when there are both parallel and antiparallel strands
Alpha helix has POS PHI and NEG PSI angles with hydrogen bonds between 1 and 4 residues.
COVALENT side chains
Side chains ROTATE
Different energy conformations determined by interaction with the atoms and other side chains
What is a hydrogen bond?
hydrogen bond is a weak bond in which a hydrogen atom attached to an electronegative atom forms a bond to another electronegative atom.
It is electrostatic as there is a partial charge difference between the hydrogen and the electronegative acceptor atom.
However the hydrogen bond shows some directionality and is in reality somewhat covalent (shares electrons).
Where can the Hydrogen bonds be found in the alpha and beta structures of proteins?
In both b-sheets and a-helices the h-bond forms between the carbonyl oxygen and the amino group.
Describe Hydrophobic/entropic interaction
All proteins have a hydrophobic core.
hydrophobic groups exposed to water lead to a decrease in entropy (ordering of water molecules) so burying hydrophobic residues away from water leads to an increase in entropy
What is a Cation–π interaction,
An interaction between the face of an electron-rich π system (e.g. benzene, ethylene, acetylene) and an adjacent cation (e.g. Li+, Na+).
This has the same energy as Hydrogen and salt bridges
Describe electrostatic interactions.
This is a complex effect that interacts with the CHARGES of amino acids (due to their polarity)
Interactions between opposite charges over short distances subject to the COULOMB equations if constant, and charges are known.
