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What is Protein Folding?

a process when a protein adapts its correct conformation.
- the polypeptide adopts its 3D structure

( when first translated - a protein starts as a random coil lacking 3D structure )

some proteins remain unfolded ( these are known as intrinsically disordered)- becoming more and more important

N.B. protein - protein interactions can be sometimes be seen as a protein folding process


What are examples of toxic protein functions ( due to failed protein folding ) ?

- neurodegenerative diseases ( form from an accumulation of misfolded proteins)


What is 3D structure important for ?

3D structure can be important for function of protein

failure to fold may result in inactive proteins or even a toxic function.


What methods can we use to examine protein folding ( or unfolding) ?

- Stimulation ( molecular dynamics- a computer simulation of physical movements )


What can be used to stimulate the process of protein folding? and what problems are associated with it ?

- molecular dynamics

- problems - the accuracy of the stimulation conditions
length of time that it needs to be studied under.


What Forces are involved in protein folding and interactions?

1. Covalent
2. hydrogen
3. entropic ( hydrophobic )


What two areas can a covalent interaction in a protein be split into ?

1. backbone bonds (most important part ) - either Cis ( only in special circumstances or Trans ( seen in most peptide bonds )
2. side chain bonds ( can rotate but there will be low energy conformers and the energy of the different states is dictated by the interactions with the backbone atoms and with other side chains. ) / side chains location is determined by energy.


Why are peptide bonds important ?

-the peptide bonds are planar and due to the partial double bond character they cannot rotate freely but instead can be in either the low energy trans confoormation or the higher energy cis conformation

n.b. double bonds cannot rotate !!! whereas single bonds can rotate !!!


Which two dihedral angles are single bonds and so can rotate ?

- Psi
- Phi

- The alpha helix is a type of regular secondary structure in which successive amino acids adopt the same Phi and Psi dihedral angles (peptide bonds all trans). It is a coiled structure

- the alpha helix has a positive Phi and negative Psi


What is the Psi and Phi structure look like ?

- they can rotate - which is dictated by steric interactions across these bonds

(refer to slide 5 from lecture 1 biochem !! ( for exact structure ! )

although they are single bonds and can rotate - close by carbons may bond and would prevent the rotation !!


What are Newman Projections?

A Newman projection, useful in alkane stereochemistry, visualizes chemical conformations of a carbon-carbon chemical bond from front to back, with the front carbon represented by a dot and the back carbon as a circle


What plot is used to show the conformational space owned by different combinations of Phi and Psi rotations ?

- Ramachandran plot

it is a way to visualize backbone dihedral angles against of amino acid residues in protein structure.

(refer to slide 7 on lecture 1 biochem for diagram of plot !)


What are hydrogen bonds?

- weak bond
-a hydrogen atom attached to an electronegative atom - forms a bind to another electronegative atom.
- the bond is often mentioned as being electrostatic because there is a partial charge difference between the hydrogen and the electronegative acceptor atom.
- in some way the hydrogen bond can be said to be somewhat covalent as it shares electrons

-important in ALL macromolecules !
- can be made or broken !
- have 1/5 strength of covalent bond !


What is an example of a Hydrogen bonding molecule?

water ( most important example )


What importance does hydrogen bonding have in protein structure?

- hydrogen bonding is an essential component of protein structure
- in both B sheets and Alpha helices , the H bond forms between the carbonyl oxygen and the amino group.


What is Hydrophobic interactions ?

- hydrophobic - does NOT dissolve in water - but dissolves in Oil.

A.K.A Entropic

- since the hydrophobic groups exposed to water lead to a decrease in entropy ( ordering of water molecules)

- therefore burying hydrophobic residues away from water leads to an increase in entropy

almost all proteins have hydrophobic core regions !

- when proteins are folded they expose their hydrophobic groups which cause their hydrophobic groups to be buried in the core !

stacking of planar aromatic groups can also lead to π- electron interactions stabilizing the arrangement

another related interaction could be Cation - π interaction ( this is equivalent to energy of a hydrogen bond )


What is electrostatic forces?

-they govern how proteins interact in environment
- its the only force that operates over long distance
- very complex
-stable structures if folded correctly
- deals with interaction between charges


What is Anfinsen's dogma?

3D structure in small globular proteins is determined by the amino acid sequence


What is Levinthal's Paradox?

- because of the very large number of degrees of freedom in an unfolded polypeptide chain, the molecule has an astronomical number of possible conformations

therefore to understand folding you need to understand the folding pathway ( pathway as important as destination)


Are the process of protein folding and protein assmebly related ?

- both processes are simultaneous folding of two random coil peptides to give folded dimer and binding of prefolded monomers


What is a good example of how subunits can fold and interact together ?

- histones !

DOES NOT EXIST ON ITS OWN !!! - do not fold stably by themselves- except when interacting with another histone - when they form a stable heterodimer

- the H4 and H3 histones are not stably folded by themselves - there is alot of exposed hydrophobic surfaces along the helix
- the H4 and H3 histones do fold together to form a heterodimer that is more stable !

the most stable is H3H4 hetero-tetramer - which has a small interface -this is enough to form a moderately stable interface,

H3 and H4 interact to form a heterotetramer - a very stable folding !


Another example of folding and assembly ?

- yeast transcriptional activator protein GCN4
- this protein is a homodimer( two identical dimers) ( held together by a parallel alpha helical coiled coil ( using a leucine zipper ( hydrophobic) - to hold helices together )

- it is more than just GCN4 - the helices from the coil extend and can interact sequence specifically with DNA in the major groove !!!


What is a leucine Zipper ?

- a common 3D structural motif in proteins. These motifs are usually found as part of a DNA-binding domain in various transcription factors, and are therefore involved in regulating gene expression.