Protein folding Flashcards
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 proteinfailure to fold may result in inactive proteins or even a toxic function.
What methods can we use to examine protein folding ( or unfolding) ?
- NMR-EPR-FTIR-Fluorescence- 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?
- Covalent 2. hydrogen 3. entropic ( hydrophobic ) 4.electrostatic
What two areas can a covalent interaction in a protein be split into ?
- 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
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 plotit 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
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.
