Question

1) how many polypeptide chains does PFK-1 consist of?

2) is it a homodimer, heterodimer, homotrimer, heterotrimer, homotetramer or heterotetramer? and how did you come to this conclusion?

3) What is involved in the folding and unfolding of a polypeptide chain? are hydrogen bonds formed and broken or covalent bonds and are they just formed/broken in the protein backbone or from one protein strand to another?

4) what kind of interaction is the interaction between one of the ADP sugar ring hydroxyl groups and a peptide backbone carbonyl? (pi-stacking, dipole-dipole, ion-ion, hydrophobic interaction and/or hydrogen bonding)

5) what interaction is found between the F6P phosphate group binding to the protein via interactions with 3 arginine sidechains? (pi-stacking, dipole-dipole, ion-ion, hydrophobic interaction and/or hydrogen bonding)

Answer 1

Please find the answers below:

Answer 1: PFK1 or phosphofructokinase 1 is a polypeptide which contains a number of polypeptide chains which combine together in a very specific 3-dimensional manner to give rise to a functional enzyme. Structural identification studies have shown that this enzyme contains a total of 2 polypeptide chains of similar kind (i.e. a homodimer).

Answer 2: The PFK-1 is a homodimer by nature. Two major points of experimental proofs support this notion. Firstly, denaturation and resolution of PFK-1 enzyme gives rise to two strong bands at 55kDa and secondarily, strutural simulation studies in silico have also confirmed the same.

Answer 3: Folding and unfolding of a protein is a complex and thermodynamically regulated process. In this process, a number of chemical bonds are formed and broken such as hydrogen bonds, covalent bonds, ionic or salt-linkages, Van der Waal's forces, sulphydryl linkages etc. Thus, experimental studies have clearly demonstrated that a number of types of bonds take part in this combination thus giving rise to a final form of polypeptide which is thermodynamically stable and biologically functional.

Answer 4: The ADP sugar ring hydroxyl group and the peptide backbone carbonyl are attached to each other by pi-stacking and dipole-dipole interactions. This is because during the chemical process of bonding between the ADP hydroxyl and the peptide carbonyl, water molecule plays a very important role. The interaction of water molecule with these bonding subunits give rise to dipole-dipole interactions along with pi-bonding.