We discussed the various interactions that drive protein folding and stabilize p

Question

We discussed the various interactions that drive protein folding and stabilize protein structure.

i) Provide an description of each of these interactions.

ii) Provide an explanation as to why the hydrogen bonds formed between the peptide bonds of a amino acid sequence may not be as strong as the hydrogen bonds that the peptide bond could form with water.

iii) Provide an explanation as to why salt-bridge interactions at the surface of a protein (exposed to water) is not as strong as a salt-bridge formed in the interior of the protein.

Explanation / Answer

1. various interactions that drive protein folding and stabilize protein structure are ionic interactions, dipole interactions, hydrogen bonds, van der Waals forces, hydrophobic interactions. Ionic interaction involves interaction of ion with charges of opposite signs.Dipole interactions are electrostatic interactions, associated with electronegative atoms such as O or N. Hydrogen bonding is formed due to OH and NH groups as donor and O or N as acceptors.  Van der Waals force is a transient, weak and resulting in temporary electric dipole. Hydrophobic interaction is aggregation of non-polar molecules in the aqueous solution.

ii) Hydrogen bond between peptide of amino acid sequence is not strong as compared with peptide form with water because hydrogen bond is formed bewteen weak acidic donar group (D-H) and aceptor (A) with lone pair, which is all provided by water during hydrogen bonding.

iii) salt bridges depends on the ionization properties of the participating groups, which is significantly influenced by the protein environment. The strong interaction of salt bridge at surface is due to strong formation of hydrogen bond with water as compared to interior.

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