Question

how does the protein environment surrounding an amino acid chain affect its chemical properties?Consider the carboxyl group on an asparate side chain in the following environments in a protein. Rank in order these environments from the highest to the lowest proportion of carboxyl groups in the -COO- form.that is in terms of pKas.

1. an aspartate side chain on the surface of protein with no other ionizable groups nearby.

2. an aspartate side chain buried in a hydrophobic pocket on the surface of a protein

3. an asparate chain in a hydrophobic pocket adjacent to a glutamte side chain

4. an asparate side chain in a hydrophobic porket adjacent to a lysine side chain.

Answer 1

Aspartic acid is a charged polar amino acid which is responsible for constituting a part of active sites of many enzymes and maintaining the solubility and ionic character of proteins. Polar groups are most capable of creating ordered hydration through hydrogen bonding and ionic interactions. It provides most electrostatically and thus energetically promising interaction, especially if there is no pre-existing order in the water that requires destruction. This non-specific electrostatic interaction gives additional advantage in aqueous environment when H-bonding extending away from bulk to surface. Since, Aspartic acid (D) possesses the smallest molar volume as compared to expected due to larger molecular weight.

The order of highest to lowest pKa would be

3>2>1>4

In 3^rd case pKa will maximum due to destabilization of alike ions of Glutamate

In 2^nd case pKa will be less than above due to no surrounding interference

In 1^st case ionization will be supported by polar molecule

In 4^th case due to presence of positive charge will reduced ionization