What would you predict about the ratio of hydrophilic to hydro- phobic amino acid residues in a series of monomeric globular proteins that range in size from a molecular weight of 10,000 g/mole to a molecular weight of 100,000 g/mole? Note that the volume of a sphere is 4/3nr³, while the sur- face area of the outside of a sphere is 4nr².
Before getting into the calculations, we have to assume that our globular protein have a spherical topography . Here we use an equation that would give you the fraction of hydrophilic amino acid residues in a globular protein. The equation agrees with the models used in CATH and SCOP databases and hence is used to easily calculate the ratio of hydrophilic to hydrophobic amino acid residues.
The distribution of amino acids on a globular protein depends on its aqueous affinities. Based on this, amino acids are divided into hydrophobic (low aqueous affinity ) and hydrophilic (high aqueous affinity). So, hydrophobic amino acids will be mainly found towards the core of the globular protein and hydrophilic amino acids will be found on the surface of the globular protein. Once this 'minimum condition' is agreed upon by a globular protein , the protein follows the HP model which is used in Bioinformatics spaces including CATH and SCOP.
First we need to find the total number of amino acid residues present in our globular proteins.
The average molecular weight (Mw) of amino acids within a protein (or simply a polypeptide chain) is 110 g/mole. The total number of amino acid residues in a globular protein which follows the HP model (satisfies the minimum condition) is represented as 'Nopt ' (Noptimum ).
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