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Basic amino acids

Of the basic amino acid side chains, histidine has the lowest pKa (around 6) and is therefore neutral at around physiological pH. This amino acid occurs very frequently in enzyme active sites as it can function as a very efficient general acid-base catalyst. It also acts as a metal ion ligand in numerous protein families. Lysine and arginine are more strongly basic and are positively charged at physiological pH's. They are generally solvated but do occasionally occur in the interior of a protein where they are usually involved in electrostatic interactions with negatively charged groups such as Asp or Glu. Lys and Arg have important roles in anion-binding proteins as they can interact electrostatically with the ligand. Here is a pdb-file for RasMol.

Conformationally important residues

Glycine and proline are unique amino acids in that they appear to influence the conformation of the polypeptide. Glycine essentially lacks a side chain and therefore can adopt conformations which are sterically forbidden for other amino acids. This confers a high degree of local flexibility on the polypeptide. Accordingly, glycine residues are frequently found in turn regions of proteins where the backbone has to make a sharp turn. Glycine occurs abundantly in certain fibrous proteins due to its flexibility and because its small size allows adjacent polypeptide chains to pack together closely. In contrast, proline is the most rigid of the twenty naturally occurring amino acids since its side chain is covalently linked with the main chain nitrogen. Here is a pdb-file for RasMol.

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j.cooper 31/1/95