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A researcher is given the task of designing a protein that will bind to a receptor very well. The receptor's binding site has strong positive charges at the edges and negative charges in the center. How would you go about designing the protein to bind to it?

Proteins are made up of amino acids, which have variable side chains. The side chains can (in one system of categorisation), be neutral, negatively charged, or positively charged at the pH of the cell (physiological pH).In this case, then, you would want to match up positive and negative charges on your protein/peptide drug with the complementary charge on the receptor. i.e., positive with negative and negative with positive.Have a look at amino acids like arginine, aspartate, lysine, and glutamate.Other types of interaction you might want to look for could be weaker, but sometimes "easier" interactions such as hydrogen bonding or "hydrophobic" bonding, between receptor and peptide (typically the "thing" binding is referred to as a ligand).In terms of actual design steps, the researcher might use a combinatorial system where he/she synthesises a broad range of peptides and assesses their activity against the receptor. X-ray crystallography may be used to help determine the key interactions necessary - in this case, since the structure of the receptor is known, this is likely to be particularly useful.
10 June 2013
A protein is made up of a chain of amino acids (the protein being the polymer and the amino acids being monomers). Each amino acids is made up of three parts; an amine group; a carboxyl group; and an R-group. The R group is a unique structure to each different type of amino acids. When a protein folds into it's specific shape, it is these R-groups that repel or attract each other to make it fold in a specific manner. The R-groups may have sulphurs in them, allowing them to form disulphide bridges. They may have hydroxide and hydrogens, forming hydrogen bonds. Alternatively, they can have positive and negative charges.When designing the protein receptor, the negatively charged amino acids must be placed where the structure would be complementary to the positively charged parts of the receptor and visa-versa. As a result, the negative charged edge of the protein would be attracted to the positive charge at the edge of the receptor, whilst the positive charge centre of the protein would be attracted to the negative charge at the centre of the receptor.
02 September 2015
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