ABSTRACT
Whole books have been written on protein analysis but what is covered in this single chapter are some of the major problems and opportunities for studying proteins. The amino acid sequence of a protein can provide clues to its function. The recognition of sequence patterns in protein-coding genes can allow predictions, many of them quite accurate, as to family membership and the role in the cell. Once translated, proteins undergo modification, which adds a further layer of expression and regulation to these sequences. Some common post-translational modifications such as phosphorylation are reversible, allowing “switches” to be turned on and off, repeatedly. These changes, in turn, influence structure, function, and translocation, making the world of proteins a very dynamic place. Amino acids, both adjacent and at distant sites, work together to create the three-dimensional form of the protein, bind other proteins or molecules, and create active sites where enzymatic reactions take place. In this chapter, several protein structures will be studied, manipulated, and optimized to better understand the relationships between sequence, structure, and function.
