Developing Bioinformatics Computer Skills

Chapter 10. Predicting Protein Structure and Function from Sequence

The amino acid sequence of a protein contains interesting information in and of itself. A protein sequence can be compared and contrasted with the sequences of other proteins to establish its relationship, if any, to known protein families, and to provide information about the evolution of biochemical function. However, for the purpose of understanding protein function, the 3D structure of a protein is far more useful than its sequence.

The key property of proteins that allows them to perform a variety of biochemical functions is the sequence of amino acids in the protein chain, which somehow uniquely determines the 3D structure of the protein.^[*] Given 20 amino acid possibilities, there are a vast number of ways they can be combined to make up even a short protein sequence, which means that given time, organisms can evolve proteins that carry out practically any imaginable purpose.

Each time a particular protein chain is synthesized in the cell, it folds together so that each of the critical chemical groups for that particular protein's function is brought into a precise geometric arrangement. The fold assumed by a protein sequence doesn't vary. Every occurrence of that particular protein folds into exactly the same structure.

Despite this consistency on the part of proteins, no one has figured out how to accurately predict the 3D structure that a protein will fold into based on its sequence alone. Patterns are ...