Predicting primary and secondary structure properties

The tool ProtParam, on the ExPASy server, calculates a protein's physical and chemical properties just from its amino acid sequence. Learn its four main results in order:

• Isoelectric point (pI): the pH at which the protein's overall charge is zero. If the pI is below 7, the protein is acidic; above 7, it is basic. Knowing the pI helps choose the right buffer to purify the protein, for example by isoelectric focusing.
• Instability index: an estimate of how stable the protein is in a test tube, based on certain pairs of amino acids in it. Below 40: predicted stable. Above 40: predicted unstable.
• Aliphatic index: the relative volume taken up by amino acids with aliphatic side chains (alanine, valine, isoleucine, leucine). A high value suggests the protein stays stable over a wide range of temperatures.
• GRAVY (grand average of hydropathy): the average water-loving or water-fearing score of all the amino acids. A low (negative) GRAVY means the protein is more water-loving and mixes well with water; a high one means it is more water-fearing.

The next step is to predict the protein's secondary structure (where it forms helices, sheets and coils), using tools such as APSSP, CFSSP, SOPMA and GOR. This helps reveal the protein's function, and is a step towards predicting its full 3-D shape.