From protein folding to vaccines

Our most simple actions like picking up a mug of coffee, or even the involuntary task of breathing, require the co-ordinated, controlled activities of many proteins. Proteins form the functional units of our body and carry out many varied functions; alteration in the synthesis or function of any part or parts of a protein has been the known cause of various diseases.

Amino acids are the building blocks of a protein. These are linked together in a protein chain which folds to form a three-dimensional structure characteristic of each protein. A small change in the amino acid sequence of a protein can affect the three dimensional shape, function and/or stability of the protein. Protein folding, or the study of how proteins take up a particular shape individual to themselves, has been the focus of many scientists all over the world. Prof Raghavan Varadarajan’s laboratory at the Indian Institute of Science aims at understanding forces that drive protein folding.

Prof. Varadarajan's group started off by studying how the burial of hydrophobic (water repelling) amino acids stabilized proteins. This was done by systematically altering the amino acids in these hydrophobic pockets, followed by tests to assess the stability and structure of the altered protein.

Prof. Varadarajan’s laboratory has managed to apply this seemingly simple approach to study many different proteins. For example, it was used to understand the basis of temperature-sensitive mutant proteins, which are widely used tools in research. His extensive work enabled the prediction of 'buried' amino acids within a protein based on the protein sequence alone; the group was also able to predict which of these amino acids, when altered, would generate a temperature-sensitive protein. With this information in hand, Prof. Varadarajan’s lab went on to successfully generate temperature-sensitive mutants in bacteria, yeast and the fruit fly.

Generation of vaccines against viral infections has been a very challenging problem. It involves the injection of some components of the virus, typically some proteins, into the body to raise an immune reaction. This 'trains' the body to recognise the component in the case of an actual viral infection. With the availability of the crystal structure of one of the subunits of the surface proteins of HIV in 1998 he saw a window of opportunity to apply this knowledge to the generation or vaccines.

Prof. Varadarajan says “I thought it would be interesting to see if we could put our understanding on how to stabilise proteins to stabilize the surface protein of the Human Immunodeficiency Virus (HIV) which causes the Acquired Immunodeficiency Syndrome (AIDS)”.

While the work on a vaccine against HIV made slow and steady progress, a search for new systems to apply this knowledge of protein folding and stabilisation led Prof. Varadarajan to the problem of vaccine generation for Influenza. The influenza virus, which causes the common flu, has many variants. This makes the process of generation of a universal vaccine for flu difficult. By applying the knowledge of protein folding to hemagglutinin, a surface protein of influenza virus, the group was able to purify a fragment of this very unstable surface protein. The unique feature of this fragment is that it is more or less common to all the known variants of the virus, strengthening its case as a candidate as an influenza vaccine which can be effective against multiple strains of the virus. This fragment emerged successful in its ability to protect mice from infection with the influenza virus. Prof. Varadarajan says that his method is a much more cost-effective and less tedious method for vaccine generation against influenza compared to the other vaccines available in the market.

On being asked if a universal vaccine can be made, Prof. Varadarajan says “That would be the ultimate dream. However, it is unlikely”. He adds “Realistically, the main applications of our work is that because these protein fragments are bacterially producible, and there are 18 different subtypes of the flu virus, we could in principle prepare vaccines against all the available subtypes of the vaccine….these can be easily stored and then be used when necessary. Also, making variants of the vaccine effective against newly emerging variants of the virus is an easier process as compared to the existing methods of vaccine generation against the influenza virus”.

The influenza protein fragments are in the process of undergoing further tests in mice and other animal models to determine their utility and broad applicability, before deciding whether to test them in humans.

Lab web page: http://mbu.iisc.ernet.in/~rvgrp/