Scientists found that the virus-fighting proteins protected against swine flu when levels were increased.
When the proteins were removed the swine flu virus was able to multiply in the body unchecked.
The accidental discovery may help to explain why some people develop serious symptoms when they contract flu and others do not.
The protein, IFITM3, and although it appeared to be connected to the functioning of the immune system, how it worked and what it did had never been understood.
Professor Stephen Elledge, from Harvard Medical School in Boston, US, who led the research, said: "We've uncovered the first-line defence in how our bodies fight the flu virus.
"The protein is there to stop the flu. Every cell has a constitutive immune response that is ready for the virus. If we get rid of that, the virus has a heyday."
The findings, reported in the journal Cell, could pave the way to new kinds of antiviral treatment, say the scientists. However, it remains to be seen what the long-term side effects of boosting levels of the proteins might be.
The news comes as Sir Liam Donaldson, Chief Medical Officer, announced the latest swine flu figures showing a further drop in cases with an estimated 9,000 new diagnoses last week.
It is thought over 800,000 people have suffered symptoms of swine flu since it first emerged in England in April.
It appears that the second wave of the disease is coming to an end but he warned that it is not know what will happen in the New Year.
Sir Liam said the NHS had coped 'brilliantly' with swine flu this year.
The vaccination programme is also progressing with three million people out of the nine million in the first priority groups already immunised.
More than 100,000 pregnant women have so far been vaccinated, Prof David Salisbury, head of immunisation said, out of around 550,000 women who are pregnant at any one time in England.
Two thirds of local NHS organisations have now reached agreements with GPs to start vaccinating children aged between six months and five years.