They believe rare individuals who progress very slowly to Aids when infected make white blood cells that are better at fighting the virus.
The findings, published in Nature, may help international efforts to design an effective Aids vaccine.
But the research team at MIT and Harvard says any such vaccine is at least a decade away.
The findings relate to so-called "elite controllers" - a small number of people who, when exposed to HIV, progress very slowly to Aids or never develop it at all. In the late 1990s it was discovered that these individuals - about one in 200 of those infected with HIV - carry a specific gene, known as HLA B57.
The research team, led by MIT Professor Arup Chakraborty and Harvard Professor Bruce Walker, found this gene causes the body to make more potent killer T cells - a type of white blood cell that fights infections.
This helps them to keep the HIV virus at bay, but also makes them more susceptible to autoimmune diseases, where the body's immune system turns on itself.
The work is based on computer modelling of how immune cells develop in a specialised organ of the immune system known as the thymus.
The researchers say the study has implications for designing an effective vaccine. It could help them develop vaccines that provoke the same response to HIV that individuals with "natural immunity" can do on their own.
But they say even if they knew exactly what vaccine they wanted to make, it would take at least a decade to reach the hands of a healthcare worker.
Prof Bruce Walker told the BBC: "Some people are able to control HIV on their own and it's really critical for us to understand how this happens. This study takes us a step forward in understanding that."
Prof Chakraborty added: "It shows another piece in the puzzle of what we want a vaccine to do."
Commenting on the study, Jason Warriner, clinical director at the Terrence Higgins Trust, said: "Anything that gives us greater insight into genetic defences related to HIV is useful in searching for a vaccine and, one day, a cure for this complex virus.
"However, these elite controllers are a tiny proportion of people and they are not immune from HIV-related illnesses.
"HIV remains the UK's fastest-growing serious health condition, with 83,000 people affected, so it is vital that people continue to use condoms to protect themselves."
The study is published online in the journal Nature.