Findings contradict widely accepted theory
A NAIT instructor and three former students are making an impact on HIV research around the world with their newly published work that shows the current, widely accepted model of the virus’ structure is wrong.
Their results could have an impact on future work in the field.
The research by Dr. Marcelo Marcet-Palacios and his team was published earlier this month in the international scientific journal, PLOS ONE. The open access, peer-reviewed journal is published by the Public Library of Science, a non-profit science advocacy organization.
“Even after our paper, we still do not know what that structure is,” says Marcet-Palacios. “But our paper tells the scientific community what it is not, for sure.”
He and then students David Barilla (Nanotechnology Systems ’16), Eduardo Reyes-Serratos (Biological Sciences Technology - Environmental Sciences ’16) and Joy Santos (Mechanical Engineering Technology ’16) have shown, through computer modeling, that the current, accepted structure of the virus is mathematically impossible.
“This model has impacted every single bit of [research] work that has been done since,” says Marcet-Palacios, a biochemist who teaches Biological Sciences Technology at NAIT.
“We’re publishing something that contradicts 10 years of research by an international community of experts,” he said. While the NAIT team’s model is unproven and needs further study by the scientific community, it is a starting point for future research, he adds.
A mathematical impossibility
Until now, HIV research has been based on a 2009 model of the structure of the virus’ inner shell that shows a sphere made up of hexagonal shapes. This shell is inside another spherical outer layer.
A pattern of hexagons alone can’t form a sphere – or, for that matter, part of HIV as had been suggested.
The accepted virus model had long nagged at Marcet-Palacios; diagrams appeared to show overlapping pieces and areas where the pattern was stretched, he thought. His doubts led him to propose the project to the students, to try and create a better model of the virus.
The research team’s success on the HIV project didn’t come easily. Barilla recalls the painstaking process of trying to recreate the old, spherical model in a new way, essentially trying to fit square pegs into round holes.
A pattern of hexagons alone can’t form a sphere – or, for that matter, part of HIV.
“We went through almost a year’s worth of attempts to make it work before it struck us that you can’t build it that way,” he says.
He and Marcet-Palacios were working together on the model one night when the instructor noticed an odd pattern appearing, Barilla recounts. “Marcelo said, ‘That looks weird. Do you see the pattern that’s evolving out of this thing?’ It was just serendipity that we noticed it and continued building it that way.”
They realized the pattern was forming a new structure that wasn’t hexagonal at all. A computer scientist, Weijie Sun, and a mathematics expert, Sean Graves, developed essential mathematical concepts and methodologies to help their work. A lab tech supervisor, Mattea Bujold, supported the students in the early stages of the project. A NAIT colleague, David Christiansen (Electronics Engineering Technology ’84), IT supervisor in the School of Applied Sciences and Technology, built the computer they needed to do the complex modelling.
As a result of their research, the NAIT team proposed an alternative to the rigid, hexagonal shell – a more flexible structure that, when closed, looks like a beachball composed of six crescent-shaped petals that don’t quite close at one end.
Between each crescent are channels where certain proteins can manoeuver to eventually bind to white blood cells in the body. They theorize that the petal-shaped structure opens, releasing the HIV cocoon, or capsid, inside to infect the cell.
“I don’t know if this is the real model. The point of the paper is that this model is equally as good, if not better than the previous one, because it is actually mathematically feasible. So let’s start from it.”
‘Holy cow, there may be something here’
The research was done without funding, on weekends and evenings outside the students’ regular program hours. “I told them, I’m willing to move things forward if you’re willing to put in your own time,” says Marcet-Palacios.
The students jumped at the chance to be involved. “Marcelo is a very charismatic and enthusiastic teacher,” says Barilla. “He has a way of making anything super-interesting, and this project and this idea had never been done before.”
Though the students each came from different programs, they had all worked with Marcet-Palacios in 2015 on a team that received a silver medal at the International Genetically Engineered Machine (iGEM) competition in Boston, which drew about 280 teams from high schools and post-secondary institutions around the world.
“That was such a fun project and we knew we worked well together,” says Reyes-Serratos. “We got a sense of accomplishment and success that was so rewarding.”
While the research project is a departure from the usual applied or hands-on research done at a polytechnic, Marcet-Palacios says in NAIT's Lab Research and Biotechnology program, doing research is practical experience for students and keeps him current in his field.
"I teach my students to do research by doing research with them.”
“I teach my students to do research by doing research with them,” he adds.
The students never expected their curiosity and hard work would result in such a significant discovery, says Barilla. “You go from thinking, ‘This isn’t going to be anything,’ to thinking, ‘Holy cow, there may be something here.’ It’s exciting, and it’s something to be proud of.”
Adds Reyes-Serratos, “Marcelo emphasizes always trying to give to the collective knowledge. The whole purpose of this is to contribute to the knowledge of humanity, and let’s see where it goes.”